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Hoohm / dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow
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Error opening file: hg19_mm10_transgenes.rRNA.intervals #24

Closed olechnwin closed 6 years ago

olechnwin commented 6 years ago

Hi,

I have another error: xception in thread "main" htsjdk.samtools.SAMException: Error opening file: /opt/dropSeqPipe/ref/hg19_mm10_transgenes.rRNA.intervals

This seems to be a new feature of Drop-seq 1.13. Can you please let me know how to fix this? Also, what does this do?

Thanks!

Hoohm commented 6 years ago

Could you please provide more context. I don't see where the error comes from.

Which step is this? Are you using the reference of the McCarroll lab or did you make your own?

olechnwin commented 6 years ago

Sorry here it is. Hard for me to tell since I'm doing multi core, but I am guessing it's the singleCellRnaSeqMetricsCollector? The rRNA.intervals file was never created. I am using the reference of the McCarroll lab. 


+ java -Xmx32g -Djava.io.tmpdir=/tmp -jar /opt/Drop-seq_tools-1.13/jar/dropseq.jar DigitalExpression I=data/sample1_N706_S2_L001_MOUSE_unfiltered.bam O=summary/sample1_N706_S2_L001_MOUSE_umi_expression_matrix.txt MIN_BC_READ_THRESHOLD=1 CELL_BC_FILE=summary/sample1_N706_S2_L001_MOUSE_barcodes.csv
+ java -Xmx32g -Djava.io.tmpdir=/tmp -jar /opt/Drop-seq_tools-1.13/jar/dropseq.jar GatherMolecularBarcodeDistributionByGene I=data/sample1_N706_S2_L001_MOUSE_unfiltered.bam O=logs/sample1_N706_S2_L001_MOUSE_umi_per_gene.tsv CELL_BC_FILE=summary/sample1_N706_S2_L001_MOUSE_barcodes.csv
+ java -Xmx32g -Djava.io.tmpdir=/tmp -jar /opt/Drop-seq_tools-1.13/jar/dropseq.jar GatherMolecularBarcodeDistributionByGene I=data/sample1_N706_S2_L001_HUMAN_unfiltered.bam O=logs/sample1_N706_S2_L001_HUMAN_umi_per_gene.tsv CELL_BC_FILE=summary/sample1_N706_S2_L001_HUMAN_barcodes.csv
[Wed Mar 14 14:36:48 EDT 2018] org.broadinstitute.dropseqrna.barnyard.SingleCellRnaSeqMetricsCollector INPUT=data/sample1_N706_S2_L001_MOUSE_unfiltered.bam OUTPUT=logs/samplel1_N706_S2_L001_MOUSE_rna_metrics.txt ANNOTATIONS_FILE=/opt/dropSeqPipe/ref/hg19_mm10_transgenes.refFlat RIBOSOMAL_INTERVALS=/opt/dropSeqPipe/ref/hg19_mm10_transgenes.rRNA.intervals CELL_BC_FILE=summary/sample1_N706_S2_L001_MOUSE_barcodes.csv    CELL_BARCODE_TAG=XC STRAND_SPECIFICITY=NONE RRNA_FRAGMENT_PERCENTAGE=0.8 READ_MQ=10 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
[Wed Mar 14 14:36:48 EDT 2018] Executing as cxx@himem01.cluster on Linux 2.6.32-504.23.4.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_121-b15; Picard version: 1.13(7bed8f4_1513008033)
[Wed Mar 14 14:36:48 EDT 2018] org.broadinstitute.dropseqrna.barnyard.DigitalExpression OUTPUT_READS_INSTEAD=true OUTPUT=summary/sample1_N706_S2_L001_MOUSE_counts_expression_matrix.txt INPUT=data/samplel1_N706_S2_L001_MOUSE_unfiltered.bam CELL_BC_FILE=summary/sample1_N706_S2_L001_MOUSE_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
[Wed Mar 14 14:36:48 EDT 2018] Executing as cxx@himem01.cluster on Linux 2.6.32-504.23.4.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_121-b15; Picard version: 1.13(7bed8f4_1513008033)
[Wed Mar 14 14:36:48 EDT 2018] org.broadinstitute.dropseqrna.barnyard.DigitalExpression OUTPUT=summary/sample1_N706_S2_L001_MOUSE_umi_expression_matrix.txt INPUT=data/sample1_N706_S2_L001_MOUSE_unfiltered.bam MIN_BC_READ_THRESHOLD=1 CELL_BC_FILE=summary/sample1_N706_S2_L001_MOUSE_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
[Wed Mar 14 14:36:48 EDT 2018] Executing as cxx@himem01.cluster on Linux 2.6.32-504.23.4.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_121-b15; Picard version: 1.13(7bed8f4_1513008033)
INFO    2018-03-14 14:36:48 SingleCellRnaSeqMetricsCollector    Found 334 cell barcodes in file
INFO    2018-03-14 14:36:48 BarcodeListRetrieval    Found 334 cell barcodes in file
INFO    2018-03-14 14:36:48 DigitalExpression   Calculating digital expression for [334] cells.
