2023-04-02 02:22:32,620 /var/log/job.log INFO     Using reference DB: UNITE ITS general FASTA release (unite); version: 8.3; source: https://files.plutof.ut.ee/public/orig/7B/23/7B235835FAF5C85D7B01E40FEF17F687914CB81A182554C5BD95E3168328E604.tgz
2023-04-02 02:22:33,095 /var/log/job.log INFO     Reference DB checksum: 4b28de370fa31b122a76f99367fafd9f
2023-04-02 02:22:33,095 /var/log/job.log INFO     Loading R module: DADA2_ITS/ITSdada2nephele.
2023-04-02 02:22:33,096 sh.command   DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>: starting process
2023-04-02 02:22:33,107 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: started process
2023-04-02 02:22:33,107 sh.command.process.streamwriter DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>.stdin: parsed stdin as a None
2023-04-02 02:22:33,108 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamWriter object at 0x7f242070ebb0> ready for more input
2023-04-02 02:22:33,108 sh.command   INFO     <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele', pid 2777>: process started
2023-04-02 02:22:33,108 sh.command.process.streamwriter DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>.stdin: done reading
2023-04-02 02:22:33,108 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: acquiring wait lock to wait for completion
2023-04-02 02:22:33,108 sh.command.process.streamwriter DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>.stdin: closing, but flushing first
2023-04-02 02:22:33,108 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: got wait lock
2023-04-02 02:22:33,109 sh.stream_bufferer DEBUG    acquiring buffering lock for flushing buffer
2023-04-02 02:22:33,109 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: exit code not set, waiting on pid
2023-04-02 02:22:33,109 sh.stream_bufferer DEBUG    got buffering lock for flushing buffer
2023-04-02 02:22:33,109 sh.stream_bufferer DEBUG    released buffering lock for flushing buffer
2023-04-02 02:22:33,109 sh.command.process.streamwriter DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>.stdin: got chunk size 0 to flush: b''
2023-04-02 02:22:33,508 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e970> ready to be read from
2023-04-02 02:22:33,508 sh.streamreader DEBUG    got chunk size 89: b'* installing to library \xe2\x80\x98/us'
2023-04-02 02:22:33,509 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:33,509 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:33,509 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:22:33,520 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e970> ready to be read from
2023-04-02 02:22:33,520 sh.streamreader DEBUG    got chunk size 56: b'* installing *source* package '
2023-04-02 02:22:33,520 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:33,520 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:33,521 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:22:33,521 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e970> ready to be read from
2023-04-02 02:22:33,521 sh.streamreader DEBUG    got chunk size 29: b'** using staged installation\n'
2023-04-02 02:22:33,521 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:33,521 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:33,521 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:22:33,538 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e970> ready to be read from
2023-04-02 02:22:33,538 sh.streamreader DEBUG    got chunk size 5: b'** R\n'
2023-04-02 02:22:33,538 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:33,539 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:33,539 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:22:33,543 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e970> ready to be read from
2023-04-02 02:22:33,543 sh.streamreader DEBUG    got chunk size 53: b'** byte-compile and prepare pa'
2023-04-02 02:22:33,543 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:33,543 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:33,544 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:22:40,835 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e970> ready to be read from
2023-04-02 02:22:40,836 sh.streamreader DEBUG    got chunk size 28: b'** building package indices\n'
2023-04-02 02:22:40,836 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:40,836 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:40,836 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:22:41,045 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e970> ready to be read from
2023-04-02 02:22:41,045 sh.streamreader DEBUG    got chunk size 24: b'** installing vignettes\n'
2023-04-02 02:22:41,045 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:41,045 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:41,045 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:22:41,049 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e970> ready to be read from
2023-04-02 02:22:41,049 sh.streamreader DEBUG    got chunk size 70: b'** testing if installed packag'
2023-04-02 02:22:41,049 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:41,049 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:41,049 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:22:47,729 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e970> ready to be read from
2023-04-02 02:22:47,730 sh.streamreader DEBUG    got chunk size 66: b'** testing if installed packag'
2023-04-02 02:22:47,730 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:47,730 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:47,730 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:22:54,408 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e970> ready to be read from
2023-04-02 02:22:54,408 sh.streamreader DEBUG    got chunk size 78: b'** testing if installed packag'
2023-04-02 02:22:54,409 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:54,409 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:54,409 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:22:54,409 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e970> ready to be read from
2023-04-02 02:22:54,409 sh.streamreader DEBUG    got chunk size 25: b'* DONE (ITSdada2nephele)\n'
2023-04-02 02:22:54,409 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:54,409 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:22:54,409 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:22:54,414 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e7c0> ready to be read from
2023-04-02 02:22:54,414 sh.command.process.streamreader DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>.stdout: got errno 5, done reading
2023-04-02 02:22:54,414 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>: <sh.StreamReader object at 0x7f242070e970> ready to be read from
2023-04-02 02:22:54,414 sh.streamreader DEBUG    got no chunk, done reading
2023-04-02 02:22:54,414 sh.stream_bufferer DEBUG    acquiring buffering lock for flushing buffer
2023-04-02 02:22:54,414 sh.stream_bufferer DEBUG    got buffering lock for flushing buffer
2023-04-02 02:22:54,414 sh.stream_bufferer DEBUG    released buffering lock for flushing buffer
2023-04-02 02:22:54,415 sh.command.process.streamreader DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele'>.<Process 2777 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele']>.stdout: got chunk size 0 to flush: b''
2023-04-02 02:22:54,415 sh.stream_bufferer DEBUG    acquiring buffering lock for flushing buffer
2023-04-02 02:22:54,415 sh.stream_bufferer DEBUG    got buffering lock for flushing buffer
2023-04-02 02:22:54,415 sh.stream_bufferer DEBUG    released buffering lock for flushing buffer
2023-04-02 02:22:54,415 sh.streamreader DEBUG    got chunk size 0 to flush: b''
2023-04-02 02:22:54,415 sh.command   DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/DADA2_ITS/ITSdada2nephele', pid 2777>: process completed
2023-04-02 02:22:54,415 /var/log/job.log INFO     Running DADA2 ITS
kwargs: {'fwd_primer': 'ACCTGCGGARGGATCA', 'rev_primer': 'GAGATCCRTTGYTRAAAGTT', 'cutadapt_path': 'cutadapt', 'min_len': 50, 'job_id': '0d8958e4aea9', 'input_dname': '/nephele_data/inputs/', 'out_dname': '/nephele_data/outputs/', 'map_fname': '/nephele_data/outputs/E23-ITS_fastq_single_end_mapping_template_qiime_corrected.txt.no_gz', 'log_fname': '/var/log/job.log', 'maxEE': 5, 'truncQ': 4, 'maxMismatch': 0, 'justConcatenate': False, 'chimera': True, 'trimOverhang': False, 'data_type': 'ITS_SE', 'band_size': <rpy2.rinterface_lib.sexp.NULLType object at 0x7f2535c81400> [RTYPES.NILSXP], 'homopolymer_gap_penalty': <rpy2.rinterface_lib.sexp.NULLType object at 0x7f2535c81400> [RTYPES.NILSXP], 'ref_db': '/mnt/EFS/dbs/ITSdada2_unite_v8.3/ITSdada2_unite_v8.3.fa', 'datafile': '/nephele_data/outputs/OTU_table.txt'}
4.0
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-1.fastq /nephele_data/outputs//filtN/E23-ITS-1.fastq
Processing single-end reads on 32 cores ...
Finished in 0.03 s (5685 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       6
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             6 (100.0%)

Total basepairs processed:           877 bp
Total written (filtered):            877 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 0 times
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-2.fastq /nephele_data/outputs//filtN/E23-ITS-2.fastq
Processing single-end reads on 32 cores ...
Finished in 0.16 s (7 µs/read; 8.32 M reads/minute).

=== Summary ===

Total reads processed:                  22,429
Reads with adapters:                         2 (0.0%)
Reads written (passing filters):        22,429 (100.0%)

Total basepairs processed:     5,265,371 bp
Total written (filtered):      5,265,365 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 100.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	350.5	0	2
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-3.fastq /nephele_data/outputs//filtN/E23-ITS-3.fastq
Processing single-end reads on 32 cores ...
Finished in 0.16 s (8 µs/read; 7.79 M reads/minute).

