LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts
Hi,
an error happened when RNAseqMaster.sh was executed. It seems there is something wrong when passing parameters to samtools in BAM2WIG.jar. The output log is:
/biosoft/LIONS/bin/java -jar -Xmx6G /biosoft/LIONS/scripts/RNAseqPipeline/bin/BAM2WIG.jar -bamFile HSB272_1.bam
-out /biosoft/LIONS/projects/test/HSB272_1/expression/wig -q 10 -F 772 -samtools /biosoft/LIONS/bin/samtools -
chr HSB272_1.bam0 >> /biosoft/LIONS/projects/test/HSB272_1/expression/wig/HSB272_1.wig.log
java.io.IOException: Stream closed
at java.base/java.io.BufferedReader.ensureOpen(BufferedReader.java:123)
at java.base/java.io.BufferedReader.readLine(BufferedReader.java:321)
at java.base/java.io.BufferedReader.readLine(BufferedReader.java:396)
at src.tools.BAM2WIG.generateWig(BAM2WIG.java:921)
at src.tools.BAM2WIG.run(BAM2WIG.java:377)
at src.tools.BAM2WIG.main(BAM2WIG.java:116)
expression/wig/HSB272_1.q10.F772.wig.gz
Wig file not generated. Errors are afoot.
============= ERROR 12: Wig Not Generated =============
The content of /biosoft/LIONS/projects/test/HSB272_1/expression/wig/HSB272_1.wig.log is:
Sun Jun 18 10:59:10 CST 2023
$Id: BAM2WIG.java 86812 2013-01-31 03:38:48Z mbilenky $
Reading BAM file: HSB272_1.bam
Output WIG file into: /biosoft/LIONS/projects/test/HSB272_1/expression/wig_multiread
Wrong BAM --> UCSC chromosome conversion file: HSB272_1.bam0. Use chromosome names from BAM.
Reading the header...
/biosoft/LIONS/bin/samtools view -H -q 0 -F 772 HSB272_1.bam
Read lengths for 455 chromosomes
RNA-seq, PET (NON Strand specific analysis): 1 wig file
Start analysis...
Parsing HSB272_1.bam
/biosoft/LIONS/bin/samtools view -X -q 0 -F 772 HSB272_1.bam
Error: samtools view: Incorrect number of arguments for -X option. Aborting.
Exception happened - here's what I know:
Hi, an error happened when RNAseqMaster.sh was executed. It seems there is something wrong when passing parameters to samtools in BAM2WIG.jar. The output log is:
The content of
/biosoft/LIONS/projects/test/HSB272_1/expression/wig/HSB272_1.wig.log
is:Could you give any suggestions? Thanks.