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file, marcelm, line, cutadapt, fastq, commented, error, ended, prematurely, problem, owner, pyblrfastqgz, sign, issue, qiime, reads, tmpqcasavaoneeightsinglelanepersampledirfmtqzgfepyblrfastqgz, tmpqiimearchivekptfmnpbbaadfefdatapyblrfastqgz, plugin, command, trimpaired, ggactachvgggtwtctaat, gtgccagcmgccgcggtaa, call, status, make, message, dataset, files, reproduce, chunks, ill, navigation, source, code, pull, requests, actions, security, closed, traceback, recent, homeqiimeminicondaenvsqiimelibpythonsitepackagescutadaptpipelinepy, run, read, iter, results, homeqiimeminicondaenvsqiimelibpythonsitepackagesqiimesdkactionpy, homeqiimeminicondaenvsqiimelibpythonsitepackagesqcutadapttrimpy, cores,

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'/tmp/qiime2-archive-kptfm8np/464bb15a-a936-48d4-8420-6f1249e567f9/data/p91_y16_b_284_l001_r1_001 '/tmp/qiime2-archive-kptfm8np/464bb15a-a936-48d4-8420-6f1249e567f9/data/p91_y16_b_285_l001_r2_001 '/tmp/q2-casavaoneeightsinglelanepersampledirfmt-q57zg2fe/p91_y16_b_284_l001_r1_001 '/tmp/q2-casavaoneeightsinglelanepersampledirfmt-q57zg2fe/p91_y16_b_285_l001_r2_001 /home/qiime2/miniconda/envs/qiime2-2017 5/site-packages/qiime2/sdk/action 5/site-packages/cutadapt/pipeline 5/site-packages/q2cli/commands 5/site-packages/q2_cutadapt/_trim 5/site-packages/cutadapt/seqio paired-end fastq files paired end reads fastq file p91_y16_b_285_l001_r2_001 src/cutadapt/_seqio marcelm closed code comment metadata assignees input fastq file run output=stdout exit status 1 data qiime plugin qza --p-front quick work diagnosing trim primers cutadapt plugin ggactachvgggtwtctaat --p-front command '['cutadapt' source resulting output fastq file qiime2 p91_y16_b_284_l001_r1_001 issue error message p91_y16_b_285_l001_r2_001 trim_paired file cd ~_seqio incorrect results cutadapt cutadapt 1 recent call works fine 12/lib/python3 bound_callable output_types callable_executor output_views = trim_paired run_commands check=true stderr=stderr '--error-rate'

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DiscussionForumPosting:
      context:https://schema.org
      headline:FASTQ file ended prematurely
      articleBody:I am using the cutadapt plugin in QIIME2 to trim primers from paired end reads. For most samples it works fine, but one sample is returning an error and I can't seem to track down the source of the problem. Any help would be appreciated. Below is the command in QIIME2 along with resulting output: qiime cutadapt trim-paired \ --i-demultiplexed-sequences ginseng/untrimmed/all-bacteria.qza \ --p-front-f GGACTACHVGGGTWTCTAAT \ --p-front-r GTGCCAGCMGCCGCGGTAA \ --p-cores 2 \ --output-dir ginseng/trimmed/all-bacteria ERROR: Traceback (most recent call last): File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/cutadapt/pipeline.py", line 454, in run (n, bp1, bp2) = self._pipeline.process_reads() File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/cutadapt/pipeline.py", line 282, in process_reads for read1, read2 in self._reader: File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/cutadapt/seqio.py", line 414, in __iter__ r2 = next(it2) File "src/cutadapt/_seqio.pyx", line 234, in __iter__ (cd ~_seqio.c:5816) cutadapt.seqio.FormatError: FASTQ file ended prematurely cutadapt: error: FASTQ file ended prematurely Traceback (most recent call last): File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 224, in __call__ results = action(**arguments) File "<decorator-gen-358>", line 2, in trim_paired File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable output_types, provenance) File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 363, in _callable_executor_ output_views = self._callable(**view_args) File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_cutadapt/_trim.py", line 172, in trim_paired run_commands(cmds) File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_cutadapt/_trim.py", line 28, in run_commands subprocess.run(cmd, check=True) File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/subprocess.py", line 398, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['cutadapt', '--cores', '2', '--error-rate', '0.1', '--times', '1', '--overlap', '3', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-q57zg2fe/P91_Y16_B_284_L001_R1_001.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-q57zg2fe/P91_Y16_B_285_L001_R2_001.fastq.gz', '--front', 'GGACTACHVGGGTWTCTAAT', '-G', 'GTGCCAGCMGCCGCGGTAA', '/tmp/qiime2-archive-kptfm8np/464bb15a-a936-48d4-8420-6f1249e567f9/data/P91_Y16_B_284_L001_R1_001.fastq.gz', '/tmp/qiime2-archive-kptfm8np/464bb15a-a936-48d4-8420-6f1249e567f9/data/P91_Y16_B_285_L001_R2_001.fastq.gz']' returned non-zero exit status 1 Plugin error from cutadapt: Command '['cutadapt', '--cores', '2', '--error-rate', '0.1', '--times', '1', '--overlap', '3', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-q57zg2fe/P91_Y16_B_284_L001_R1_001.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-q57zg2fe/P91_Y16_B_285_L001_R2_001.fastq.gz', '--front', 'GGACTACHVGGGTWTCTAAT', '-G', 'GTGCCAGCMGCCGCGGTAA', '/tmp/qiime2-archive-kptfm8np/464bb15a-a936-48d4-8420-6f1249e567f9/data/P91_Y16_B_284_L001_R1_001.fastq.gz', '/tmp/qiime2-archive-kptfm8np/464bb15a-a936-48d4-8420-6f1249e567f9/data/P91_Y16_B_285_L001_R2_001.fastq.gz']' returned non-zero exit status 1 See above for debug info.
