The "File not found CMD" error in running run_purge_dups.py

[nozabey]

Dear developer,

I am new to this tool. I apologize in advance in case that I made very primitive mistakes.

I run run_purge_dups.py as follows.

/home/software/tools/purge_dups-1.2.6/scripts/run_purge_dups.py \
purge_dups.json /home/software/Links/bin tri_Sha4M

Then, the following error appeared. Could you please let me know the possible issues and a solution?

Best,
Fumi

---

calculate coverage and self-alignment
File not found CMD: ['bsub', '-K', '-q', 'normal', '-M', '20000', '-n', '12', '-R"select[mem>20000] rusage[mem=20000] span[hosts=1]"', '-J', 'minimap_tri_Sha4M_all_passed_trim_filtered.fastq', '-o', 'dtri-Sha4M-heterochromatin-scaffold-v1.2canu/coverage/minimap_tri_Sha4M_all_passed_trim_filtered.fastq_%J.o', '-e', 'dtri-Sha4M-heterochromatin-scaffold-v1.2canu/coverage/minimap_tri_Sha4M_all_passed_trim_filtered.fastq_%J.e', 'minimap2 -I 4G -x map-pb -t 12 /home4/assembly/nozawa/tri_sha4M/canu/purge_dups/dtri-Sha4M-heterochromatin-scaffold-v1.2canu.fasta /home2/assembly/nozawa/triSha4M/tri_Sha4M_all_passed_trim_filtered.fastq.gz >dtri-Sha4M-heterochromatin-scaffold-v1.2canu/coverage/tri_Sha4M_all_passed_trim_filtered.fastq.paf']
command minimap2 -I 4G -x map-pb -t 12 /home4/assembly/nozawa/tri_sha4M/canu/purge_dups/dtri-Sha4M-heterochromatin-scaffold-v1.2canu.fasta /home2/assembly/nozawa/triSha4M/tri_Sha4M_all_passed_trim_filtered.fastq.gz >dtri-Sha4M-heterochromatin-scaffold-v1.2canu/coverage/tri_Sha4M_all_passed_trim_filtered.fastq.paf failed, return code: 1
File not found CMD: ['bsub', '-K', '-q', 'normal', '-M', '5000', '-n', '1', '-R"select[mem>5000] rusage[mem=5000] span[hosts=1]"', '-J', 'split_tri_Sha4M', '-o', 'dtri-Sha4M-heterochromatin-scaffold-v1.2canu/split_aln/split_tri_Sha4M_%J.o', '-e', 'dtri-Sha4M-heterochromatin-scaffold-v1.2canu/split_aln/split_tri_Sha4M_%J.e', '/home/software/Links/bin/split_fa /home4/assembly/nozawa/tri_sha4M/canu/purge_dups/dtri-Sha4M-heterochromatin-scaffold-v1.2canu.fasta > dtri-Sha4M-heterochromatin-scaffold-v1.2canu/split_aln/dtri-Sha4M-heterochromatin-scaffold-v1.2canu.split.fa']
command /home/software/Links/bin/split_fa /home4/assembly/nozawa/tri_sha4M/canu/purge_dups/dtri-Sha4M-heterochromatin-scaffold-v1.2canu.fasta > dtri-Sha4M-heterochromatin-scaffold-v1.2canu/split_aln/dtri-Sha4M-heterochromatin-scaffold-v1.2canu.split.fa failed, return code: 1
purge duplicates

[lalomartinez]

Hi @nozabey, I have the same problem, how did you solve it?

[nozabey]

Hi, No, I have not resolved the issue. I also hope someone reply to this message and help us to resolve the issue. Best, Fumi

…

________________________________ 差出人: ***@***.*** ***@***.***> 送信日時: 2023年10月4日 0:00 宛先: dfguan/purge_dups ***@***.***> CC: 野澤　昌文 ***@***.***>; Mention ***@***.***> 件名: Re: [dfguan/purge_dups] The "File not found CMD" error in running run_purge_dups.py (Issue #130) Hi @nozabey<https://github.com/nozabey>, I have the same problem, how did you solve it? — Reply to this email directly, view it on GitHub<#130 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AL6PMAE4OO3SHTCCODHOQD3X5QSARAVCNFSM6AAAAAAZVVV3USVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBVGE3DAMZWHE>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[additive3]

Hi @nozabey, @lalomartinez

Can I ask what environment you are trying to run purge_dups in?

[Thamos]

I had the same problem when I wanted to run it locally. Adding "-p bash" to the run_purge_dups.py command fixed it for me.