Hello,
I am trying to merge reads for 943 samples and I keep getting the same error with some fastqs that I have concatenated as some samples were sequenced more than once:
Fatal error: More reverse reads than forward reads
Traceback (most recent call last):
File “/Users/mteachey/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in join_pairs
File “/Users/mteachey/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 232, in bound_callable
output_types, provenance)
File “/Users/mteachey/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 367, in callable_executor
output_views = self._callable(**view_args)
File “/Users/mteachey/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_vsearch/_join_pairs.py”, line 57, in join_pairs
qmax, qmaxout)
File “/Users/mteachey/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_vsearch/_join_pairs.py”, line 141, in _join_pairs_w_command_output
run_command(cmd)
File “/Users/mteachey/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_vsearch/_cluster_features.py”, line 33, in run_command
subprocess.run(cmd, check=True)
File “/Users/mteachey/miniconda3/envs/qiime2-2018.6/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘vsearch’, ‘–fastq_mergepairs’, ‘/var/folders/v4/06g73zxx0_3315vbt6xc4869ch0sww/T/qiime2-archive-dhiivbem/dff142a2-6b76-42f1-acec-c7fd4f97f2f8/data/SP13-MIDO806_54_L001_R1_001.fastq.gz’, ‘–reverse’, ‘/var/folders/v4/06g73zxx0_3315vbt6xc4869ch0sww/T/qiime2-archive-dhiivbem/dff142a2-6b76-42f1-acec-c7fd4f97f2f8/data/SP13-MIDO806_55_L001_R2_001.fastq.gz’, ‘–fastqout’, ‘/var/folders/v4/06g73zxx0_3315vbt6xc4869ch0sww/T/q2-SingleLanePerSampleSingleEndFastqDirFmt-gdul6_qr/SP13-MIDO806_256_L001_R1_001.fastq’, ‘–fastq_ascii’, ‘33’, ‘–fastq_minlen’, ‘1’, ‘–fastq_minovlen’, ‘10’, ‘–fastq_maxdiffs’, ‘10’, ‘–fastq_qmin’, ‘0’, ‘–fastq_qminout’, ‘0’, ‘–fastq_qmax’, ‘41’, ‘–fastq_qmaxout’, ‘41’, ‘–fastq_allowmergestagger’]’ returned non-zero exit status 1
I have tried to reconcile the apparent differences in sequence reads in the following ways:
- re-concatenating the files and replacing the old ones (this didn’t work)
- removing the trouble sample entirely (this worked until it hit another sample that it deemed had different numbers of reads)
I checked the file size of the sample in the error above and R1 was 88.2 MB and R2 was 88.5 MB. While there is a difference in size, other samples for which multiple fastqs were merged and of slightly different sizes passed through fine. For example, a sample from the same collection date and Miseq run with an R1 of 123.2 MB and an R2 of 123.6 MB merged at 100%. Can someone help me figure out how to resolve this without removing each sample that fails in this way, as I have so many samples to deal with?
Thanks in advance for the help!