=== Summary ===

Total reads processed:                  20,428
Reads with adapters:                        12 (0.1%)
Reads written (passing filters):        20,428 (100.0%)

Total basepairs processed:     4,455,381 bp
Total written (filtered):      4,455,337 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 13 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 61.5%
  C: 7.7%
  G: 23.1%
  T: 7.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	8	319.2	0	8
4	5	79.8	0	5
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-4.fastq /nephele_data/outputs//filtN/E23-ITS-4.fastq
Processing single-end reads on 32 cores ...
Finished in 0.16 s (6 µs/read; 9.72 M reads/minute).

=== Summary ===

Total reads processed:                  26,411
Reads with adapters:                         3 (0.0%)
Reads written (passing filters):        26,411 (100.0%)

Total basepairs processed:     6,316,782 bp
Total written (filtered):      6,316,773 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 3 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 66.7%
  C: 0.0%
  G: 33.3%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	3	412.7	0	3
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-5.fastq /nephele_data/outputs//filtN/E23-ITS-5.fastq
Processing single-end reads on 32 cores ...
Finished in 0.17 s (7 µs/read; 9.06 M reads/minute).

=== Summary ===

Total reads processed:                  25,286
Reads with adapters:                         4 (0.0%)
Reads written (passing filters):        25,286 (100.0%)

Total basepairs processed:     5,835,400 bp
Total written (filtered):      5,835,384 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 5 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 40.0%
  C: 20.0%
  G: 20.0%
  T: 20.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	4	395.1	0	4
4	1	98.8	0	1
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-6.fastq /nephele_data/outputs//filtN/E23-ITS-6.fastq
Processing single-end reads on 32 cores ...
Finished in 0.20 s (5 µs/read; 13.27 M reads/minute).

=== Summary ===

Total reads processed:                  44,017
Reads with adapters:                        16 (0.0%)
Reads written (passing filters):        44,017 (100.0%)

Total basepairs processed:     9,997,811 bp
Total written (filtered):      9,997,762 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-16 bp: 1

Overview of removed sequences
length	count	expect	max.err	error counts
3	1	687.8	0	1


=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 15 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 20.0%
  C: 20.0%
  G: 60.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	14	687.8	0	14
4	1	171.9	0	1
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-7.fastq /nephele_data/outputs//filtN/E23-ITS-7.fastq
Processing single-end reads on 32 cores ...
Finished in 0.16 s (7 µs/read; 8.47 M reads/minute).

=== Summary ===

Total reads processed:                  23,036
Reads with adapters:                         2 (0.0%)
Reads written (passing filters):        23,036 (100.0%)

Total basepairs processed:     5,502,923 bp
Total written (filtered):      5,502,917 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 100.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	359.9	0	2
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-8.fastq /nephele_data/outputs//filtN/E23-ITS-8.fastq
Processing single-end reads on 32 cores ...
Finished in 0.03 s (11636 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           707 bp
Total written (filtered):            707 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 0 times
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-9.fastq /nephele_data/outputs//filtN/E23-ITS-9.fastq
Processing single-end reads on 32 cores ...
Finished in 0.04 s (89 µs/read; 0.67 M reads/minute).

=== Summary ===

Total reads processed:                     398
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):           398 (100.0%)

Total basepairs processed:        93,859 bp
Total written (filtered):         93,859 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 0 times
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-10.fastq /nephele_data/outputs//filtN/E23-ITS-10.fastq
Processing single-end reads on 32 cores ...
Finished in 0.18 s (7 µs/read; 8.37 M reads/minute).

=== Summary ===

Total reads processed:                  25,753
Reads with adapters:                         1 (0.0%)
Reads written (passing filters):        25,753 (100.0%)

Total basepairs processed:     5,778,021 bp
Total written (filtered):      5,778,018 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 100.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	1	402.4	0	1
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-11.fastq /nephele_data/outputs//filtN/E23-ITS-11.fastq
Processing single-end reads on 32 cores ...
Finished in 0.15 s (7 µs/read; 8.32 M reads/minute).

=== Summary ===

Total reads processed:                  21,167
Reads with adapters:                         3 (0.0%)
Reads written (passing filters):        21,167 (100.0%)

Total basepairs processed:     4,989,601 bp
Total written (filtered):      4,989,586 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 25.0%
  C: 25.0%
  G: 25.0%
  T: 25.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	330.7	0	2
4	1	82.7	0	1
5	1	20.7	0	1
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-12.fastq /nephele_data/outputs//filtN/E23-ITS-12.fastq
Processing single-end reads on 32 cores ...
Finished in 0.20 s (7 µs/read; 8.90 M reads/minute).

=== Summary ===

Total reads processed:                  29,240
Reads with adapters:                         4 (0.0%)
Reads written (passing filters):        29,240 (100.0%)

Total basepairs processed:     7,137,495 bp
Total written (filtered):      7,137,483 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 25.0%
  C: 0.0%
  G: 50.0%
  T: 25.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	4	456.9	0	4
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-13.fastq /nephele_data/outputs//filtN/E23-ITS-13.fastq
Processing single-end reads on 32 cores ...
Finished in 0.16 s (8 µs/read; 7.27 M reads/minute).

=== Summary ===

Total reads processed:                  19,757
Reads with adapters:                         6 (0.0%)
Reads written (passing filters):        19,757 (100.0%)

Total basepairs processed:     4,349,220 bp
Total written (filtered):      4,349,199 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 7 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 57.1%
  C: 42.9%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	7	308.7	0	7
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-14.fastq /nephele_data/outputs//filtN/E23-ITS-14.fastq
Processing single-end reads on 32 cores ...
Finished in 0.22 s (7 µs/read; 8.90 M reads/minute).

=== Summary ===

Total reads processed:                  32,930
Reads with adapters:                         4 (0.0%)
Reads written (passing filters):        32,930 (100.0%)

Total basepairs processed:     8,149,495 bp
Total written (filtered):      8,149,483 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 75.0%
  C: 0.0%
  G: 25.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	4	514.5	0	4
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-15.fastq /nephele_data/outputs//filtN/E23-ITS-15.fastq
Processing single-end reads on 32 cores ...
Finished in 0.16 s (8 µs/read; 7.86 M reads/minute).

=== Summary ===

Total reads processed:                  21,183
Reads with adapters:                         3 (0.0%)
Reads written (passing filters):        21,183 (100.0%)

Total basepairs processed:     5,337,184 bp
Total written (filtered):      5,337,167 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 5 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 40.0%
  C: 20.0%
  G: 0.0%
  T: 40.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	3	331.0	0	3
4	2	82.7	0	2
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-16.fastq /nephele_data/outputs//filtN/E23-ITS-16.fastq
Processing single-end reads on 32 cores ...
Finished in 0.10 s (19 µs/read; 3.21 M reads/minute).

=== Summary ===

Total reads processed:                   5,606
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):         5,606 (100.0%)

Total basepairs processed:     1,307,340 bp
Total written (filtered):      1,307,340 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 0 times
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-17.fastq /nephele_data/outputs//filtN/E23-ITS-17.fastq
Processing single-end reads on 32 cores ...
Finished in 0.04 s (174 µs/read; 0.35 M reads/minute).

=== Summary ===

Total reads processed:                     203
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):           203 (100.0%)

Total basepairs processed:        43,687 bp
Total written (filtered):         43,687 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 0 times
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-18.fastq /nephele_data/outputs//filtN/E23-ITS-18.fastq
Processing single-end reads on 32 cores ...
Finished in 0.16 s (8 µs/read; 7.31 M reads/minute).

=== Summary ===

Total reads processed:                  18,960
Reads with adapters:                         1 (0.0%)
Reads written (passing filters):        18,960 (100.0%)

Total basepairs processed:     4,660,338 bp
Total written (filtered):      4,660,335 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 100.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	1	296.2	0	1
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-19.fastq /nephele_data/outputs//filtN/E23-ITS-19.fastq
Processing single-end reads on 32 cores ...
Finished in 0.13 s (11 µs/read; 5.38 M reads/minute).

=== Summary ===

Total reads processed:                  11,949
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):        11,949 (100.0%)

Total basepairs processed:     3,019,224 bp
Total written (filtered):      3,019,224 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 0 times
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-20.fastq /nephele_data/outputs//filtN/E23-ITS-20.fastq
Processing single-end reads on 32 cores ...
Finished in 0.18 s (6 µs/read; 10.40 M reads/minute).

