Error while running kma

[rafalkolenda]

I was thinking that I was able to get through the hard process of installing this software, but after some success with few reads I got this error:

subprocess.CalledProcessError: Command 'kma -ipe /home/ubuntu/kingsley-group/Food_Isolates/ConFindr/MC1883-1887-29S55/trimmed_R1.fastq.gz /home/ubuntu/kingsley-group/Food_Isolates/ConFindr/MC1883-1887-29S55/trimmed_R2.fastq.gz -t_db /home/ubuntu/kingsley-group/Rafal_Kolenda/confindr_databases/rMLST/rMLST_combined_kma -o /home/ubuntu/kingsley-group/Food_Isolates/ConFindr/MC1883-1887-29S55/kma_rmlst -t 4' returned non-zero exit status 1

[pcrxn]

Hi @rafalkolenda, could you please provide the command that you used to run ConFindr, the names of your files, and the output of running ls on the directory containing your files?

[rafalkolenda]

Hello, command: from confindr_src import confindr

# Find read files.
paired_reads = confindr.find_paired_reads('/home/ubuntu/kingsley-group/Food_Isolates/raw_reads/', forward_id='R1', reverse_id='R2')
for pair in paired_reads:
    confindr.find_contamination(pair=pair,
                                forward_id='R1', # change if yours is different
                                threads=8,
                                xmx='30g',
                                output_folder='/home/ubuntu/kingsley-group/Food_Isolates/ConFindr',
                                databases_folder='/home/ubuntu/kingsley-group/Rafal_Kolenda/confindr_databases/rMLST',
                                use_rmlst=True,
                                cross_details=True)

Name of my files: MC1883-1887-29_S55_R1_001.fastq.gz, MC1883-1887-29_S55_R2_001.fastq.gz ls of directory containing the results of my run: A20contamination.csv LA_GT63rmlst.csv A20rmlst.csv LA_GT64contamination.csv B101contamination.csv LA_GT64rmlst.csv B101rmlst.csv LA_GT65contamination.csv B104contamination.csv LA_GT65rmlst.csv B104rmlst.csv LA_GT67contamination.csv B105contamination.csv LA_GT67rmlst.csv B105rmlst.csv LA_GT68contamination.csv B111contamination.csv LA_GT68rmlst.csv B111rmlst.csv LA_GT70contamination.csv B113contamination.csv LA_GT70rmlst.csv B113rmlst.csv LA_GT71contamination.csv B118contamination.csv LA_GT71rmlst.csv B118rmlst.csv LA_GT72contamination.csv B119contamination.csv LA_GT72rmlst.csv B119rmlst.csv LA_GT73contamination.csv B35contamination.csv LA_GT73rmlst.csv B35rmlst.csv LA_GT74contamination.csv B82contamination.csv LA_GT74rmlst.csv B82rmlst.csv LA_GT75contamination.csv B90contamination.csv LA_GT75rmlst.csv B90rmlst.csv LA_GT76contamination.csv B98contamination.csv LA_GT76rmlst.csv B98rmlst.csv LA_GT77contamination.csv confindr_log.txt LA_GT77rmlst.csv confindr_report.csv LA_GT78contamination.csv LA_GT50contamination.csv LA_GT78__rmlst.csv LA_GT50rmlst.csv LA_GT79contamination.csv LA_GT51__contamination.csv LA_GT79rmlst.csv LA_GT51rmlst.csv MC1018-1022-45_S45__contamination.csv LA_GT52contamination.csv MC1018-1022-45_S45rmlst.csv LA_GT52__rmlst.csv MC1023-1027-49_S46contamination.csv LA_GT53contamination.csv MC1023-1027-49_S46__rmlst.csv LA_GT53rmlst.csv MC1023-1027-50_S47contamination.csv LA_GT54__contamination.csv MC1023-1027-50_S47rmlst.csv LA_GT54rmlst.csv MC1033-1037-63_S48__contamination.csv LA_GT55contamination.csv MC1033-1037-63_S48rmlst.csv LA_GT55__rmlst.csv MC1043-1047-67_S49contamination.csv LA_GT56contamination.csv MC1043-1047-67_S49__rmlst.csv LA_GT56rmlst.csv MC1053-1057-78_S50contamination.csv LA_GT57__contamination.csv MC1053-1057-78_S50rmlst.csv LA_GT57rmlst.csv MC1368-1372-11_S63__contamination.csv LA_GT58contamination.csv MC1368-1372-11_S63rmlst.csv LA_GT58__rmlst.csv MC1863-1867-10_S52contamination.csv LA_GT59contamination.csv MC1863-1867-10_S52__rmlst.csv LA_GT59rmlst.csv MC1863-1867-9_S51contamination.csv LA_GT60__contamination.csv MC1863-1867-9_S51rmlst.csv LA_GT60rmlst.csv MC1883-1887-28_S54__contamination.csv LA_GT61contamination.csv MC1883-1887-28_S54rmlst.csv LA_GT61__rmlst.csv MC1883-1887-29S55 LA_GT63contamination.csv

[pcrxn]

Hi @rafalkolenda,

Thanks for sharing that output. Can you please run the following within the same environment as before, and share the output?

kma -ipe /home/ubuntu/kingsley-group/Food_Isolates/ConFindr/MC1883-1887-29_S55_/trimmed_R1.fastq.gz /home/ubuntu/kingsley-group/Food_Isolates/ConFindr/MC1883-1887-29_S55_/trimmed_R2.fastq.gz -t_db /home/ubuntu/kingsley-group/Rafal_Kolenda/confindr_databases/rMLST/rMLST_combined_kma -o /home/ubuntu/kingsley-group/Food_Isolates/ConFindr/MC1883-1887-29_S55_/kma_rmlst -t 4

[pcrxn]

Will close this in a couple of weeks unless an update is provided from the author.

[pcrxn]

Closed due to inactivity.