[Wed Mar 14 14:36:48 EDT 2018] org.broadinstitute.dropseqrna.barnyard.DigitalExpression OUTPUT_READS_INSTEAD=true OUTPUT=summary/sample1_N706_S2_L001_HUMAN_counts_expression_matrix.txt INPUT=data/samplel1_N706_S2_L001_HUMAN_unfiltered.bam CELL_BC_FILE=summary/sample1_N706_S2_L001_HUMAN_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
[Wed Mar 14 14:36:48 EDT 2018] Executing as cxx@himem01.cluster on Linux 2.6.32-504.23.4.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_121-b15; Picard version: 1.13(7bed8f4_1513008033)
[Wed Mar 14 14:36:48 EDT 2018] org.broadinstitute.dropseqrna.barnyard.SingleCellRnaSeqMetricsCollector INPUT=data/samplel1_N706_S2_L001_HUMAN_unfiltered.bam OUTPUT=logs/sample1_N706_S2_L001_HUMAN_rna_metrics.txt ANNOTATIONS_FILE=/opt/dropSeqPipe/ref/hg19_mm10_transgenes.refFlat RIBOSOMAL_INTERVALS=/opt/dropSeqPipe/ref/hg19_mm10_transgenes.rRNA.intervals CELL_BC_FILE=summary/sample1_N706_S2_L001_HUMAN_barcodes.csv    CELL_BARCODE_TAG=XC STRAND_SPECIFICITY=NONE RRNA_FRAGMENT_PERCENTAGE=0.8 READ_MQ=10 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
[Wed Mar 14 14:36:48 EDT 2018] org.broadinstitute.dropseqrna.barnyard.DigitalExpression OUTPUT=summary/samplel1_N706_S2_L001_HUMAN_umi_expression_matrix.txt INPUT=data/sample1_N706_S2_L001_HUMAN_unfiltered.bam MIN_BC_READ_THRESHOLD=1 CELL_BC_FILE=summary/sample1_N706_S2_L001_HUMAN_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
INFO    2018-03-14 14:36:48 BarcodeListRetrieval    Found 334 cell barcodes in file
INFO    2018-03-14 14:36:48 DigitalExpression   Calculating digital expression for [334] cells.
[Wed Mar 14 14:36:48 EDT 2018] Executing as cxx@himem01.cluster on Linux 2.6.32-504.23.4.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_121-b15; Picard version: 1.13(7bed8f4_1513008033)
[Wed Mar 14 14:36:48 EDT 2018] Executing as cxx@himem01.cluster on Linux 2.6.32-504.23.4.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_121-b15; Picard version: 1.13(7bed8f4_1513008033)
[Wed Mar 14 14:36:48 EDT 2018] org.broadinstitute.dropseqrna.barnyard.GatherMolecularBarcodeDistributionByGene OUTPUT=logs/sample1_N706_S2_L001_MOUSE_umi_per_gene.tsv INPUT=data/sample1_N706_S2_L001_MOUSE_unfiltered.bam CELL_BC_FILE=summary/sample1_N706_S2_L001_MOUSE_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
[Wed Mar 14 14:36:48 EDT 2018] Executing as cxx@himem01.cluster on Linux 2.6.32-504.23.4.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_121-b15; Picard version: 1.13(7bed8f4_1513008033)
[Wed Mar 14 14:36:48 EDT 2018] org.broadinstitute.dropseqrna.barnyard.GatherMolecularBarcodeDistributionByGene OUTPUT=logs/sample1_N706_S2_L001_HUMAN_umi_per_gene.tsv INPUT=data/sample1_N706_S2_L001_HUMAN_unfiltered.bam CELL_BC_FILE=summary/sample1_N706_S2_L001_HUMAN_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
[Wed Mar 14 14:36:48 EDT 2018] Executing as cxx@himem01.cluster on Linux 2.6.32-504.23.4.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_121-b15; Picard version: 1.13(7bed8f4_1513008033)
INFO    2018-03-14 14:36:48 BarcodeListRetrieval    Found 141 cell barcodes in file
INFO    2018-03-14 14:36:48 DigitalExpression   Calculating digital expression for [141] cells.
INFO    2018-03-14 14:36:48 SingleCellRnaSeqMetricsCollector    Found 141 cell barcodes in file
INFO    2018-03-14 14:36:48 BarcodeListRetrieval    Found 141 cell barcodes in file
INFO    2018-03-14 14:36:48 DigitalExpression   Calculating digital expression for [141] cells.
INFO    2018-03-14 14:36:48 BarcodeListRetrieval    Found 334 cell barcodes in file
INFO    2018-03-14 14:36:48 BarcodeListRetrieval    Found 141 cell barcodes in file
INFO    2018-03-14 14:36:49 FilterBAM   Processed    12,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    1s.  Last read position: */*
INFO    2018-03-14 14:36:52 FilterBAM   Processed     6,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:   12s.  Last read position: MOUSE_2:122,011,881
