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[2023-06-04T07:45:16Z INFO coverm::contig] In sample 'cdhit_rep_seq.fna/SRR13083091_1.fq.gz', found 0 reads mapped out of 0 total (NaN%) #169

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JiaLonghao1997 opened this issue Jun 4, 2023 · 3 comments

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@JiaLonghao1997
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When we run coverm:

/home1/jialh/anaconda3/envs/MAG/bin/coverm contig  \
-t 8 -r /home1/jialh/brain/CAGs/CAGs/cdhit_rep_seq.fna  \
-1 /home1/jialh/brain/JPN/preprocessing/01_processing/05_sync/SRR13083091_1.fq.gz \
-2 /home1/jialh/brain/JPN/preprocessing/01_processing/05_sync/SRR13083091_2.fq.gz     \
--bam-file-cache-directory /home1/jialh/brain/CAGs/CAGs/coverm/SRR13083091_coverm_temp     \
--output-file /home1/jialh/brain/CAGs/CAGs/coverm/SRR13083091_gene_abundance.txt

We got the next error. The reference file cdhit_rep_seq.fna is from hundreds of samples, which include the sample SRR13083091. Why do we got this error? How to deal with this issue?
image

@wwood
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wwood commented Jun 4, 2023

Hi,

From the timestamps it seems minimap2 finishes instantly, which isn't a good sign. Is something wrong with the input files or minimap2 executable?

@Wanning888
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Hello,

I was wondering if you have managed to solve this problem. I'm having a similar issue and would greatly appreciate any help you can give me.

@JiaLonghao1997
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JiaLonghao1997 commented Jun 26, 2023 via email

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3 participants