ChaoLab
commented
2 years ago Hi @AnyiHu It could be due to many reasons. Did you check that all the bowtie2, samtools, sambamba, and other relevant dependencies are well-installed? And if you can mask (using '#') the lines of removing bam, sam, sorted bam files in the METABOLIC-C script, you can troubleshoot which step was going wrong.
Hi Chao,
I met a problem that the bam file cann't be found when I tried to run either the test file or my real data. I have check the read address and made sure they were correct. Could you provide some suggestions? Thanks.
Please find the log information below.
[2021-11-27 22:32:49] The Prodigal annotation is running... [2021-11-27 22:33:46] The Prodigal annotation is finished [2021-11-27 22:33:46] The hmmsearch is running with 60 cpu threads... [2021-11-27 22:37:50] The hmmsearch is finished [2021-11-27 22:37:57] Generating each hmm faa collection... [2021-11-27 22:37:57] Each hmm faa collection has been made [2021-11-27 22:37:57] The KEGG module result is calculating... [2021-11-27 22:43:29] The KEGG identifier (KO id) result is calculating... [2021-11-27 22:43:29] The KEGG identifier (KO id) seaching result is finished [2021-11-27 22:43:29] Searching CAZymes by dbCAN2... [2021-11-27 22:50:10] dbCAN2 searching is done [2021-11-27 22:50:10] Searching MEROPS peptidase... [2021-11-27 22:51:46] MEROPS peptidase searching is done [2021-11-27 22:51:48] METABOLIC table has been generated [2021-11-27 22:51:48] Drawing element cycling diagrams... [E::hts_open_format] Failed to open file "METABOLIC_out/All_gene_collections_mapped.1.sorted.bam" : No such file or directory samtools index: failed to open "METABOLIC_out/All_gene_collections_mapped.1.sorted.bam": No such file or directory rm: cannot remove 'METABOLIC_out/.bam': No such file or directory rm: cannot remove 'METABOLIC_out/.bai': No such file or directory Loading required package: shape [2021-11-27 22:53:14] Drawing element cycling diagrams finished [2021-11-27 22:53:14] Drawing metabolic handoff diagrams... [2021-11-27 22:53:18] Drawing metabolic handoff diagrams finished [2021-11-27 22:53:18] Drawing energy flow chart... ==> Processed 112/120 markers (93%) |██████████████ | [384.93marker/s, ETA 00:00 ==> Processed 22/45560 sequences (0%) | | [214.84sequence/s, ETA 0==> Processed 44/45560 sequences (0%) | | [209.74sequence/s, ETA 0==> Processed 95/45560 sequences (0%) | | [316.98sequence/s, ETA 0==> Processed 146/45560 sequences (0%) | | [370.88sequence/s, ETA ==> Processed 197/45560 sequences (0%) | | [403.23sequence/s, ETA ==> Processed 245/45560 sequences (1%) | | [418.63sequence/s, ETA ==> Processed 296/45560 sequences (1%) | | [435.30sequence/s, ETA