INFO    2018-03-14 14:36:53 FilterBAM   Processed    13,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    3s.  Last read position: */*
INFO    2018-03-14 14:36:54 SingleCellRnaSeqMetricsCollector    Loaded 94207 genes.
[Wed Mar 14 14:36:54 EDT 2018] org.broadinstitute.dropseqrna.barnyard.SingleCellRnaSeqMetricsCollector done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=2595749888
Exception in thread "main" htsjdk.samtools.SAMException: Error opening file: /opt/dropSeqPipe/ref/hg19_mm10_transgenes.rRNA.intervals
    at htsjdk.samtools.util.IOUtil.openFileForReading(IOUtil.java:529)
    at htsjdk.samtools.util.IOUtil.openFileForBufferedReading(IOUtil.java:786)
    at htsjdk.samtools.util.IntervalList.fromPath(IntervalList.java:408)
    at htsjdk.samtools.util.IntervalList.fromFile(IntervalList.java:399)
    at picard.analysis.directed.RnaSeqMetricsCollector.makeOverlapDetector(RnaSeqMetricsCollector.java:69)
    at org.broadinstitute.dropseqrna.barnyard.SingleCellRnaSeqMetricsCollector$CollectorFactory.<init>(SingleCellRnaSeqMetricsCollector.java:253)
    at org.broadinstitute.dropseqrna.barnyard.SingleCellRnaSeqMetricsCollector.getRNASeqMetricsCollector(SingleCellRnaSeqMetricsCollector.java:169)
    at org.broadinstitute.dropseqrna.barnyard.SingleCellRnaSeqMetricsCollector.doWork(SingleCellRnaSeqMetricsCollector.java:135)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
    at org.broadinstitute.dropseqrna.cmdline.DropSeqMain.main(DropSeqMain.java:42)
Caused by: java.nio.file.NoSuchFileException: /opt/dropSeqPipe/ref/hg19_mm10_transgenes.rRNA.intervals
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214)
    at java.nio.file.Files.newByteChannel(Files.java:361)
    at java.nio.file.Files.newByteChannel(Files.java:407)
    at java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:384)
    at java.nio.file.Files.newInputStream(Files.java:152)
    at htsjdk.samtools.util.IOUtil.openFileForReading(IOUtil.java:525)
    ... 10 more
INFO    2018-03-14 14:36:54 SingleCellRnaSeqMetricsCollector    Loaded 94207 genes.
[Wed Mar 14 14:36:54 EDT 2018] org.broadinstitute.dropseqrna.barnyard.SingleCellRnaSeqMetricsCollector done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=2595749888
Exception in thread "main" htsjdk.samtools.SAMException: Error opening file: /opt/dropSeqPipe/ref/hg19_mm10_transgenes.rRNA.intervals
    at htsjdk.samtools.util.IOUtil.openFileForReading(IOUtil.java:529)
    at htsjdk.samtools.util.IOUtil.openFileForBufferedReading(IOUtil.java:786)
    at htsjdk.samtools.util.IntervalList.fromPath(IntervalList.java:408)
    at htsjdk.samtools.util.IntervalList.fromFile(IntervalList.java:399)
    at picard.analysis.directed.RnaSeqMetricsCollector.makeOverlapDetector(RnaSeqMetricsCollector.java:69)
    at org.broadinstitute.dropseqrna.barnyard.SingleCellRnaSeqMetricsCollector$CollectorFactory.<init>(SingleCellRnaSeqMetricsCollector.java:253)
    at org.broadinstitute.dropseqrna.barnyard.SingleCellRnaSeqMetricsCollector.getRNASeqMetricsCollector(SingleCellRnaSeqMetricsCollector.java:169)
    at org.broadinstitute.dropseqrna.barnyard.SingleCellRnaSeqMetricsCollector.doWork(SingleCellRnaSeqMetricsCollector.java:135)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
    at org.broadinstitute.dropseqrna.cmdline.DropSeqMain.main(DropSeqMain.java:42)
Caused by: java.nio.file.NoSuchFileException: /opt/dropSeqPipe/ref/hg19_mm10_transgenes.rRNA.intervals
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214)
    at java.nio.file.Files.newByteChannel(Files.java:361)
    at java.nio.file.Files.newByteChannel(Files.java:407)
    at java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:384)
    at java.nio.file.Files.newInputStream(Files.java:152)
    at htsjdk.samtools.util.IOUtil.openFileForReading(IOUtil.java:525)
    ... 10 more
Error in rule SingleCellRnaSeqMetricsCollector_whitelist_species:
    jobid: 27
    output: logs/sample1_N706_S2_L001_MOUSE_rna_metrics.txt

