Xi Chen

thanks for the explanation, but why `ms` dropped from 8942 to 2916 even if the two alignments can be seen as identical? Is this a feature of `ms`?

After some digging I saw by default the sam file is sorted like (for a single query sequence): ``` line 1 -- primary 1 line 2 -- secondary 1 of...

It seems your metadata files have a third column called "unnamed: 3", please remove the space in the header. It may cause the error.

Sry I missed this. This warning means some sequences IDs in your .fasta file cannot be found in the structure file. You may write a simple script to check the...

hi, args-oap can only handle short reads so if your metatranscriptomic data are generated by e.g. Illumina data then ok, but the results may not be directly comparable with metagenomic...

RPKM requires normalising against read counts. For metagenomic, reads are randomly distributed along the genomes; for metatranscriptomic, only genes that express will be sequenced. So the total number of reads...

Your fastq file is truncated/incomplete somehow. Did you by any chance concatenated a fastq with a fasta file? The + line is missing in line 29480427, please double check the...

I would recommand to run `seqkit sana` on your fastq file to see whether there are malformed records. Reference: https://bioinf.shenwei.me/seqkit/usage/#sana

Did you check file ? Although its named after .fa, `diamond` identifies it as a fq file. Based on your screenshot, the file indeed should be a fq file, so...

try `seqkit fq2fa` to convert your file into fa format, then run `args_oap` on the converted files. If something is wrong with your file seqkit should raise errors.