Entering edit mode
19 months ago
styagi
•
0
python3 /pipeline/MetaPro.py -c $config -1 $read1 -2 $read2 -o $output
[main] Version: 0.7.17-r1188
[main] CMD: /pipeline_tools/BWA/bwa mem -t 24 -B 40 -O 60 -E 10 -L 50 /Lung_data/output/assemble_contigs/data/1_mgm/contigs.fasta /Lung_data/output/duplicate_repopulation/final_results/pair_1.fastq /Lung_data/output/duplicate_repopulation/final_results/pair_2.fastq
[main] Real time: 148.480 sec; CPU: 1792.060 sec
BWA singleton contigs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 3376560 sequences (240000012 bp)...
[M::process] read 89655 sequences (4073930 bp)...
[M::mem_process_seqs] Processed 3376560 reads in 227.818 CPU sec, 9.559 real sec
[M::mem_process_seqs] Processed 89655 reads in 4.090 CPU sec, 0.185 real sec
[main] Version: 0.7.17-r1188
[main] CMD: /pipeline_tools/BWA/bwa mem -t 24 -B 40 -O 60 -E 10 -L 50 /Lung_data/output/assemble_contigs/data/1_mgm/contigs.fasta /Lung_data/output/duplicate_repopulation/final_results/singletons.fastq
[main] Real time: 22.546 sec; CPU: 238.069 sec
Making contig map
/pipeline/Scripts/assembly_make_contig_map.py:170: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead
See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
unmapped_sample_df["ID"] = "@" + unmapped_sample_df["ID"]
flush bad contigs
moving gene report
Traceback (most recent call last):
File "/pipeline/MetaPro.py", line 250, in <module>
main(config_file, pair_1, pair_2, single, contig, output_folder, args_pack, tutorial_mode)
File "/pipeline/MetaPro.py", line 68, in main
metapro_stage_obj.mp_assemble()
File "/pipeline/MetaPro_stages.py", line 778, in mp_assemble
sys.exit(dt.today(), "SPADes did not run. this is not normal. Contact admin immediately")
TypeError: exit expected at most 1 arguments, got 2
I'm working on metatranscriptomics datasets and using metapro pipeline for this, which uses docker. This error is coming again and again ..I m new to this programming...Please help me with the error