died with ret 6400

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veronic...@gmail.com

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Mar 19, 2018, 3:23:45 PM3/19/18
to STAR-Fusion
Hi,

The error shows like:

CMD: mkdir -p /project/bioinformatics/Xiao_lab/s171162/fusionpro/STARfus/result/test

CMD: mkdir -p /project/bioinformatics/Xiao_lab/s171162/fusionpro/STARfus/result/test/_starF_checkpoints

CMD: mkdir -p /project/bioinformatics/Xiao_lab/s171162/fusionpro/STARfus/result/test/star-fusion.preliminary

* Running CMD: /cm/shared/apps/star/2.5.2b/STAR/STAR/bin/Linux_x86_64_static/STAR --genomeDir /project/bioinformatics/Xiao_lab/s171162/fusionpro/STARfus/hg38/new/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --readFilesIn /project/bioinformatics/Xiao_lab/s171162/fusionpro/SOAPdata/RNAseq/T6_FASTQ/T6_1.fastq /project/bioinformatics/Xiao_lab/s171162/fusionpro/SOAPdata/RNAseq/T6_FASTQ/T6_2.fastq  --outReadsUnmapped None  --chimSegmentMin 12  --chimJunctionOverhangMin 12  --alignSJDBoverhangMin 10  --alignMatesGapMax 100000  --alignIntronMax 100000  --alignSJstitchMismatchNmax 5 -1 5 5  --runThreadN 4 --outSAMstrandField intronMotif  --outSAMunmapped Within  --outSAMtype BAM Unsorted  --outSAMattrRGline ID:GRPundef  --chimSegmentReadGapMax 3  --genomeLoad NoSharedMemory  --twopassMode Basic 

* Running CMD: mv Aligned.out.bam std.STAR.bam

* Running CMD: mv Chimeric.out.junction std.Chimeric.out.junction

* Running CMD: mv Chimeric.out.sam std.Chimeric.out.sam

* Running CMD: ln -s std.Chimeric.out.junction Chimeric.out.junction

* Running CMD: /project/bioinformatics/Xiao_lab/s171162/fusionpro/software/STAR-Fusion-v1.3.2/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /project/bioinformatics/Xiao_lab/s171162/fusionpro/STARfus/hg38/new/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir  -J Chimeric.out.junction  > /project/bioinformatics/Xiao_lab/s171162/fusionpro/STARfus/result/test/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt

-building interval tree based on /project/bioinformatics/Xiao_lab/s171162/fusionpro/STARfus/hg38/new/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu

Intervals must have positive width at /project/bioinformatics/Xiao_lab/s171162/fusionpro/software/STAR-Fusion-v1.3.2/util/STAR-Fusion.map_chimeric_reads_to_genes line 570, <$fh> line 109024.

Error, cmd: /project/bioinformatics/Xiao_lab/s171162/fusionpro/software/STAR-Fusion-v1.3.2/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /project/bioinformatics/Xiao_lab/s171162/fusionpro/STARfus/hg38/new/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir  -J Chimeric.out.junction  > /project/bioinformatics/Xiao_lab/s171162/fusionpro/STARfus/result/test/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt died with ret 6400 No such file or directory at /project/bioinformatics/Xiao_lab/s171162/fusionpro/software/STAR-Fusion-v1.3.2/PerlLib/Pipeliner.pm line 178.

        Pipeliner::run(Pipeliner=HASH(0x794a40)) called at /project/bioinformatics/Xiao_lab/s171162/fusionpro/software/STAR-Fusion-v1.3.2/STAR-Fusion line 659



It said died with ret 6400 No such file or directory at a directory. I checked all the files in the this cmd, every file is there.
The output shows like this:

Mar 18 16:52:14 ..... started STAR run

Mar 18 16:52:14 ..... loading genome

Mar 18 16:53:46 ..... started 1st pass mapping

Mar 18 17:16:00 ..... finished 1st pass mapping

Mar 18 17:16:01 ..... inserting junctions into the genome indices

Mar 18 17:17:26 ..... started mapping

Mar 18 17:24:22 ..... finished successfully

sbatch_output_603509 (END) 



The output files are:

Chimeric.out.junction  Log.progress.out       _starF_checkpoints       _STARpass1                 std.STAR.bam

Log.final.out          pipeliner.141848.cmds  star-fusion.preliminary  std.Chimeric.out.junction  

Log.out                SJ.out.tab             _STARgenome              std.Chimeric.out.sam



I cannot find the file: star-fusion.fusion_predictions.abridged.tsv'.

I am not sure the exact error in this case. Could you please give some insights on it?

Thanks a lot!!
Tianshi

Brian Haas

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Mar 19, 2018, 3:28:30 PM3/19/18
to veronic...@gmail.com, STAR-Fusion
Hi,

Just run 'make' in the base installation directory and then try rerunning your original command.

best,

~b

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 
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Brian Haas

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Mar 20, 2018, 7:17:54 AM3/20/18
to veronic...@gmail.com, STAR-Fusion
Great!  Thanks for the update,

~b

On Mon, Mar 19, 2018 at 4:11 PM, <veronic...@gmail.com> wrote:
Hi Brian,

Thank you so much for your prompt reply. It perfectly solve the problem!!

Tianshi
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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

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