=== Summary ===

Total reads processed:                  30,612
Reads with adapters:                         4 (0.0%)
Reads written (passing filters):        30,612 (100.0%)

Total basepairs processed:     7,149,390 bp
Total written (filtered):      7,149,377 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 25.0%
  C: 25.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	3	478.3	0	3
4	1	119.6	0	1
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-21.fastq /nephele_data/outputs//filtN/E23-ITS-21.fastq
Processing single-end reads on 32 cores ...
Finished in 0.18 s (8 µs/read; 7.61 M reads/minute).

=== Summary ===

Total reads processed:                  23,409
Reads with adapters:                         7 (0.0%)
Reads written (passing filters):        23,409 (100.0%)

Total basepairs processed:     4,889,461 bp
Total written (filtered):      4,889,440 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 7 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 42.9%
  C: 28.6%
  G: 28.6%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	7	365.8	0	7
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-22.fastq /nephele_data/outputs//filtN/E23-ITS-22.fastq
Processing single-end reads on 32 cores ...
Finished in 0.19 s (5 µs/read; 11.03 M reads/minute).

=== Summary ===

Total reads processed:                  35,704
Reads with adapters:                        10 (0.0%)
Reads written (passing filters):        35,704 (100.0%)

Total basepairs processed:     7,804,621 bp
Total written (filtered):      7,804,591 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 10 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 10.0%
  C: 30.0%
  G: 40.0%
  T: 20.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	10	557.9	0	10
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-23.fastq /nephele_data/outputs//filtN/E23-ITS-23.fastq
Processing single-end reads on 32 cores ...
Finished in 0.17 s (7 µs/read; 9.02 M reads/minute).

=== Summary ===

Total reads processed:                  26,064
Reads with adapters:                         5 (0.0%)
Reads written (passing filters):        26,064 (100.0%)

Total basepairs processed:     5,829,834 bp
Total written (filtered):      5,829,816 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 5 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 60.0%
  C: 0.0%
  G: 40.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	3	407.2	0	3
4	1	101.8	0	1
5	1	25.5	0	1
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-24.fastq /nephele_data/outputs//filtN/E23-ITS-24.fastq
Processing single-end reads on 32 cores ...
Finished in 0.15 s (10 µs/read; 6.18 M reads/minute).

=== Summary ===

Total reads processed:                  15,088
Reads with adapters:                         2 (0.0%)
Reads written (passing filters):        15,088 (100.0%)

Total basepairs processed:     3,410,113 bp
Total written (filtered):      3,410,107 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	235.8	0	2
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-25.fastq /nephele_data/outputs//filtN/E23-ITS-25.fastq
Processing single-end reads on 32 cores ...
Finished in 0.03 s (1146 µs/read; 0.05 M reads/minute).

=== Summary ===

Total reads processed:                      30
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):            30 (100.0%)

Total basepairs processed:         7,382 bp
Total written (filtered):          7,382 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 0 times
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-26.fastq /nephele_data/outputs//filtN/E23-ITS-26.fastq
Processing single-end reads on 32 cores ...
Finished in 0.24 s (4 µs/read; 14.41 M reads/minute).

=== Summary ===

Total reads processed:                  57,453
Reads with adapters:                        16 (0.0%)
Reads written (passing filters):        57,453 (100.0%)

Total basepairs processed:    12,838,952 bp
Total written (filtered):     12,838,902 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 16 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 25.0%
  C: 18.8%
  G: 43.8%
  T: 12.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	14	897.7	0	14
4	2	224.4	0	2
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-27.fastq /nephele_data/outputs//filtN/E23-ITS-27.fastq
Processing single-end reads on 32 cores ...
Finished in 0.16 s (7 µs/read; 8.56 M reads/minute).

=== Summary ===

Total reads processed:                  22,790
Reads with adapters:                        11 (0.0%)
Reads written (passing filters):        22,790 (100.0%)

Total basepairs processed:     5,050,412 bp
Total written (filtered):      5,050,379 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-16 bp: 1

Overview of removed sequences
length	count	expect	max.err	error counts
3	1	356.1	0	1


=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 10 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 20.0%
  C: 10.0%
  G: 60.0%
  T: 10.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	10	356.1	0	10
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-28.fastq /nephele_data/outputs//filtN/E23-ITS-28.fastq
Processing single-end reads on 32 cores ...
Finished in 0.19 s (7 µs/read; 9.21 M reads/minute).

=== Summary ===

Total reads processed:                  28,497
Reads with adapters:                         3 (0.0%)
Reads written (passing filters):        28,497 (100.0%)

Total basepairs processed:     6,663,610 bp
Total written (filtered):      6,663,597 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 50.0%
  C: 25.0%
  G: 0.0%
  T: 25.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	3	445.3	0	3
4	1	111.3	0	1
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-29.fastq /nephele_data/outputs//filtN/E23-ITS-29.fastq
Processing single-end reads on 32 cores ...
Finished in 0.16 s (7 µs/read; 9.20 M reads/minute).

=== Summary ===

Total reads processed:                  25,169
Reads with adapters:                         2 (0.0%)
Reads written (passing filters):        25,169 (100.0%)

Total basepairs processed:     6,188,299 bp
Total written (filtered):      6,188,293 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 100.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	393.3	0	2
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-30.fastq /nephele_data/outputs//filtN/E23-ITS-30.fastq
Processing single-end reads on 32 cores ...
Finished in 0.22 s (5 µs/read; 12.25 M reads/minute).

=== Summary ===

Total reads processed:                  44,712
Reads with adapters:                         5 (0.0%)
Reads written (passing filters):        44,712 (100.0%)

Total basepairs processed:    11,184,674 bp
Total written (filtered):     11,184,659 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 5 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 60.0%
  C: 0.0%
  G: 40.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	5	698.6	0	5
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-31.fastq /nephele_data/outputs//filtN/E23-ITS-31.fastq
Processing single-end reads on 32 cores ...
Finished in 0.16 s (7 µs/read; 8.14 M reads/minute).

=== Summary ===

Total reads processed:                  21,534
Reads with adapters:                         2 (0.0%)
Reads written (passing filters):        21,534 (100.0%)

Total basepairs processed:     5,220,224 bp
Total written (filtered):      5,220,218 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 50.0%
  C: 0.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	336.5	0	2
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-32.fastq /nephele_data/outputs//filtN/E23-ITS-32.fastq
Processing single-end reads on 32 cores ...
Finished in 0.10 s (19 µs/read; 3.09 M reads/minute).

=== Summary ===

Total reads processed:                   5,047
Reads with adapters:                         1 (0.0%)
Reads written (passing filters):         5,047 (100.0%)

Total basepairs processed:     1,296,818 bp
Total written (filtered):      1,296,815 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.0%
  C: 100.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	1	78.9	0	1
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-33.fastq /nephele_data/outputs//filtN/E23-ITS-33.fastq
Processing single-end reads on 32 cores ...
Finished in 0.04 s (78 µs/read; 0.77 M reads/minute).

=== Summary ===

Total reads processed:                     454
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):           454 (100.0%)

Total basepairs processed:       107,508 bp
Total written (filtered):        107,508 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 0 times
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-34.fastq /nephele_data/outputs//filtN/E23-ITS-34.fastq
Processing single-end reads on 32 cores ...
Finished in 0.07 s (20 µs/read; 3.06 M reads/minute).

=== Summary ===

Total reads processed:                   3,442
Reads with adapters:                         1 (0.0%)
Reads written (passing filters):         3,442 (100.0%)

Total basepairs processed:       804,842 bp
Total written (filtered):        804,839 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 100.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	1	53.8	0	1
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-35.fastq /nephele_data/outputs//filtN/E23-ITS-35.fastq
Processing single-end reads on 32 cores ...
Finished in 0.17 s (5 µs/read; 11.65 M reads/minute).

=== Summary ===

Total reads processed:                  33,952
Reads with adapters:                         2 (0.0%)
Reads written (passing filters):        33,952 (100.0%)

Total basepairs processed:     8,652,559 bp
Total written (filtered):      8,652,553 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 50.0%
  C: 0.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	530.5	0	2
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-36.fastq /nephele_data/outputs//filtN/E23-ITS-36.fastq
Processing single-end reads on 32 cores ...
Finished in 0.21 s (4 µs/read; 13.97 M reads/minute).