Error in rule SingleCellRnaSeqMetricsCollector_whitelist_species:
    jobid: 30
    output: logs/sample1_N706_S2_L001_HUMAN_rna_metrics.txt

RuleException:
CalledProcessError in line 66 of /opt/dropSeqPipe/rules/extract_expression_species.smk:
Command ' set -euo pipefail;  /opt/Drop-seq_tools-1.13/drop-seq-tools-wrapper.sh -t ~/tmp -m 32g -p SingleCellRnaSeqMetricsCollector        INPUT=data/sample1_N706_S2_L001_MOUSE_unfiltered.bam        OUTPUT=logs/sample1_N706_S2_L001_MOUSE_rna_metrics.txt      ANNOTATIONS_FILE=/opt/dropSeqPipe/ref/hg19_mm10_transgenes.refFlat      CELL_BC_FILE=summary/sample1_N706_S2_L001_MOUSE_barcodes.csv        RIBOSOMAL_INTERVALS=/opt/dropSeqPipe/ref/hg19_mm10_transgenes.rRNA.intervals ' returned non-zero exit status 1.
  File "/opt/dropSeqPipe/rules/extract_expression_species.smk", line 66, in __rule_SingleCellRnaSeqMetricsCollector_whitelist_species
  File "opt/miniconda3/envs/dropSeqPipe/lib/python3.6/concurrent/futures/thread.py", line 56, in run
RuleException:
CalledProcessError in line 66 of /opt/dropSeqPipe/rules/extract_expression_species.smk:
Command ' set -euo pipefail;  /opt/Drop-seq_tools-1.13/drop-seq-tools-wrapper.sh -t ~/tmp -m 32g -p SingleCellRnaSeqMetricsCollector        INPUT=data/sample1_N706_S2_L001_HUMAN_unfiltered.bam        OUTPUT=logs/sample1_N706_S2_L001_HUMAN_rna_metrics.txt      ANNOTATIONS_FILE=/opt/dropSeqPipe/ref/hg19_mm10_transgenes.refFlat      CELL_BC_FILE=summary/sample1_N706_S2_L001_HUMAN_barcodes.csv        RIBOSOMAL_INTERVALS=/opt/dropSeqPipe/ref/hg19_mm10_transgenes.rRNA.intervals ' returned non-zero exit status 1.
  File "/opt/dropSeqPipe/rules/extract_expression_species.smk", line 66, in __rule_SingleCellRnaSeqMetricsCollector_whitelist_species
  File "/opt/miniconda3/envs/dropSeqPipe/lib/python3.6/concurrent/futures/thread.py", line 56, in run
[Wed Mar 14 14:36:54 EDT 2018] org.broadinstitute.dropseqrna.utils.FilterBAM done. Elapsed time: 0.87 minutes.
Runtime.totalMemory()=2611478528
Finished job 24.
6 of 36 steps (17%) done
Hoohm commented 6 years ago

Yes, that is the problem is here: https://github.com/Hoohm/dropSeqPipe/blob/1fe59178579ec373c5224001d0faf9ce055c5308/rules/extract_expression_species.smk#L60

This should be in input instead of params so that it would create it. What you can do is simply run meta once and it will create it. It will run after that.

