error with common.smk
anjanaanilkumar1289 opened this issue · comments
I am getting error from line 10 in https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling/blob/master/rules/common.smk
line 10 samples = pd.read_table(config["samples"]).set_index("sample", drop=False)
TypeError: string indices must be integers
Can you please help me to fix the error.
Can you show me your config file? Did you change anything in either the Snakefile or any of the files ending with .smk?
Dear Johannes,
I didn't change the Snakefile and the rules. I am attaching the edited
config file herewith.
Regards,
Anjana
…On Tue, Jan 29, 2019 at 3:19 PM Johannes Köster ***@***.***> wrote:
Can you show me your config file? Did you change anything in either the
Snakefile or any of the files ending with .smk?
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I cannot see the config (I guess email attachments are not included here). Maybe you can just post it inside a comment?
Hi,
I have pasted the config file below.
#######################################################################
samples:
/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/samples.tsv
units:
/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/units.tsv
ref:
# name used in snpeff database
name: GRCh38
genome: /data/Priyanka/breast_fastq/Reference/GRCh38.p12.genome.fa
# known variants (e.g. DBSNP)
known-variants: /data/anjana/data/clinvar_20190114.vcf
filtering:
# Set to true in order to apply machine learning based recalibration of
# quality scores instead of hard filtering.
vqsr: false
hard:
# hard filtering as outlined in GATK docs
# (
https://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set
)
snvs:
"QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 ||
ReadPosRankSum < -8.0"
indels:
"QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0"
processing:
remove-duplicates: false
# point to a bed file with e.g. captured regions if necessary,
# see
https://gatkforums.broadinstitute.org/gatk/discussion/4133/when-should-i-use-l-to-pass-in-a-list-of-intervals
# restrict-regions: ../raw/captured_regions.bed
# If regions are restricted, use this to enlarge them in order to include
# flanking areas.
# region-padding: 100
params:
gatk:
HaplotypeCaller: ""
BaseRecalibrator: ""
GenotypeGVCFs: ""
VariantRecalibrator: ""
picard:
MarkDuplicates: "REMOVE_DUPLICATES=true"
trimmomatic:
pe:
trimmer:
-
"ILLUMINACLIP:/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/test/TruSeq3-PE.fa"
- "LEADING:3"
- "TRAILING:3"
- "SLIDINGWINDOW:4:15"
- "MINLEN:36"
se:
trimmer:
-
"ILLUMINACLIP:/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/test/TruSeq3-SE.fa"
- "LEADING:3"
- "TRAILING:3"
- "SLIDINGWINDOW:4:15"
- "MINLEN:36"
#########################################################################################
…On Wed, Jan 30, 2019 at 1:42 PM Johannes Köster ***@***.***> wrote:
I cannot see the config (I guess email attachments are not included here).
Maybe you can just post it inside a comment?
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Ok, can you also post the full stack trace of the error?
Hi,
Unfortunately I am not getting the TypeError anymore. But still there is an
error with trimmomatic that I am pasting here.
```
Traceback (most recent call last):
File
"/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/.snakemake/scripts/
tmpv2f735y6.wrapper.py", line 56, in <module>
"trimmomatic PE {extra} "
File
"/home/anjana/anaconda3/lib/python3.6/site-packages/snakemake/shell.py",
line 142, in __new__
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ' set -euo pipefail; trimmomatic PE
-trimlog trimmed/A-1.trimlog.txt
/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/test/reads/a.chr21.1.fq
/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/test/reads/a.chr21.2.fq
(pigz -5 > trimmed/A-1.1.fastq.gz) >(pigz -5 >
trimmed/A-1.1.unpaired.fastq.gz) >(pigz -5 > trimmed/A-1.2.fastq.gz) >(pigz
-5 > trimmed/A-1.2.unpaired.fastq.gz)
ILLUMINACLIP:/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/test/TruSeq3-PE.fa
LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 >
logs/trimmomatic/A-1.log 2>&1 ' returned non-zero exit status 127.
/usr/bin/bash: fastqc: command not found
Traceback (most recent call last):
File
"/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/.snakemake/scripts/
tmp3wrr9ead.wrapper.py", line 34, in <module>
shell("fastqc {snakemake.params} --quiet "
File
"/home/anjana/anaconda3/lib/python3.6/site-packages/snakemake/shell.py",
line 142, in __new__
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ' set -euo pipefail; fastqc
--quiet --outdir /tmp/tmp4v5myicp
/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/test/reads/b.chr21.1.fq
' returned non-zero exit status 127.
Traceback (most recent call last):
File
"/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/.snakemake/scripts/
tmpe88k4qc0.wrapper.py", line 56, in <module>
"trimmomatic PE {extra} "
File
"/home/anjana/anaconda3/lib/python3.6/site-packages/snakemake/shell.py",
line 142, in __new__
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ' set -euo pipefail; trimmomatic PE
-trimlog trimmed/B-1.trimlog.txt
/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/test/reads/b.chr21.1.fq
/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/test/reads/b.chr21.2.fq
(pigz -5 > trimmed/B-1.1.fastq.gz) >(pigz -5 >
trimmed/B-1.1.unpaired.fastq.gz) >(pigz -5 > trimmed/B-1.2.fastq.gz) >(pigz
-5 > trimmed/B-1.2.unpaired.fastq.gz)
ILLUMINACLIP:/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/test/TruSeq3-PE.fa
LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 >
logs/trimmomatic/B-1.log 2>&1 ' returned non-zero exit status 127.
[Wed Jan 30 15:02:52 2019]
Error in rule trim_reads_pe:
jobid: 25
output: trimmed/A-1.1.fastq.gz, trimmed/A-1.2.fastq.gz,
trimmed/A-1.1.unpaired.fastq.gz, trimmed/A-1.2.unpaired.fastq.gz,
trimmed/A-1.trimlog.txt
log: logs/trimmomatic/A-1.log
RuleException:
CalledProcessError in line 31 of
/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/rules/mapping.smk:
Command ' set -euo pipefail; /home/anjana/anaconda3/bin/python
/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/.snakemake/scripts/
tmpv2f735y6.wrapper.py ' returned non-zero exit status 1.
File
"/data/anjana/variant-calling/dna-seq-gatk-variant-calling-master/rules/mapping.smk",
line 31, in __rule_trim_reads_pe
File "/home/anjana/anaconda3/lib/python3.6/concurrent/futures/thread.py",
line 56, in run
```
Regards,
Anjana
You have to look into the log file. Did you run the pipeline with --use-conda?
log file shows "*/usr/bin/bash: trimmomatic: command not found*"
I didn't run with --use-conda. I used -j .
…On Wed, Jan 30, 2019 at 3:50 PM Johannes Köster ***@***.***> wrote:
You have to look into the log file. Did you run the pipeline with
--use-conda?
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That's the issue. You need --use-conda, in order to tell Snakemake to deploy the required software before running the workflow. Otherwise, you need to install all required tools manually. I strongly discourage the latter because it defeats reproducibility.
-j just tells Snakemake to use as many cores as possible, which is unrelated to the software deployment.
Thank you so much!! I will try with --use-conda
…On Wed, Jan 30, 2019 at 4:14 PM Johannes Köster ***@***.***> wrote:
-j just tells Snakemake to use as many cores as possible, which is
unrelated to the software deployment.
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Ok, I am therefore closing this for now.