=== Summary ===

Total reads processed:                  48,950
Reads with adapters:                        15 (0.0%)
Reads written (passing filters):        48,950 (100.0%)

Total basepairs processed:    10,646,247 bp
Total written (filtered):     10,646,200 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 15 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 33.3%
  C: 33.3%
  G: 26.7%
  T: 6.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	13	764.8	0	13
4	2	191.2	0	2
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-37.fastq /nephele_data/outputs//filtN/E23-ITS-37.fastq
Processing single-end reads on 32 cores ...
Finished in 0.19 s (5 µs/read; 12.82 M reads/minute).

=== Summary ===

Total reads processed:                  39,713
Reads with adapters:                        24 (0.1%)
Reads written (passing filters):        39,713 (100.0%)

Total basepairs processed:     8,215,814 bp
Total written (filtered):      8,215,738 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 24 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 16.7%
  C: 37.5%
  G: 37.5%
  T: 8.3%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	20	620.5	0	20
4	4	155.1	0	4
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-38.fastq /nephele_data/outputs//filtN/E23-ITS-38.fastq
Processing single-end reads on 32 cores ...
Finished in 0.25 s (3 µs/read; 19.02 M reads/minute).

=== Summary ===

Total reads processed:                  80,063
Reads with adapters:                        14 (0.0%)
Reads written (passing filters):        80,063 (100.0%)

Total basepairs processed:    19,223,974 bp
Total written (filtered):     19,223,929 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 14 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 35.7%
  C: 7.1%
  G: 57.1%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	11	1251.0	0	11
4	3	312.7	0	3
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-NTC1.fastq /nephele_data/outputs//filtN/E23-ITS-NTC1.fastq
Processing single-end reads on 32 cores ...
Finished in 0.29 s (3 µs/read; 17.50 M reads/minute).

=== Summary ===

Total reads processed:                  83,238
Reads with adapters:                        10 (0.0%)
Reads written (passing filters):        83,238 (100.0%)

Total basepairs processed:    19,593,825 bp
Total written (filtered):     19,593,780 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 13 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 46.2%
  C: 15.4%
  G: 7.7%
  T: 30.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	7	1300.6	0	7
4	6	325.1	0	6
This is cutadapt 4.0 with Python 3.8.13
Command line parameters: -g ACCTGCGGARGGATCA -a AACTTTYARCAAYGGATCTC --cores 0 -n 2 --output /nephele_data/outputs//cutadapt/E23-ITS-NTC2.fastq /nephele_data/outputs//filtN/E23-ITS-NTC2.fastq
Processing single-end reads on 32 cores ...
Finished in 0.23 s (5 µs/read; 10.96 M reads/minute).

=== Summary ===

Total reads processed:                  41,176
Reads with adapters:                        12 (0.0%)
Reads written (passing filters):        41,176 (100.0%)

Total basepairs processed:     9,181,068 bp
Total written (filtered):      9,181,032 bp (100.0%)

=== Adapter 1 ===

Sequence: ACCTGCGGARGGATCA; Type: regular 5'; Length: 16; Trimmed: 0 times

=== Adapter 2 ===

Sequence: AACTTTYARCAAYGGATCTC; Type: regular 3'; Length: 20; Trimmed: 12 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 25.0%
  C: 50.0%
  G: 25.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	12	643.4	0	12
2023-04-02 02:33:52,119 /var/log/job.log INFO     Summarizing biom file to /nephele_data/outputs/OTU_summary_table.txt.
2023-04-02 02:33:52,133 /var/log/job.log INFO     Creating a phylogenetic tree with 12 threads
2023-04-02 02:33:52,134 /var/log/job.log INFO     phylogeny version 2022.2.0. This QIIME 2 plugin supports generating and manipulating phylogenetic trees.
2023-04-02 02:33:52,134 /var/log/job.log INFO     Artifact.import_data(type='FeatureData[Sequence]', view=/nephele_data/outputs/seq.fasta)
2023-04-02 02:33:52,172 /var/log/job.log INFO     align_to_tree_mafft_fasttree(sequences=seqs, n_threads=num_threads)
inputfile = orig
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: mafft --preservecase --inputorder --thread 12 /nephele_data/tmp/qiime2-archive-czh0lvng/4afabd2f-8f3d-4f75-a06f-730812a53358/data/dna-sequences.fasta

492 x 300 - 88 d
nthread = 12
nthreadpair = 12
nthreadtb = 12
ppenalty_ex = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

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done.

Constructing a UPGMA tree (efffree=0) ... 

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done.

Progressive alignment 1/2... 

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STEP     4 / 491 (thread    3) f
STEP     6 / 491 (thread    5) f f f
STEP     5 / 491 (thread    4) f
STEP    12 / 491 (thread   11) f
STEP    11 / 491 (thread   10) f
STEP     8 / 491 (thread    7) f
STEP     9 / 491 (thread    8)
STEP    10 / 491 (thread    9) f f
STEP     7 / 491 (thread    6) f
STEP    19 / 491 (thread   11) f
STEP    15 / 491 (thread    0) f
STEP    14 / 491 (thread    3) f
STEP    23 / 491 (thread    7) f
STEP    13 / 491 (thread    5) f
STEP    25 / 491 (thread    9) f
STEP    18 / 491 (thread    1) f
STEP    26 / 491 (thread    0) f
STEP    22 / 491 (thread    8) f
STEP    29 / 491 (thread    9) f
STEP    16 / 491 (thread    2) f
STEP    30 / 491 (thread    1) f
STEP    21 / 491 (thread   10) f
Reallocating..done. *alloclen = 1602

