Hi there! I am processing reads to generate contigs (using make.file) and I got the following error:
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Processing file pair 1T802G_S45_L001_R1_001.fastq - 1T802G_S45_L001_R2_001.fastq (files 44 of 53)
Making contigs…
M02149_635_000000000-KPLGJ_1_2103_14044_27106 is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
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Segmentation fault
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The error message repeated many times before ultimately saying “Segmentation fault” and quitting Mothur.
Any help or suggestions are appreciated!
Hi there - I suspect that someone preprocessed/trimmed the sequences before you go ahold of them. Would it be possible to go back and get the sequence files as they came off the sequencer?
Pat
Hello! Thank you for your reply!
Yes the sequencing center demultiplexed the sequence files for us, and to my knowledge that is all that they did. I do have access to the sequencing files as they came off the sequencer.
A couple additional questions:
- I am sorry to ask this - but do you think it would be worth running the fastq files through Trimmomatic prior to hopefully remove the unpaired reads from the paired end fastq files in question?
- I ran remove-seqs() but was unsure how to integrate the output from that command into the continuation of contig building using make.contigs(). Is there a tutorial or online resource for integrating those two pipelines?
Many thanks!!
In my experience, trimming the sequences outside of mothur always results in a loss of quality. I wouldn’t bother with trimmomatic.
Pat