When checking the *_bowtie2_unaligned.fa file, there is *. I have sucessfully run humann, but failed with a different batch of sequencing data. Could you please give me some suggestions? Thank you very much in advance.
* will sometimes occur as a STOP codon in protein sequences but I don’t think it should be occurring in your sequencing reads? Can you share a portion of the reads file containing the *(s)? That appears to be what is tripping up DIAMOND.
Hi Franzosa,
Thank you very much for your reply.
I double-checked the data and found that * was generated during cutadapt step. After discarding lines with *, HUMANN was running successfully. Appreciate your response again.
Hi @Xia
I am facing the same issue, what do you mean by discarded the line with *. Can you share how you did this exactly?
Any help would be appreciated. Thank you
Hi @franzosa, I have the same error. I am using version 3.8 and I have the temp folder but not the 3 main output files.
For instance my error says (path names have been changed):
CRITICAL ERROR: Error executing: /install/software/restart/py3/naga//bin/diamond blastx --query /path/to/humann_temp/sample_bowtie2_unaligned.fa --evalue 1.0 --threads 2 --top 1 --outfmt 6 --db /databases/humann3.8/uniref/uniref90_201901b_full --out /H3/sample_L001_h3/humann_temp/tmpb3yiqtuw/diamond_m8_2v9dte3w --tmpdir /path/to/humann_temp/tmpb3yiqtuw
From the earlier reply, it sounds like some QC that was done to the sequencing reads included * characters in the output, which are then tripping up DIAMOND. Have you checked your FASTQ input to make sure it doesn’t have * characters on the sequence lines?