STEP    31 / 491 (thread    5) f
STEP    27 / 491 (thread    3) f
STEP    35 / 491 (thread    1) f
STEP    34 / 491 (thread    9) f
STEP    36 / 491 (thread   10) f
STEP    33 / 491 (thread    8) f
STEP    17 / 491 (thread    4) f
STEP    39 / 491 (thread    1) f
STEP    40 / 491 (thread    9) f
STEP    41 / 491 (thread    5) f
STEP    37 / 491 (thread    2) f
STEP    42 / 491 (thread    8) f
STEP    43 / 491 (thread    1) f
STEP    44 / 491 (thread    9) f
STEP    20 / 491 (thread   11) f
STEP    47 / 491 (thread   10) f
STEP    48 / 491 (thread    2) f
STEP    49 / 491 (thread    1) f
STEP    50 / 491 (thread    8) f
STEP    46 / 491 (thread    4) f
STEP    51 / 491 (thread   10) f
STEP    52 / 491 (thread    9) f
STEP    53 / 491 (thread   11) f
STEP    24 / 491 (thread    6) f
STEP    55 / 491 (thread    1) f
STEP    56 / 491 (thread    8) f
STEP    57 / 491 (thread   10) f
STEP    58 / 491 (thread    9) f
STEP    59 / 491 (thread   11) f
STEP    54 / 491 (thread    2) f
STEP    60 / 491 (thread    6) f
STEP    28 / 491 (thread    0) f
STEP    61 / 491 (thread    8) f
STEP    62 / 491 (thread    9) f
STEP    63 / 491 (thread    4) f
STEP    64 / 491 (thread   10) f
STEP    65 / 491 (thread    1) f
STEP    66 / 491 (thread   11) f
STEP    67 / 491 (thread    0) f
STEP    32 / 491 (thread    7) f
STEP    68 / 491 (thread    8) f
STEP    69 / 491 (thread    9) f
STEP    70 / 491 (thread    1) f
STEP    71 / 491 (thread   10) f
STEP    74 / 491 (thread    4) f
STEP    76 / 491 (thread    7) f
STEP    38 / 491 (thread    3) f
STEP    77 / 491 (thread    0) f
STEP    75 / 491 (thread    6) f
STEP    78 / 491 (thread    8) f
STEP    72 / 491 (thread    2) f
STEP    79 / 491 (thread    9) f
STEP    73 / 491 (thread   11) f
STEP    80 / 491 (thread    7) f
STEP    81 / 491 (thread    3) f
STEP    45 / 491 (thread    5) f
STEP    82 / 491 (thread    8) f
STEP    83 / 491 (thread    0) f
STEP    84 / 491 (thread    1) f
STEP    85 / 491 (thread   10) f
STEP    86 / 491 (thread    4) f
STEP    87 / 491 (thread    9) f
STEP    89 / 491 (thread    1) f
STEP    90 / 491 (thread   10) f
STEP    88 / 491 (thread    3) f
STEP    93 / 491 (thread    4) f
STEP    94 / 491 (thread    5) f
STEP    95 / 491 (thread   11) f
STEP    96 / 491 (thread    8) f
STEP    97 / 491 (thread    7) f
STEP    98 / 491 (thread    2) f
STEP    99 / 491 (thread    9) f
STEP   100 / 491 (thread    1) f
STEP   101 / 491 (thread   10) f
STEP    91 / 491 (thread    6) f
STEP   102 / 491 (thread    3) f
STEP   103 / 491 (thread    2) f
STEP   104 / 491 (thread    5) f
STEP   106 / 491 (thread    8) f
STEP   107 / 491 (thread    9) f
STEP   108 / 491 (thread   11) f
STEP   109 / 491 (thread    7) f
STEP   111 / 491 (thread   10) f
STEP   113 / 491 (thread    5) f
STEP    92 / 491 (thread    0) f
STEP   115 / 491 (thread    6) f
STEP   116 / 491 (thread    9) f
STEP   117 / 491 (thread   11) f
STEP   123 / 491 (thread    9) f
STEP   124 / 491 (thread    0) f
STEP   105 / 491 (thread    4) f
STEP   118 / 491 (thread    8) f
STEP   125 / 491 (thread   11) f
STEP   126 / 491 (thread    9) f
STEP   127 / 491 (thread    0) f
STEP   128 / 491 (thread   11) f
STEP   119 / 491 (thread    7) f
STEP   130 / 491 (thread    8) f
STEP   131 / 491 (thread    4) f
STEP   110 / 491 (thread    1) f
STEP   133 / 491 (thread    0) f
STEP   132 / 491 (thread   11) f
STEP   120 / 491 (thread   10) f
STEP   136 / 491 (thread    1) f
STEP   112 / 491 (thread    2) f
STEP   135 / 491 (thread    4) f
STEP   138 / 491 (thread    0) f
STEP   139 / 491 (thread   11) f
STEP   134 / 491 (thread    7) f
STEP   140 / 491 (thread    1) f
STEP   122 / 491 (thread    6) f
STEP   142 / 491 (thread    4) f
STEP   137 / 491 (thread    8) f
STEP   143 / 491 (thread    2) f
STEP   114 / 491 (thread    3) f
STEP   141 / 491 (thread   10) f
STEP   144 / 491 (thread   11) f
STEP   145 / 491 (thread    0) f
STEP   146 / 491 (thread    7) f
STEP   149 / 491 (thread    4) f
STEP   148 / 491 (thread    2) f
STEP   147 / 491 (thread    1) f
STEP   150 / 491 (thread    0) f
STEP   152 / 491 (thread    8) f
STEP   155 / 491 (thread    7) f
STEP   121 / 491 (thread    5) f
STEP   157 / 491 (thread    2) f
STEP   153 / 491 (thread    6) f
STEP   158 / 491 (thread    1) f
STEP   160 / 491 (thread    7) f
STEP   159 / 491 (thread    8) f
STEP   161 / 491 (thread    1) f
STEP   162 / 491 (thread    0) f
STEP   151 / 491 (thread   11) f
STEP   164 / 491 (thread    4) f
STEP   129 / 491 (thread    9) f
STEP   166 / 491 (thread    7) f
STEP   167 / 491 (thread    1) f
STEP   168 / 491 (thread    6) f
STEP   169 / 491 (thread    8) f
STEP   165 / 491 (thread    5) f
STEP   170 / 491 (thread    6) f
STEP   171 / 491 (thread    0) f
STEP   172 / 491 (thread    1) f
STEP   173 / 491 (thread    8) f
STEP   174 / 491 (thread    7) f
STEP   176 / 491 (thread   11) f
STEP   154 / 491 (thread   10) f
STEP   178 / 491 (thread    1) f
STEP   179 / 491 (thread    0) f
STEP   175 / 491 (thread    4) f
STEP   180 / 491 (thread    5) f
STEP   181 / 491 (thread    7) f
STEP   182 / 491 (thread    8) f
STEP   185 / 491 (thread    1) f
STEP   186 / 491 (thread    0) f
STEP   188 / 491 (thread   10) f
STEP   156 / 491 (thread    3) f
STEP   189 / 491 (thread    4) f
STEP   177 / 491 (thread    9) f
STEP   190 / 491 (thread    5) f
STEP   191 / 491 (thread    8) f
STEP   192 / 491 (thread    4) f
STEP   193 / 491 (thread    1) f
STEP   187 / 491 (thread    7) f
STEP   183 / 491 (thread    6) f
STEP   163 / 491 (thread    2) f
STEP   198 / 491 (thread    3) f
STEP   199 / 491 (thread    4) f
STEP   197 / 491 (thread    9) f
STEP   194 / 491 (thread   10) f
STEP   203 / 491 (thread    3) f
STEP   204 / 491 (thread    6) f
STEP   184 / 491 (thread   11) f
STEP   205 / 491 (thread    3) f
STEP   206 / 491 (thread    6) f
STEP   207 / 491 (thread    4) f
STEP   208 / 491 (thread    9) f
STEP   209 / 491 (thread    2) f
STEP   201 / 491 (thread    1) f
STEP   213 / 491 (thread    2) f
STEP   214 / 491 (thread   11) f
STEP   195 / 491 (thread    8) f
STEP   215 / 491 (thread    6) f
STEP   216 / 491 (thread    4) f
STEP   217 / 491 (thread    6) f
STEP   218 / 491 (thread    1) f
STEP   210 / 491 (thread    9) f
STEP   219 / 491 (thread    4) f
STEP   222 / 491 (thread   11) f
STEP   224 / 491 (thread    6) f
STEP   221 / 491 (thread    4) f
STEP   225 / 491 (thread    8) f
STEP   196 / 491 (thread    5) f
STEP   226 / 491 (thread    6) f
STEP   227 / 491 (thread   11) f
STEP   228 / 491 (thread    8) f
STEP   229 / 491 (thread    9) f
STEP   231 / 491 (thread    4) f
STEP   232 / 491 (thread    5) f
STEP   234 / 491 (thread    6) f
STEP   200 / 491 (thread    7) f
STEP   235 / 491 (thread    9) f
STEP   236 / 491 (thread    4) f
STEP   237 / 491 (thread    4) f
STEP   238 / 491 (thread    6) f
STEP   239 / 491 (thread    5) f
STEP   241 / 491 (thread    7) f
STEP   202 / 491 (thread    0) f
STEP   242 / 491 (thread    6) f
STEP   243 / 491 (thread    5) f
STEP   244 / 491 (thread    7) f
STEP   245 / 491 (thread    6) f
STEP   246 / 491 (thread    5) f
STEP   247 / 491 (thread    4) f
STEP   248 / 491 (thread    7) f
STEP   249 / 491 (thread    0) f
STEP   211 / 491 (thread   10) f
STEP   251 / 491 (thread    7) f
STEP   253 / 491 (thread    5) f
STEP   254 / 491 (thread    0) f
STEP   255 / 491 (thread    7) f
STEP   256 / 491 (thread    0) f
STEP   257 / 491 (thread    5) f
STEP   258 / 491 (thread   10) f
STEP   212 / 491 (thread    3) f
STEP   259 / 491 (thread    7) f
STEP   260 / 491 (thread    7) f
STEP   262 / 491 (thread    7) f
STEP   261 / 491 (thread    0) f
STEP   263 / 491 (thread    7) f
STEP   264 / 491 (thread    5) f
STEP   265 / 491 (thread   10) f
STEP   266 / 491 (thread    7) f
