I am using deblur denoise-other (with the SILVA 132 DB as the reference) on 18S amplicon data. I have merged the paired-end reads using the VSearch End-Joining tool in QIIME.
Traceback (most recent call last):
File "/bigdata/biklab/shared/pkgs/conda/qiime2-2018.8/lib/python3.5/site-packages/skbio/io/registry.py", line 914, in wrapped_sniffer
return sniffer(fh)
File "/bigdata/biklab/shared/pkgs/conda/qiime2-2018.8/lib/python3.5/site-packages/skbio/io/format/fastq.py", line 320, in _fastq_sniffer
if split_length == 10 and description[1] in 'YN':
IndexError: list index out of range
FormatIdentificationWarning)
/bigdata/biklab/shared/pkgs/conda/qiime2-2018.8/lib/python3.5/site-packages/deblur/workflow.py:92: UserWarning: input file /tmp/qiime2-archive-_acuosa6/f851d4b9-c777-4e87-b7b6-e527f2b61f0e/data/NPRB3_WLK_02_125_L001_R1_001.fastq.gz does not appear to be FASTA or FASTQ
warnings.warn(msg, UserWarning)
/bigdata/biklab/shared/pkgs/conda/qiime2-2018.8/lib/python3.5/site-packages/deblur/workflow.py:851: UserWarning: Problem removing artifacts from file /tmp/qiime2-archive-_acuosa6/f851d4b9-c777-4e87-b7b6-e527f2b61f0e/data/NPRB3_WLK_02_125_L001_R1_001.fastq.gz
seqs_fp, UserWarning)
/bigdata/biklab/shared/pkgs/conda/qiime2-2018.8/lib/python3.5/site-packages/skbio/io/registry.py:922: FormatIdentificationWarning: '_fastq_sniffer' has encountered a problem.
My files are FASTQ Format, so I don’t know what is causing this error.
When I run it with the --verbose flag I get the following:
INFO(47056145847104)2018-12-18 15:36:11,096:launch_workflow for file /tmp/qiime2-archive-_acuosa6/f851d4b9-c777-4e87-b7b6-e527f2b61f0e/data/NPRB3_SF007_r2_111_L001_R1_001.fastq.gz
WARNING(47056145847104)2018-12-18 15:36:11,101:input file /tmp/qiime2-archive-_acuosa6/f851d4b9-c777-4e87-b7b6-e527f2b61f0e/data/NPRB3_SF007_r2_111_L001_R1_001.fastq.gz does not appear to be FASTA or FASTQ
INFO(47056145847104)2018-12-18 15:36:11,101:dereplicate seqs file /tmp/tmpx5iaokx6/deblur_working_dir/NPRB3_SF007_r2_111_L001_R1_001.fastq.gz.trim
ERROR(47056145847104)2018-12-18 15:36:11,120:Problem running vsearch dereplication on file /tmp/tmpx5iaokx6/deblur_working_dir/NPRB3_SF007_r2_111_L001_R1_001.fastq.gz.trim
INFO(47056145847104)2018-12-18 15:36:11,121:remove_artifacts_seqs file /tmp/tmpx5iaokx6/deblur_working_dir/NPRB3_SF007_r2_111_L001_R1_001.fastq.gz.trim.derep
WARNING(47056145847104)2018-12-18 15:36:11,121:file /tmp/tmpx5iaokx6/deblur_working_dir/NPRB3_SF007_r2_111_L001_R1_001.fastq.gz.trim.derep has size 0, continuing
WARNING(47056145847104)2018-12-18 15:36:11,121:remove artifacts failed, aborting
WARNING(47056145847104)2018-12-18 15:36:11,122:deblurring failed for file /tmp/qiime2-archive-_acuosa6/f851d4b9-c777-4e87-b7b6-e527f2b61f0e/data/NPRB3_SF007_r2_111_L001_R1_001.fastq.gz
Indeed, that file does not look empty at all! Though that is what that error message implied.
So the plot thickens — pls give me some more time to mull this over. Maybe you could share a link to that sequence file? That will help us troubleshoot locally. Thanks!
@DeSantiago,
One more test: could you try running in deblur directly? (not q2-deblur.) That will help diagnose whether this is an issue with deblur itself or if this is isolated to q2-deblur.
Thanks!