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Pipeline Error #1
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Normally, the generate-plot should create a file in the summary file. So there is something wrong there |
Can you provide the config.yaml file? |
I can't attach the file here. I copied the settings from here: https://github.com/Hoohm/dropSeqPipe/wiki/Create-config-files Anyway this is my config file: Samples: |
Ok, so datatype has to be either bulk or singleCell. And it is case sensitive. |
Ok, I can try running the pipeline on another sample, setting singleCell instead of SingleCell in the config file. |
Added a check for Data_type value. |
Still getting the error at the fastqc... /programs/FastQC-0.11.5/ MLW4_R1.fastq.gz MLW4_R2.fastq.gz -t 2 -o logs --extract Pipeline has been updated to 0.24 |
Oh, I see now. |
Oh ok, now I get the following error: Mode is generate-plots |
Hello, |
Gotcha, I think the problems are arising from a bad configuration file anyway. Now I get the following: Mode is generate-plots My config.yaml is as follows: Samples: So I don't get which lines I'm missing..... |
@davidepisu the issue should be resolved thanks to @duyck |
Hello @davidepisu, |
No response so I'll close the issue. |
Got this error while generating the Expression Matrix:
[Sun Sep 10 01:02:04 2017] Finished job 1.
[Sun Sep 10 01:02:04 2017] 4 of 5 steps (80%) done
[Sun Sep 10 01:02:04 2017]
[Sun Sep 10 01:02:04 2017] localrule all:
input: logs/MLW12_hist_out_cell.txt
log: logs/Dropseq_post_align.log
jobid: 0
[Sun Sep 10 01:02:04 2017]
[Sun Sep 10 01:02:04 2017] Finished job 0.
[Sun Sep 10 01:02:04 2017] 5 of 5 steps (100%) done
Mode is generate-plots
Generating multiqc report
[INFO ] multiqc : This is MultiQC v1.2
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '/SSD/MLW12/logs'
[INFO ] multiqc : Searching '/SSD/MLW12/summary'
Searching 62 files.. [####################################] 100%
[INFO ] star : Found 2 reports
[INFO ] fastqc : Found 2 reports
[INFO ] multiqc : Compressing plot data
[INFO ] multiqc : Report : MLW12/multiqc_report.html
[INFO ] multiqc : Data : MLW12/multiqc_data
[INFO ] multiqc : MultiQC complete
Extracting expression
[Sun Sep 10 01:02:43 2017] Provided cores: 20
[Sun Sep 10 01:02:43 2017] Rules claiming more threads will be scaled down.
[Sun Sep 10 01:02:43 2017] Job counts:
count jobs
1 all
1 extract_expression
1 extract_umi_per_gene
1 gunzip
4
[Sun Sep 10 01:02:43 2017]
[Sun Sep 10 01:02:43 2017] rule extract_umi_per_gene:
input: MLW12_final.bam
output: logs/MLW12_umi_per_gene.tsv
jobid: 1
wildcards: sample=MLW12
[Sun Sep 10 01:02:43 2017]
[Sun Sep 10 01:02:43 2017] /programs/Drop-seq_tools-1.12/GatherMolecularBarcodeDistributionByGene I=MLW12_final.bam O=logs/MLW12_umi_per_gene.tsv CELL_BC_FILE=summary/MLW12_barcodes.csv
[Sun Sep 10 01:02:43 2017] rule extract_expression:
input: MLW12_final.bam
output: summary/MLW12_expression_matrix.txt.gz
jobid: 3
wildcards: sample=MLW12
[Sun Sep 10 01:02:43 2017]
[Sun Sep 10 01:02:43 2017] /programs/Drop-seq_tools-1.12/DigitalExpression I=MLW12_final.bam O=summary/MLW12_expression_matrix.txt.gz SUMMARY=summary/MLW12_dge.summary.txt CELL_BC_FILE=summary/MLW12_barcodes.csv MIN_BC_READ_THRESHOLD=1
[Sun Sep 10 01:02:44 EDT 2017] org.broadinstitute.dropseqrna.barnyard.DigitalExpression SUMMARY=summary/MLW12_dge.summary.txt OUTPUT=summary/MLW12_expression_matrix.txt.gz INPUT=MLW12_final.bam MIN_BC_READ_THRESHOLD=1 CELL_BC_FILE=summary/MLW12_barcodes.csv OUTPUT_READS_INSTEAD=false CELL_BARCODE_TAG=XC MOLECULAR_BARCODE_TAG=XM GENE_EXON_TAG=GE STRAND_TAG=GS EDIT_DISTANCE=1 READ_MQ=10 USE_STRAND_INFO=true RARE_UMI_FILTER_THRESHOLD=0.0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Sun Sep 10 01:02:44 EDT 2017] org.broadinstitute.dropseqrna.barnyard.GatherMolecularBarcodeDistributionByGene OUTPUT=logs/MLW12_umi_per_gene.tsv INPUT=MLW12_final.bam CELL_BC_FILE=summary/MLW12_barcodes.csv CELL_BARCODE_TAG=XC MOLECULAR_BARCODE_TAG=XM GENE_EXON_TAG=GE STRAND_TAG=GS EDIT_DISTANCE=1 READ_MQ=10 MIN_BC_READ_THRESHOLD=0 USE_STRAND_INFO=true RARE_UMI_FILTER_THRESHOLD=0.0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Sun Sep 10 01:02:44 EDT 2017] Executing as [email protected] on Linux 3.10.0-229.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Picard version: 1.12(d3aeea7_1452606774) IntelDeflater