STEP   267 / 491 (thread    0) f
STEP   268 / 491 (thread    5) f
STEP   269 / 491 (thread   10) f
STEP   270 / 491 (thread    7) f
STEP   271 / 491 (thread    5) f
STEP   272 / 491 (thread   10) f
STEP   220 / 491 (thread    2) f
STEP   274 / 491 (thread    0) f
STEP   275 / 491 (thread    5) f
STEP   276 / 491 (thread    7) f
STEP   277 / 491 (thread    0) f
STEP   280 / 491 (thread    5) f
STEP   223 / 491 (thread    1) f
STEP   281 / 491 (thread    2) f
STEP   279 / 491 (thread    7) f
STEP   283 / 491 (thread    5) f
STEP   285 / 491 (thread    7) f
STEP   286 / 491 (thread    5) f
STEP   284 / 491 (thread    2) f
STEP   230 / 491 (thread    8) f
STEP   288 / 491 (thread    7) f
STEP   287 / 491 (thread    1) f
STEP   289 / 491 (thread    5) f
STEP   290 / 491 (thread    5) f
STEP   291 / 491 (thread    5) f
STEP   292 / 491 (thread    2) f
STEP   294 / 491 (thread    7) f
STEP   233 / 491 (thread   11) f
STEP   296 / 491 (thread    7) f
STEP   295 / 491 (thread    8) f
STEP   293 / 491 (thread    5) f
STEP   299 / 491 (thread    7) f
STEP   301 / 491 (thread    8) f
STEP   298 / 491 (thread    2) f
STEP   302 / 491 (thread   11) f
STEP   240 / 491 (thread    9) f
STEP   303 / 491 (thread   11) f
STEP   305 / 491 (thread    2) f
STEP   300 / 491 (thread    5) f
STEP   306 / 491 (thread    8) f
STEP   307 / 491 (thread   11) f
STEP   308 / 491 (thread    2) f
STEP   310 / 491 (thread    5) f
STEP   311 / 491 (thread    9) f
STEP   312 / 491 (thread   11) f
STEP   250 / 491 (thread    6) f
STEP   313 / 491 (thread    9) f
STEP   314 / 491 (thread   11) f
STEP   315 / 491 (thread    5) f
STEP   316 / 491 (thread    2) f
STEP   319 / 491 (thread   11) f
STEP   320 / 491 (thread    2) f
STEP   318 / 491 (thread    5) f
STEP   321 / 491 (thread    5) f
STEP   322 / 491 (thread    6) f
STEP   252 / 491 (thread    4) f
STEP   323 / 491 (thread    6) f
STEP   326 / 491 (thread    5) f
STEP   325 / 491 (thread   11) f
STEP   327 / 491 (thread    6) f
STEP   329 / 491 (thread   11) f
STEP   331 / 491 (thread    4) f
STEP   273 / 491 (thread    3) f
STEP   332 / 491 (thread   11) f
STEP   334 / 491 (thread   11) f
STEP   335 / 491 (thread   11) f
STEP   278 / 491 (thread   10) f
STEP   337 / 491 (thread   11) f
STEP   338 / 491 (thread   10) f
STEP   282 / 491 (thread    0) f
STEP   340 / 491 (thread   10) f
STEP   342 / 491 (thread    0) f
STEP   297 / 491 (thread    1) f
STEP   344 / 491 (thread    1) f
STEP   304 / 491 (thread    7) f
STEP   345 / 491 (thread    1) f
STEP   347 / 491 (thread    7) f
STEP   309 / 491 (thread    8) f
STEP   348 / 491 (thread    7) f
STEP   350 / 491 (thread    8) f
STEP   317 / 491 (thread    9) f
STEP   352 / 491 (thread    9) f
STEP   324 / 491 (thread    2) f
STEP   353 / 491 (thread    9) f
STEP   328 / 491 (thread    5) f
STEP   356 / 491 (thread    5) f
STEP   330 / 491 (thread    6) f
STEP   358 / 491 (thread    6) f
STEP   333 / 491 (thread    4) f
STEP   359 / 491 (thread    6) f
STEP   361 / 491 (thread    6) f
STEP   336 / 491 (thread    3) f
STEP   362 / 491 (thread    6) f
STEP   363 / 491 (thread    6) f
STEP   364 / 491 (thread    6) f
STEP   365 / 491 (thread    6) f
STEP   367 / 491 (thread    3) f
STEP   339 / 491 (thread   11) f
STEP   368 / 491 (thread    3) f
STEP   369 / 491 (thread    3) f
STEP   371 / 491 (thread   11) f
STEP   341 / 491 (thread   10) f
STEP   372 / 491 (thread   11) f
STEP   373 / 491 (thread   11) f
STEP   375 / 491 (thread   10) f
STEP   343 / 491 (thread    0) f
STEP   376 / 491 (thread   10) f
STEP   377 / 491 (thread   10) f
STEP   378 / 491 (thread    0) f
STEP   346 / 491 (thread    1) f
STEP   379 / 491 (thread   10) f
STEP   380 / 491 (thread    0) f
STEP   381 / 491 (thread   10) f
STEP   383 / 491 (thread   10) f
STEP   384 / 491 (thread   10) f
STEP   386 / 491 (thread    1) f
STEP   349 / 491 (thread    7) f
STEP   387 / 491 (thread    1) f
STEP   388 / 491 (thread    1) f
STEP   389 / 491 (thread    1) f
STEP   390 / 491 (thread    1) f
STEP   391 / 491 (thread    1) f
STEP   392 / 491 (thread    1) f
STEP   351 / 491 (thread    8) f
STEP   394 / 491 (thread    1) f
STEP   395 / 491 (thread    1) f
STEP   397 / 491 (thread    8) f
STEP   354 / 491 (thread    9) f
STEP   398 / 491 (thread    8) f
STEP   399 / 491 (thread    8) f
STEP   400 / 491 (thread    8) f
STEP   401 / 491 (thread    8) f
STEP   402 / 491 (thread    9) f
STEP   355 / 491 (thread    2) f
STEP   403 / 491 (thread    8) f
STEP   404 / 491 (thread    8) f
STEP   405 / 491 (thread    8) f
STEP   406 / 491 (thread    9) f
STEP   407 / 491 (thread    8) f
STEP   408 / 491 (thread    9) f
STEP   409 / 491 (thread    8) f
STEP   410 / 491 (thread    9) f
STEP   411 / 491 (thread    8) f
STEP   412 / 491 (thread    2) f
STEP   357 / 491 (thread    5) f
STEP   414 / 491 (thread    9) f
STEP   415 / 491 (thread    8) f
STEP   417 / 491 (thread    9) f
STEP   418 / 491 (thread    5) f
STEP   360 / 491 (thread    4) f
STEP   419 / 491 (thread    5) f
STEP   420 / 491 (thread    9) f
STEP   421 / 491 (thread    5) f
STEP   422 / 491 (thread    9) f
STEP   423 / 491 (thread    5) f
STEP   424 / 491 (thread    9) f
STEP   425 / 491 (thread    9) f
STEP   427 / 491 (thread    9) f
STEP   428 / 491 (thread    9) f
STEP   430 / 491 (thread    4) f
STEP   366 / 491 (thread    6) f
STEP   431 / 491 (thread    4) f
STEP   432 / 491 (thread    4) f
STEP   433 / 491 (thread    4) f
STEP   434 / 491 (thread    4) f
STEP   436 / 491 (thread    6) f
STEP   370 / 491 (thread    3) f
STEP   437 / 491 (thread    6) f
STEP   438 / 491 (thread    6) f
STEP   439 / 491 (thread    6) f
STEP   440 / 491 (thread    6) f
STEP   441 / 491 (thread    6) f
STEP   442 / 491 (thread    3) f
STEP   374 / 491 (thread   11) f
STEP   443 / 491 (thread    6) f
STEP   444 / 491 (thread    6) f
STEP   446 / 491 (thread    6) f
STEP   447 / 491 (thread    6) f
STEP   382 / 491 (thread    0) f
STEP   448 / 491 (thread   11) f
STEP   449 / 491 (thread    6) f
STEP   451 / 491 (thread    6) f
STEP   453 / 491 (thread    0) f
STEP   385 / 491 (thread   10) f
STEP   454 / 491 (thread    0) f
STEP   455 / 491 (thread    0) f
STEP   456 / 491 (thread    0) f
STEP   458 / 491 (thread   10) f
STEP   393 / 491 (thread    7) f
STEP   460 / 491 (thread    7) f
STEP   396 / 491 (thread    1) f
STEP   461 / 491 (thread    7) f
STEP   463 / 491 (thread    1) f
STEP   413 / 491 (thread    2) f
STEP   464 / 491 (thread    1) f
STEP   416 / 491 (thread    8) f
STEP   467 / 491 (thread    8) f
STEP   426 / 491 (thread    5) f
STEP   429 / 491 (thread    9) f
STEP   435 / 491 (thread    4) f
STEP   471 / 491 (thread    4) f
STEP   445 / 491 (thread    3) f
STEP   472 / 491 (thread    4) f
STEP   474 / 491 (thread    3) f
STEP   450 / 491 (thread   11) d
STEP   475 / 491 (thread    3) f
STEP   452 / 491 (thread    6) d h
STEP   478 / 491 (thread    6) f
STEP   457 / 491 (thread    0) d h
STEP   459 / 491 (thread   10) d h
STEP   462 / 491 (thread    7) d h
STEP   482 / 491 (thread    7) f
STEP   465 / 491 (thread    1) d h
STEP   466 / 491 (thread    2) d h
STEP   468 / 491 (thread    8) d h
STEP   469 / 491 (thread    5) d h
STEP   470 / 491 (thread    9) d h
STEP   473 / 491 (thread    4) d h
STEP   476 / 491 (thread    3) d h
STEP   477 / 491 (thread   11) d h
STEP   479 / 491 (thread    6) d h
STEP   480 / 491 (thread    0) d h
STEP   481 / 491 (thread   10) d h
STEP   483 / 491 (thread    7) d h
STEP   484 / 491 (thread    1) d h
STEP   485 / 491 (thread    2) d h
STEP   486 / 491 (thread    8) d h
STEP   487 / 491 (thread    5) d h
STEP   488 / 491 (thread    9) d h
STEP   489 / 491 (thread    4) d h
STEP   490 / 491 (thread    3) d h
STEP   491 / 491 (thread   11) d h
done.