      author:
         url:https://github.com/dk267
         type:Person
         name:dk267
      datePublished:2018-02-19T18:28:49.000Z
      interactionStatistic:
         type:InteractionCounter
         interactionType:https://schema.org/CommentAction
         userInteractionCount:7
      url:https://github.com/291/cutadapt/issues/291
      context:https://schema.org
      headline:FASTQ file ended prematurely
      articleBody:I am using the cutadapt plugin in QIIME2 to trim primers from paired end reads. For most samples it works fine, but one sample is returning an error and I can't seem to track down the source of the problem. Any help would be appreciated. Below is the command in QIIME2 along with resulting output: qiime cutadapt trim-paired \ --i-demultiplexed-sequences ginseng/untrimmed/all-bacteria.qza \ --p-front-f GGACTACHVGGGTWTCTAAT \ --p-front-r GTGCCAGCMGCCGCGGTAA \ --p-cores 2 \ --output-dir ginseng/trimmed/all-bacteria ERROR: Traceback (most recent call last): File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/cutadapt/pipeline.py", line 454, in run (n, bp1, bp2) = self._pipeline.process_reads() File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/cutadapt/pipeline.py", line 282, in process_reads for read1, read2 in self._reader: File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/cutadapt/seqio.py", line 414, in __iter__ r2 = next(it2) File "src/cutadapt/_seqio.pyx", line 234, in __iter__ (cd ~_seqio.c:5816) cutadapt.seqio.FormatError: FASTQ file ended prematurely cutadapt: error: FASTQ file ended prematurely Traceback (most recent call last): File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 224, in __call__ results = action(**arguments) File "<decorator-gen-358>", line 2, in trim_paired File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable output_types, provenance) File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 363, in _callable_executor_ output_views = self._callable(**view_args) File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_cutadapt/_trim.py", line 172, in trim_paired run_commands(cmds) File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_cutadapt/_trim.py", line 28, in run_commands subprocess.run(cmd, check=True) File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/subprocess.py", line 398, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['cutadapt', '--cores', '2', '--error-rate', '0.1', '--times', '1', '--overlap', '3', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-q57zg2fe/P91_Y16_B_284_L001_R1_001.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-q57zg2fe/P91_Y16_B_285_L001_R2_001.fastq.gz', '--front', 'GGACTACHVGGGTWTCTAAT', '-G', 'GTGCCAGCMGCCGCGGTAA', '/tmp/qiime2-archive-kptfm8np/464bb15a-a936-48d4-8420-6f1249e567f9/data/P91_Y16_B_284_L001_R1_001.fastq.gz', '/tmp/qiime2-archive-kptfm8np/464bb15a-a936-48d4-8420-6f1249e567f9/data/P91_Y16_B_285_L001_R2_001.fastq.gz']' returned non-zero exit status 1 Plugin error from cutadapt: Command '['cutadapt', '--cores', '2', '--error-rate', '0.1', '--times', '1', '--overlap', '3', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-q57zg2fe/P91_Y16_B_284_L001_R1_001.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-q57zg2fe/P91_Y16_B_285_L001_R2_001.fastq.gz', '--front', 'GGACTACHVGGGTWTCTAAT', '-G', 'GTGCCAGCMGCCGCGGTAA', '/tmp/qiime2-archive-kptfm8np/464bb15a-a936-48d4-8420-6f1249e567f9/data/P91_Y16_B_284_L001_R1_001.fastq.gz', '/tmp/qiime2-archive-kptfm8np/464bb15a-a936-48d4-8420-6f1249e567f9/data/P91_Y16_B_285_L001_R2_001.fastq.gz']' returned non-zero exit status 1 See above for debug info.
      author:
         url:https://github.com/dk267
         type:Person
         name:dk267
      datePublished:2018-02-19T18:28:49.000Z
      interactionStatistic:
         type:InteractionCounter
         interactionType:https://schema.org/CommentAction
         userInteractionCount:7
      url:https://github.com/291/cutadapt/issues/291
Person:
      url:https://github.com/dk267
      name:dk267
      url:https://github.com/dk267
      name:dk267
InteractionCounter:
      interactionType:https://schema.org/CommentAction
      userInteractionCount:7
      interactionType:https://schema.org/CommentAction
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