gene_markers_identification crashed

[jiaojiaoguan]

Dear authors,

Thanks for your tools! I have also the problems,
[e] Command '['/home/xxx/miniconda3/envs/phylophlan/bin/diamond', 'blastx', '--quiet', '--threads', '1', '--outfmt', '6', '--more-sensitive', '--id', '50', '--max-hsps', '35', '-k', '0', '--query-gencode', '11', '--query', 'output_meta_vlp_SGB_medium_diversity/tmp/clean_dna/Rat226_bin.29.fa', '--db', 'phylophlan_databases/phylophlan/phylophlan.dmnd', '--out', 'output_meta_vlp_SGB_medium_diversity/tmp/map_dna/Rat226_bin.29.b6o.bkp']' returned non-zero exit status 1.

I have followed your instruction and run the diamond blastx directly and found that the file output_meta_vlp_SGB_medium_diversity/tmp/clean_dna/Rat226_bin.29.fa is empty. That's the reason. But I want to know what it mean. The original Rat226_bin.29.fa file is not empty. what operation have done for the clean steps? Can I remove Rat226_bin.29.fa file directly from the input?

thanks very much!

Best,
Jiaojiao

[apoosakkannu]

Hi, I have similar issue of gene_markers_identifications crashed. I hereby attached my script, out and error files. Please give some suggestions to get through. Please consider i am new to phylophlan.

phylophlan_err_27850540_4294967294.txt
phylophlan_out_27850540_4294967294.txt

phytoplan.txt

[fasnicar]

Dear both, thank you for using PhyloPhlAn and for reporting this issue.

The cleaning step has limited impact on genomes. Your logs should show you that --min_num_proteins is set to 1 and --min_len_protein to 50. This means that any input (genome or proteome) will be discarded if it contains fewer than 1 contig. Additionally, sequences within that input shorter than 50 units (nucleotides for genomes, amino acids for proteomes) will be excluded from the cleaned output.

So, it is strange that you find empty files, unless all contigs in your genomes have fewer than 50 nucleotides.

Another thing to double-check, which I noticed in the error output from @apoosakkannu, is the file name. The error file provided reports on line 4:

/usr/local/bin/diamond blastx --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0 --query-gencode 11 --query /scratch/project_2003832/shotgun/arg_search/host_removal/trimreads/bins/ecoli_bins/phyloplan_output/tmp/clean_dna/bin.1_15AVilppulaWood .fna --db /scratch/project_2003832/shotgun/arg_search/phyloplan_db/phylophlan/phylophlan.dmnd --out /scratch/project_2003832/shotgun/arg_search/host_removal/trimreads/bins/ecoli_bins/phyloplan_output/tmp/map_dna/bin.1_15AVilppulaWood .b6o.bkp

If you notice, the --query param has:

/scratch/project_2003832/shotgun/arg_search/host_removal/trimreads/bins/ecoli_bins/phyloplan_output/tmp/clean_dna/bin.1_15AVilppulaWood .fna

with a space at the end of the file name. I'm not 100% sure, but I guess that the space can cause problems with the execution of diamond.

Thanks,
Francesco