Making a distance matrix from msa.. 

    0 / 492 (thread    0)
  100 / 492 (thread    2)
  200 / 492 (thread    6)
  300 / 492 (thread    7)
  400 / 492 (thread    8)
done.

Constructing a UPGMA tree (efffree=1) ... 

    0 / 492
   10 / 492
   20 / 492
   30 / 492
   40 / 492
   50 / 492
   60 / 492
   70 / 492
   80 / 492
   90 / 492
  100 / 492
  110 / 492
  120 / 492
  130 / 492
  140 / 492
  150 / 492
  160 / 492
  170 / 492
  180 / 492
  190 / 492
  200 / 492
  210 / 492
  220 / 492
  230 / 492
  240 / 492
  250 / 492
  260 / 492
  270 / 492
  280 / 492
  290 / 492
  300 / 492
  310 / 492
  320 / 492
  330 / 492
  340 / 492
  350 / 492
  360 / 492
  370 / 492
  380 / 492
  390 / 492
  400 / 492
  410 / 492
  420 / 492
  430 / 492
  440 / 492
  450 / 492
  460 / 492
  470 / 492
  480 / 492
  490 / 492
done.

Progressive alignment 2/2... 

STEP     1 / 491 (thread    0) f
STEP     2 / 491 (thread    1) f
STEP     3 / 491 (thread    2) f
STEP     4 / 491 (thread    3) f
STEP     5 / 491 (thread    4) f
STEP     6 / 491 (thread    5) f
STEP     7 / 491 (thread    6) f
STEP     8 / 491 (thread    7) f
STEP     9 / 491 (thread    8) f
STEP    10 / 491 (thread    9) f
STEP    11 / 491 (thread   10) f
STEP    14 / 491 (thread    0) f
STEP    13 / 491 (thread    9) f
STEP    18 / 491 (thread    5) f
STEP    19 / 491 (thread    1) f
STEP    23 / 491 (thread    6)
STEP    22 / 491 (thread    0) f f
STEP    12 / 491 (thread   11) f
Reallocating..done. *alloclen = 1604

STEP    21 / 491 (thread    8) f
STEP    16 / 491 (thread    3) f
STEP    29 / 491 (thread    6) f
STEP    30 / 491 (thread    6) f
STEP    24 / 491 (thread   10) f
STEP    33 / 491 (thread    6) f
STEP    31 / 491 (thread    8) f
STEP    34 / 491 (thread    6) f
STEP    35 / 491 (thread    6) f
STEP    36 / 491 (thread    8) f
STEP    37 / 491 (thread   10) f
STEP    26 / 491 (thread    5) f
STEP    38 / 491 (thread    6) f
STEP    41 / 491 (thread    6) f
STEP    39 / 491 (thread    8) f
STEP    40 / 491 (thread   10) f
STEP    42 / 491 (thread    5) f
STEP    44 / 491 (thread    8) f
STEP    47 / 491 (thread    8) f
STEP    48 / 491 (thread    8) f
STEP    49 / 491 (thread    8) f
STEP    51 / 491 (thread   11) f
STEP    15 / 491 (thread    2) f
STEP    52 / 491 (thread   11) f
STEP    53 / 491 (thread    2) f
STEP    17 / 491 (thread    4) f
STEP    54 / 491 (thread    2) f
STEP    55 / 491 (thread   11) f
STEP    56 / 491 (thread   11) f
STEP    57 / 491 (thread   11) f
STEP    58 / 491 (thread    4) f
STEP    20 / 491 (thread    7) f
STEP    59 / 491 (thread    2) f
STEP    60 / 491 (thread   11) f
STEP    61 / 491 (thread    2) f
STEP    62 / 491 (thread    4) f
STEP    63 / 491 (thread    4) f
STEP    64 / 491 (thread    2) f
STEP    65 / 491 (thread    4) f
STEP    66 / 491 (thread   11) f
STEP    67 / 491 (thread    4) f
STEP    68 / 491 (thread   11) f
STEP    69 / 491 (thread    2) f
STEP    70 / 491 (thread    7) f
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STEP   491 / 491 (thread    2) d h
done.

disttbfast (nuc) Version 7.505
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
12 thread(s)


Strategy:
 FFT-NS-2 (Fast but rough)
 Progressive method (guide trees were built 2 times.)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

FastTree Version 2.1.10 Double precision (No SSE3), OpenMP (12 threads)
Alignment: /nephele_data/tmp/qiime2-archive-hiux3lpj/b9cf02ad-13ad-40b6-924d-69d1486e390b/data/aligned-dna-sequences.fasta
Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Jukes-Cantor, CAT approximation with 20 rate categories
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: FastTreeMP -quote -nt /nephele_data/tmp/qiime2-archive-hiux3lpj/b9cf02ad-13ad-40b6-924d-69d1486e390b/data/aligned-dna-sequences.fasta