This is fixed in the next version.

olechnwin commented 6 years ago

Sorry. can you please clarify? What does that mean to run meta? Never mind. Got it. Going to run it now.

Hoohm commented 6 years ago

Sure. When you run the pipeline you can run different steps separately. so running: snakemake meta will run the meta data creation as one thing. This will create the missing files you need.

olechnwin commented 6 years ago

Thank you for all your help. That fix the error. Closing this issue.

Jun-Lizst commented 6 years ago

I continue to encounter this problem. please give some suggestion: u2510@GenekServer-0:~/ncbi/public/sra/dropSeqPipe-0.31$ snakemake --cores 8 extract --use-conda --directory /home/u2510/ncbi/public/sra/dropSeqPipe-0.31/dropSeqPipe_mydata Building DAG of jobs... Using shell: /bin/bash Provided cores: 8 Rules claiming more threads will be scaled down. Job counts: count jobs 1 SingleCellRnaSeqMetricsCollector 1 create_intervals 1 extract 1 plot_rna_metrics 4

[Sat Nov 17 09:21:57 2018] localrule create_intervals: input: /home/u2510/lj/rnaseq/10Xdata/refdata_scRNAseq/refdata-cellranger-mm10-1.2.0/genes/genes.reduced.gtf, /home/u2510/lj/rnaseq/10Xdata/refdata_scRNAseq/refdata-cellranger-mm10-1.2.0/fasta/genome.fa.dict output: /home/u2510/lj/rnaseq/10Xdata/refdata_scRNAseq/refdata-cellranger-mm10-1.2.0/fasta/genome.fa.rRNA.intervals jobid: 10

Activating conda environment: /home/u2510/ncbi/public/sra/dropSeqPipe-0.31/dropSeqPipe_mydata/.snakemake/conda/59f26949 Error: Invalid or corrupt jarfile /home/u2510/ncbi/public/sra/dropSeqPipe-0.31/drop-seq-tools-wrapper.sh [Sat Nov 17 09:21:57 2018] Error in rule create_intervals: jobid: 10 output: /home/u2510/lj/rnaseq/10Xdata/refdata_scRNAseq/refdata-cellranger-mm10-1.2.0/fasta/genome.fa.rRNA.intervals conda-env: /home/u2510/ncbi/public/sra/dropSeqPipe-0.31/dropSeqPipe_mydata/.snakemake/conda/59f26949

RuleException: CalledProcessError in line 73 of /home/u2510/ncbi/public/sra/dropSeqPipe-0.31/rules/generate_meta.smk: Command 'source activate /home/u2510/ncbi/public/sra/dropSeqPipe-0.31/dropSeqPipe_mydata/.snakemake/conda/59f26949; set -euo pipefail; java -Xmx70g -jar -Djava.io.tmpdir=/home/u2510/ncbi/public/sra/dropSeqPipe-0.31/temp-directory /home/u2510/ncbi/public/sra/dropSeqPipe-0.31/drop-seq-tools-wrapper.sh -p CreateIntervalsFiles REDUCED_GTF=/home/u2510/lj/rnaseq/10Xdata/refdata_scRNAseq/refdata-cellranger-mm10-1.2.0/genes/genes.reduced.gtf SEQUENCE_DICTIONARY=/home/u2510/lj/rnaseq/10Xdata/refdata_scRNAseq/refdata-cellranger-mm10-1.2.0/fasta/genome.fa.dict OUTPUT=/home/u2510/lj/rnaseq/10Xdata/refdata_scRNAseq/refdata-cellranger-mm10-1.2.0 PREFIX=/home/u2510/lj/rnaseq/10Xdata/refdata_scRNAseq/refdata-cellranger-mm10-1.2.0/fasta/genome.fa ' returned non-zero exit status 1. File "/home/u2510/ncbi/public/sra/dropSeqPipe-0.31/rules/generate_meta.smk", line 73, in __rule_create_intervals File "/home/u2510/miniconda3/lib/python3.6/concurrent/futures/thread.py", line 56, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/u2510/ncbi/public/sra/dropSeqPipe-0.31/dropSeqPipe_mydata/.snakemake/log/2018-11-17T092137.104780.snakemake.log