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Hoohm / dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow
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I can not find the jar directory! help!!! #62

Closed Jun-Lizst closed 5 years ago

Jun-Lizst commented 5 years ago

Error: Unable to access jarfile /home/u2510/ncbi/public/sra/dropSeqPipe-0.31/jar/dropseq.jar

Hoohm commented 5 years ago

@Jun-NIBS You need to give more context to your issues. Just the error is not enough.

Jun-Lizst commented 5 years ago

My another question going to be like this when I run: snakemake --cores 8 meta --use-conda --directory /home/u2510/ncbi/public/sra/dropSeqPipe-0.31/dropSeqPipe_mydata Other rules it finished well. there remain one issue that I try many many times and cannot fix: [Sat Nov 17 13:18:26 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: 3

Activating conda environment: /home/u2510/ncbi/public/sra/dropSeqPipe-0.31/dropSeqPipe_mydata/.snakemake/conda/59f26949 Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/home/u2510/ncbi/public/sra/dropSeqPipe-0.31/temp-directory [Sat Nov 17 13:18:27 CST 2018] org.broadinstitute.dropseqrna.annotation.CreateIntervalsFiles SEQUENCE_DICTIONARY=/home/u2510/lj/rnaseq/10Xdata/refdata_scRNAseq/refdata-cellranger-mm10-1.2.0/fasta/genome.fa.dict REDUCED_GTF=/home/u2510/lj/rnaseq/10Xdata/refdata_scRNAseq/refdata-cellranger-mm10-1.2.0/genes/genes.reduced.gtf 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 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 [Sat Nov 17 13:18:27 CST 2018] Executing as u2510@GenekServer-0 on Linux 4.4.0-130-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Picard version: 1.13(7bed8f4_1513008033) [Sat Nov 17 13:18:32 CST 2018] org.broadinstitute.dropseqrna.annotation.CreateIntervalsFiles done. Elapsed time: 0.08 minutes. Runtime.totalMemory()=2708471808 Exception in thread "main" htsjdk.samtools.SAMException: Error opening file for writing: genome.fa.genes.intervals at htsjdk.samtools.util.IOUtil.openFileForWriting(IOUtil.java:589) at htsjdk.samtools.util.IOUtil.openFileForBufferedWriting(IOUtil.java:597) at htsjdk.samtools.util.IOUtil.openFileForBufferedWriting(IOUtil.java:604) at htsjdk.samtools.util.IntervalList.write(IntervalList.java:525) at org.broadinstitute.dropseqrna.annotation.CreateIntervalsFiles.write(CreateIntervalsFiles.java:215) at org.broadinstitute.dropseqrna.annotation.CreateIntervalsFiles.doWork(CreateIntervalsFiles.java:160) 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.io.FileNotFoundException: /home/u2510/lj/rnaseq/10Xdata/refdata_scRNAseq/refdata-cellranger-mm10-1.2.0/home/u2510/lj/rnaseq/10Xdata/refdata_scRNAseq/refdata-cellranger-mm10-1.2.0/fasta/genome.fa.genes.intervals (No such file or directory) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(FileOutputStream.java:270) at java.io.FileOutputStream.(FileOutputStream.java:213) at htsjdk.samtools.util.IOUtil.openFileForWriting(IOUtil.java:585) ... 8 more [Sat Nov 17 13:18:32 2018]

The file seem can not write into expected dirctory and named wrong. Please give me some suggestion!! Thanks!

Jun-Lizst commented 5 years ago

@Hoohm

Puriney commented 5 years ago

As the author mentioned, you'd better answer the details first to give the developers more clues about what is happening.

In addition, you might reconsider a more friendly and precise title rather than 'abcdxyz, help!!!'. And be wise about using the @ feature in Github as email bombing is not a suggested way to get attention.

Good luck.