      0.12 seconds: Joined    400 of    473
Initial topology in 0.15 seconds
Refining topology: 36 rounds ME-NNIs, 2 rounds ME-SPRs, 18 rounds ML-NNIs
      0.25 seconds: SPR round   1 of   2, 101 of 950 nodes
      0.38 seconds: SPR round   1 of   2, 401 of 950 nodes
      0.50 seconds: SPR round   1 of   2, 701 of 950 nodes
      0.61 seconds: ME NNI round 13 of 36, 1 of 474 splits
      0.72 seconds: SPR round   2 of   2, 201 of 950 nodes
      0.82 seconds: SPR round   2 of   2, 501 of 950 nodes
      0.94 seconds: SPR round   2 of   2, 801 of 950 nodes
Total branch-length 6.916 after 1.05 sec
      1.05 seconds: ML Lengths 1 of 474 splits
      1.16 seconds: ML Lengths 401 of 474 splits
      1.28 seconds: ML NNI round 1 of 18, 201 of 474 splits, 80 changes (max delta 7.861)
ML-NNI round 1: LogLk = -10797.247 NNIs 163 max delta 7.86 Time 1.41
      1.41 seconds: Site likelihoods with rate category 1 of 20
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.832 so that average rate = 1.0
CAT-based log-likelihoods may not be comparable across runs
Use -gamma for approximate but comparable Gamma(20) log-likelihoods
      1.55 seconds: ML NNI round 2 of 18, 101 of 474 splits, 24 changes (max delta 2.114)
      1.65 seconds: ML NNI round 2 of 18, 301 of 474 splits, 67 changes (max delta 4.193)
ML-NNI round 2: LogLk = -8368.184 NNIs 116 max delta 4.19 Time 1.75
      1.80 seconds: ML NNI round 3 of 18, 101 of 474 splits, 13 changes (max delta 0.834)
      1.90 seconds: ML NNI round 3 of 18, 301 of 474 splits, 63 changes (max delta 4.744)
ML-NNI round 3: LogLk = -8333.725 NNIs 85 max delta 4.74 Time 1.97
      2.02 seconds: ML NNI round 4 of 18, 101 of 474 splits, 11 changes (max delta 0.977)
      2.12 seconds: ML NNI round 4 of 18, 301 of 474 splits, 45 changes (max delta 2.921)
ML-NNI round 4: LogLk = -8312.306 NNIs 47 max delta 2.92 Time 2.14
      2.23 seconds: ML NNI round 5 of 18, 201 of 474 splits, 26 changes (max delta 1.089)
ML-NNI round 5: LogLk = -8305.164 NNIs 33 max delta 1.09 Time 2.27
ML-NNI round 6: LogLk = -8280.543 NNIs 21 max delta 9.49 Time 2.36
      2.35 seconds: ML NNI round 7 of 18, 1 of 474 splits
ML-NNI round 7: LogLk = -8274.485 NNIs 13 max delta 2.25 Time 2.44
      2.48 seconds: ML NNI round 8 of 18, 101 of 474 splits, 6 changes (max delta 0.449)
ML-NNI round 8: LogLk = -8273.026 NNIs 6 max delta 0.45 Time 2.49
ML-NNI round 9: LogLk = -8271.596 NNIs 6 max delta 0.98 Time 2.52
ML-NNI round 10: LogLk = -8269.816 NNIs 4 max delta 1.00 Time 2.56
ML-NNI round 11: LogLk = -8269.186 NNIs 3 max delta 0.06 Time 2.58
Turning off heuristics for final round of ML NNIs (converged)
      2.63 seconds: ML NNI round 12 of 18, 101 of 474 splits, 2 changes (max delta 0.003)
      2.77 seconds: ML NNI round 12 of 18, 401 of 474 splits, 11 changes (max delta 1.385)
ML-NNI round 12: LogLk = -8266.216 NNIs 12 max delta 1.39 Time 2.81 (final)
      2.88 seconds: ML Lengths 401 of 474 splits
Optimize all lengths: LogLk = -8265.924 Time 2.90
      3.02 seconds: ML split tests for    100 of    473 internal splits
      3.13 seconds: ML split tests for    200 of    473 internal splits
      3.25 seconds: ML split tests for    300 of    473 internal splits
      3.37 seconds: ML split tests for    400 of    473 internal splits
Total time: 3.46 seconds Unique: 476/492 Bad splits: 2/473 Worst delta-LogLk 0.645
2023-04-02 02:33:58,677 /var/log/job.log INFO     Saving trees to /nephele_data/outputs/phylo
2023-04-02 02:33:58,678 /var/log/job.log INFO     Checking output file from dada2 pipeline required by data visualization pipeline.
2023-04-02 02:33:58,687 /var/log/job.log INFO     Loading R module: datavis16s.
2023-04-02 02:33:58,687 sh.command   DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>: starting process
2023-04-02 02:33:58,719 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: started process
2023-04-02 02:33:58,720 sh.command.process.streamwriter DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>.stdin: parsed stdin as a None
2023-04-02 02:33:58,721 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamWriter object at 0x7f2407f19460> ready for more input
2023-04-02 02:33:58,721 sh.command   INFO     <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s', pid 6009>: process started
2023-04-02 02:33:58,721 sh.command.process.streamwriter DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>.stdin: done reading
2023-04-02 02:33:58,721 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: acquiring wait lock to wait for completion
2023-04-02 02:33:58,721 sh.command.process.streamwriter DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>.stdin: closing, but flushing first
2023-04-02 02:33:58,721 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: got wait lock
2023-04-02 02:33:58,721 sh.stream_bufferer DEBUG    acquiring buffering lock for flushing buffer
2023-04-02 02:33:58,722 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: exit code not set, waiting on pid
2023-04-02 02:33:58,722 sh.stream_bufferer DEBUG    got buffering lock for flushing buffer
2023-04-02 02:33:58,722 sh.stream_bufferer DEBUG    released buffering lock for flushing buffer
2023-04-02 02:33:58,722 sh.command.process.streamwriter DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>.stdin: got chunk size 0 to flush: b''
2023-04-02 02:33:59,126 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamReader object at 0x7f2407e75880> ready to be read from
2023-04-02 02:33:59,126 sh.streamreader DEBUG    got chunk size 89: b'* installing to library \xe2\x80\x98/us'
2023-04-02 02:33:59,126 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:33:59,126 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:33:59,126 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:33:59,135 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamReader object at 0x7f2407e75880> ready to be read from
2023-04-02 02:33:59,136 sh.streamreader DEBUG    got chunk size 51: b'* installing *source* package '
2023-04-02 02:33:59,136 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:33:59,136 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:33:59,136 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:33:59,136 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamReader object at 0x7f2407e75880> ready to be read from
2023-04-02 02:33:59,136 sh.streamreader DEBUG    got chunk size 29: b'** using staged installation\n'
2023-04-02 02:33:59,136 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:33:59,136 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:33:59,136 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:33:59,153 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamReader object at 0x7f2407e75880> ready to be read from
2023-04-02 02:33:59,153 sh.streamreader DEBUG    got chunk size 5: b'** R\n'
2023-04-02 02:33:59,153 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:33:59,153 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:33:59,153 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:33:59,158 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamReader object at 0x7f2407e75880> ready to be read from
2023-04-02 02:33:59,159 sh.streamreader DEBUG    got chunk size 53: b'** byte-compile and prepare pa'
2023-04-02 02:33:59,159 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:33:59,159 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:33:59,159 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:34:01,290 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamReader object at 0x7f2407e75880> ready to be read from
2023-04-02 02:34:01,291 sh.streamreader DEBUG    got chunk size 28: b'** building package indices\n'
2023-04-02 02:34:01,291 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:34:01,291 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:34:01,291 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:34:01,502 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamReader object at 0x7f2407e75880> ready to be read from
2023-04-02 02:34:01,502 sh.streamreader DEBUG    got chunk size 70: b'** testing if installed packag'
2023-04-02 02:34:01,502 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:34:01,502 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:34:01,502 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:34:03,128 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamReader object at 0x7f2407e75880> ready to be read from
2023-04-02 02:34:03,128 sh.streamreader DEBUG    got chunk size 66: b'** testing if installed packag'
2023-04-02 02:34:03,128 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:34:03,128 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:34:03,128 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:34:04,763 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamReader object at 0x7f2407e75880> ready to be read from
2023-04-02 02:34:04,763 sh.streamreader DEBUG    got chunk size 78: b'** testing if installed packag'
2023-04-02 02:34:04,763 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:34:04,763 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:34:04,763 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:34:04,764 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamReader object at 0x7f2407e75880> ready to be read from
2023-04-02 02:34:04,764 sh.streamreader DEBUG    got chunk size 20: b'* DONE (datavis16s)\n'
2023-04-02 02:34:04,764 sh.stream_bufferer DEBUG    acquiring buffering lock to process chunk (buffering: 1)
2023-04-02 02:34:04,764 sh.stream_bufferer DEBUG    got buffering lock to process chunk (buffering: 1)
2023-04-02 02:34:04,764 sh.stream_bufferer DEBUG    released buffering lock for processing chunk (buffering: 1)
2023-04-02 02:34:04,769 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamReader object at 0x7f2407f19580> ready to be read from
2023-04-02 02:34:04,769 sh.command.process.streamreader DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>.stdout: got errno 5, done reading
2023-04-02 02:34:04,769 sh.command.process DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>: <sh.StreamReader object at 0x7f2407e75880> ready to be read from
2023-04-02 02:34:04,769 sh.streamreader DEBUG    got no chunk, done reading
2023-04-02 02:34:04,770 sh.stream_bufferer DEBUG    acquiring buffering lock for flushing buffer
2023-04-02 02:34:04,770 sh.stream_bufferer DEBUG    got buffering lock for flushing buffer
2023-04-02 02:34:04,770 sh.stream_bufferer DEBUG    released buffering lock for flushing buffer
2023-04-02 02:34:04,770 sh.command.process.streamreader DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s'>.<Process 6009 [b'/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R', b'CMD', b'INSTALL', b'--no-help', b'--use-vanilla', b'--preclean', b'/usr/local/src/nephele2/pipelines/datavis16s']>.stdout: got chunk size 0 to flush: b''
2023-04-02 02:34:04,770 sh.stream_bufferer DEBUG    acquiring buffering lock for flushing buffer
2023-04-02 02:34:04,770 sh.stream_bufferer DEBUG    got buffering lock for flushing buffer
2023-04-02 02:34:04,770 sh.stream_bufferer DEBUG    released buffering lock for flushing buffer
2023-04-02 02:34:04,770 sh.streamreader DEBUG    got chunk size 0 to flush: b''
2023-04-02 02:34:04,770 sh.command   DEBUG    <Command '/usr/local/bin/miniconda3/envs/qiime2-2022.2/bin/R CMD INSTALL --no-help --use-vanilla --preclean /usr/local/src/nephele2/pipelines/datavis16s', pid 6009>: process completed
2023-04-02 02:34:04,771 /var/log/job.log INFO     Running data visualization pipeline.
2023-04-02 02:34:17,001 /var/log/job.log INFO     DADA2 pipeline complete.