[Sun Sep 10 01:02:44 EDT 2017] Executing as [email protected] on Linux 3.10.0-229.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Picard version: 1.12(d3aeea7_1452606774) IntelDeflater
[Sun Sep 10 01:02:44 EDT 2017] org.broadinstitute.dropseqrna.barnyard.DigitalExpression done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2022178816
Exception in thread "main" [Sun Sep 10 01:02:44 EDT 2017] org.broadinstitute.dropseqrna.barnyard.GatherMolecularBarcodeDistributionByGene done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2022178816
Exception in thread "main" htsjdk.samtools.SAMException: Error opening file: MLW12_barcodes.csvhtsjdk.samtools.SAMException: Error opening file: MLW12_barcodes.csv
Caused by: java.io.FileNotFoundException: summary/MLW12_barcodes.csv (No such file or directory)Caused by: java.io.FileNotFoundException: summary/MLW12_barcodes.csv (No such file or directory)
[Sun Sep 10 01:02:44 2017] Error in job extract_expression while creating output file summary/MLW12_expression_matrix.txt.gz.
[Sun Sep 10 01:02:44 2017] Error in job extract_umi_per_gene while creating output file logs/MLW12_umi_per_gene.tsv.
[Sun Sep 10 01:02:44 2017] RuleException:
CalledProcessError in line 21 of /programs/dropSeqPipe/lib/python3.6/site-packages/dropSeqPipe/Snakefiles/singleCell/extract_expression_single.snake:
Command '/programs/Drop-seq_tools-1.12/DigitalExpression I=MLW12_final.bam O=summary/MLW12_expression_matrix.txt.gz SUMMARY=summary/MLW12_dge.summary.txt CELL_BC_FILE=summary/MLW12_barcodes.csv MIN_BC_READ_THRESHOLD=1' returned non-zero exit status 1.
File "/programs/dropSeqPipe/lib/python3.6/site-packages/dropSeqPipe/Snakefiles/singleCell/extract_expression_single.snake", line 21, in __rule_extract_expression
File "/usr/local/lib/python3.6/concurrent/futures/thread.py", line 55, in run
[Sun Sep 10 01:02:44 2017] RuleException:
CalledProcessError in line 34 of /programs/dropSeqPipe/lib/python3.6/site-packages/dropSeqPipe/Snakefiles/singleCell/extract_expression_single.snake:
Command '/programs/Drop-seq_tools-1.12/GatherMolecularBarcodeDistributionByGene I=MLW12_final.bam O=logs/MLW12_umi_per_gene.tsv CELL_BC_FILE=summary/MLW12_barcodes.csv' returned non-zero exit status 1.
File "/programs/dropSeqPipe/lib/python3.6/site-packages/dropSeqPipe/Snakefiles/singleCell/extract_expression_single.snake", line 34, in __rule_extract_umi_per_gene
File "/usr/local/lib/python3.6/concurrent/futures/thread.py", line 55, in run
[Sun Sep 10 01:02:44 2017] Removing output files of failed job extract_umi_per_gene since they might be corrupted:
logs/MLW12_umi_per_gene.tsv
[Sun Sep 10 01:02:44 2017] Will exit after finishing currently running jobs.
[Sun Sep 10 01:02:44 2017] Exiting because a job execution failed. Look above for error message
Traceback (most recent call last):
File "/programs/dropSeqPipe/bin/dropSeqPipe", line 11, in
load_entry_point('dropSeqPipe==0.23a0', 'console_scripts', 'dropSeqPipe')()
File "/programs/dropSeqPipe/lib/python3.6/site-packages/dropSeqPipe/main.py", line 223, in main
shell(extract_expression_single)
File "/usr/local/lib/python3.6/site-packages/snakemake/shell.py", line 88, in new
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'snakemake -s /programs/dropSeqPipe/lib/python3.6/site-packages/dropSeqPipe/Snakefiles/singleCell/extract_expression_single.snake --cores 20 -pT -d /SSD/MLW12 --configfile /SSD/local.yaml ' returned non-zero exit status 1.
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