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Opened by Shaman Narayanasamy@shaman.narayanasamy
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No filtering problem

$ python3.4 /home/snarayanasamy/Work/tools/IMP/IMP -m /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/A01/Lux_Lipids_Community-041010_DNA_TCTCACGG_L007_R1_001.fastq.bz2 -m /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/A01/Lux_Lipids_Community-041010_DNA_TCTCACGG_L007_R2_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/A01/Lux_Lipids_Community-041010_RNA_ATCACG_L006_R1_0012.fastq.bz2 -t /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/A01/Lux_Lipids_Community-041010_RNA_ATCACG_L006_R2_0012.fastq.bz2 -o /mnt/md1200/snarayanasamy/LAO_TS/A01 -c /home/snarayanasamy/Work/tools/IMP/conf/LAO_bigbug_config.imp.json -a megahit -d /home/snarayanasamy/Work/tools/IMP/db -v 1.3 snakemake -np
[x] Found IMP docker-r3lab.uni.lu/imp/imp 1.3
Executing " docker run -v /mnt/md1200/snarayanasamy/archived_raw_data/LAO:/home/imp/data -v /mnt/md1200/snarayanasamy/LAO_TS/A01:/home/imp/output -v /home/snarayanasamy/Work/tools/IMP/db:/home/imp/databases -v /home/snarayanasamy/Work/tools/IMP/conf:/home/imp/conf -e MG="/home/imp/data/Metagenomic/time_series/A01/Lux_Lipids_Community-041010_DNA_TCTCACGG_L007_R1_001.fastq.bz2 /home/imp/data/Metagenomic/time_series/A01/Lux_Lipids_Community-041010_DNA_TCTCACGG_L007_R2_001.fastq.bz2" -e MT="/home/imp/data/Metatranscriptomic/time_series/A01/Lux_Lipids_Community-041010_RNA_ATCACG_L006_R1_0012.fastq.bz2 /home/imp/data/Metatranscriptomic/time_series/A01/Lux_Lipids_Community-041010_RNA_ATCACG_L006_R2_0012.fastq.bz2" -e CONFIGFILE=/home/imp/conf/LAO_bigbug_config.imp.json -e IMP_ASSEMBLER=megahit --rm -e "LOCAL_USER_ID=`id -u $USER`" -e "LOCAL_GROUP_ID=`id -g $USER`" --name mnt_md1200_snarayanasamy_LAO_TS_A01 docker-r3lab.uni.lu/imp/imp:1.3 snakemake -np -s /home/imp/code/Snakefile "
InputFunctionException in line 21 of /home/imp/code/rules/Preprocessing/no-filtering.rules:
AttributeError: 'Wildcards' object has no attribute 'step'
Wildcards:
type=mg

When I do a real run, the following is error is received.

rule prepare_data_input:
        input: /home/imp/data/Metagenomic/time_series/A01/Lux_Lipids_Community-041010_DNA_TCTCACGG_L007_R1_001.fastq.bz2, /home/imp/data/Metagenomic/time_series/A01/Lux_Lipids_Community-041010_DNA_TCTCACGG_L007_R2_001.fastq.bz2
        output: Preprocessing/mg.r1.fq, Preprocessing/mg.r2.fq
        wildcards: type=mg
5 of 58 steps (9%) done
rule no_filtering:
        input: Preprocessing/mt.r1.trimmed.rna_filtered.fq, Preprocessing/mt.r2.trimmed.rna_filtered.fq, Preprocessing/mt.se.trimmed.rna_filtered.fq
        output: Preprocessing/mt.r1.preprocessed.fq, Preprocessing/mt.r2.preprocessed.fq, Preprocessing/mt.se.preprocessed.fq
        wildcards: type=mt
Waiting at most 5 seconds for missing files.
Error in job no_filtering while creating output files Preprocessing/mt.r1.preprocessed.fq, Preprocessing/mt.r2.preprocessed.fq, Preprocessing/mt.se.preprocessed.fq.
MissingOutputException in line 21 of /home/imp/code/rules/Preprocessing/no-filtering.rules:
Missing files after 5 seconds:
Preprocessing/mt.r1.preprocessed.fq
Preprocessing/mt.r2.preprocessed.fq
Preprocessing/mt.se.preprocessed.fq
Will exit after finishing currently running jobs.
/home/imp/data/Metatranscriptomic/time_series/A01/Lux_Lipids_Community-041010_RNA_ATCACG_L006_R1_0012.fastq.bz2 => Preprocessing/mt.r1.fq
/home/imp/data/Metatranscriptomic/time_series/A01/Lux_Lipids_Community-041010_RNA_ATCACG_L006_R2_0012.fastq.bz2 => Preprocessing/mt.r2.fq
/home/imp/data/Metagenomic/time_series/A01/Lux_Lipids_Community-041010_DNA_TCTCACGG_L007_R1_001.fastq.bz2 => Preprocessing/mg.r1.fq
/home/imp/data/Metagenomic/time_series/A01/Lux_Lipids_Community-041010_DNA_TCTCACGG_L007_R2_001.fastq.bz2 => Preprocessing/mg.r2.fq
Exiting because a job execution failed. Look above for error message
[x] Found IMP docker-r3lab.uni.lu/imp/imp 1.4.1
Executing " docker run -v /mnt/md1200/snarayanasamy/archived_raw_data/LAO:/home/imp/data -v /mnt/md1200/snarayanasamy/LAO_TS/A01_renamed:/home/imp/output -v /home/snarayanasamy/Work/tools/IMP/db:/home/imp/databases -v /home/snarayanasamy/Work/tools/IMP/conf:/home/imp/conf -v /home/snarayanasamy/Work/tools/IMP:/home/imp/code -e MG="/home/imp/data/Metagenomic/time_series/A01/Lux_Lipids_Community-041010_DNA_TCTCACGG_L007_R1_001.fastq.bz2 /home/imp/data/Metagenomic/time_series/A01/Lux_Lipids_Community-041010_DNA_TCTCACGG_L007_R2_001.fastq.bz2" -e MT="/home/imp/data/Metatranscriptomic/time_series/A01/Lux_Lipids_Community-041010_RNA_ATCACG_L006_R1_0012.fastq.bz2 /home/imp/data/Metatranscriptomic/time_series/A01/Lux_Lipids_Community-041010_RNA_ATCACG_L006_R2_0012.fastq.bz2" -e CONFIGFILE=/home/imp/conf/LAO_bigbug_config.imp.json -e IMP_ASSEMBLER=megahit --rm -e "LOCAL_USER_ID=`id -u $USER`" -e "LOCAL_GROUP_ID=`id -g $USER`" --name mnt_md1200_snarayanasamy_LAO_TS_A01_renamed docker-r3lab.uni.lu/imp/imp:1.4.1 snakemake ALL -s /home/imp/code/Snakefile "

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