Dear Peter,
Thanks for help !
I downloaded the new version. I use this command:
java NGSrich summarize -r /stockage/ngs-client-01/tools/samtools/test_target/sam/align_LBC03.sam -o /stockage/ngs-client-01/tools/samtools/test_target/sam/
Error: Argument -i is mandatory
Apparently missing the-i option
For this command :
java NGSrich evaluate -r /stockage/ngs-client-01/tools/samtools/test_target/sam/align_LBC03.sam -a /stockage/ngs-client-01/tools/samtools/test_target/ref/hg19_refGene.txt -t /stockage/ngs-client-01/tools/samtools/test_target/bed/baits_chr17_brca1.bed
I get this response:
>>> STEP 1: reducing files
READS FILE:
/stockage/ngs-client-01/tools/samtools/test_target/sam/align_LBC03.sam reduced to /tmp/1311070026218/NGSrich_align_LBC03_s-ngs-client-linux.10819.txt
Reduced file /tmp/1311070026218/NGSrich_align_LBC03_s-ngs-client-linux.10819.txt sorted
GENOME ANNOTATION FILE:
/tmp/1311070026218/hg19_refGene.genome reduced to /tmp/1311070026218/NGSrich_genome_s-ngs-client-linux.10819.txt
TARGET REGIONS FILE:
/tmp/1311070026218/baits_chr17_brca1.target reduced to /tmp/1311070026218/NGSrich_target_s-ngs-client-linux.10819.txt
Reduced file /tmp/1311070026218/NGSrich_target_s-ngs-client-linux.10819.txt sorted
STEP 1 successfully completed
=====================2=========================
>>> STEP 2: computing target coverage data
Target BED coverage file created (/stockage/ngs-client-01/tools/samtools/test_target/sam/enrichment/data/align_LBC03_enrichment.bed)
Per-base coverage file created (/tmp/1311070026218/coverage_s-ngs-client-linux.10819.txt)
Summary statistics file created (/stockage/ngs-client-01/tools/samtools/test_target/sam/enrichment/data/align_LBC03_enrichment.xml)
STEP 2 successfully completed
=====================3=========================
>>> STEP 3: evaluating enrichment files
java.io.IOException: Cannot run program "Rscript": java.io.IOException: error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:475)
at java.lang.Runtime.exec(Runtime.java:610)
at java.lang.Runtime.exec(Runtime.java:448)
at java.lang.Runtime.exec(Runtime.java:345)
at Enrichment.evaluate(Enrichment.java:179)
at NGSrichEvaluate.main(NGSrichEvaluate.java:122)
at NGSrich.main(NGSrich.java:26)
Caused by: java.io.IOException: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.<init>(UNIXProcess.java:164)
at java.lang.ProcessImpl.start(ProcessImpl.java:81)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:468)
... 6 more
=====================4=========================
>>> STEP 4: computing targets wiggle data
Computing wiggle file for on-target reads
Wiggle file for on-target reads created
Output written to /stockage/ngs-client-01/tools/samtools/test_target/sam/enrichment/data/align_LBC03_onTarget.wig
STEP 4 successfully completed.
=====================5=========================
>>> STEP 5: computing overall wiggle data
Computing wiggle file for all reads
Wiggle file for all reads created
Output written to /stockage/ngs-client-01/tools/samtools/test_target/sam/enrichment/data/align_LBC03.wig
STEP 5 successfully completed.
It's normal ?
I hold you informed of progress!
Regards
Antoine
Thanks for help !
I downloaded the new version. I use this command:
java NGSrich summarize -r /stockage/ngs-client-01/tools/samtools/test_target/sam/align_LBC03.sam -o /stockage/ngs-client-01/tools/samtools/test_target/sam/
Error: Argument -i is mandatory
Apparently missing the-i option
For this command :
java NGSrich evaluate -r /stockage/ngs-client-01/tools/samtools/test_target/sam/align_LBC03.sam -a /stockage/ngs-client-01/tools/samtools/test_target/ref/hg19_refGene.txt -t /stockage/ngs-client-01/tools/samtools/test_target/bed/baits_chr17_brca1.bed
I get this response:
>>> STEP 1: reducing files
READS FILE:
/stockage/ngs-client-01/tools/samtools/test_target/sam/align_LBC03.sam reduced to /tmp/1311070026218/NGSrich_align_LBC03_s-ngs-client-linux.10819.txt
Reduced file /tmp/1311070026218/NGSrich_align_LBC03_s-ngs-client-linux.10819.txt sorted
GENOME ANNOTATION FILE:
/tmp/1311070026218/hg19_refGene.genome reduced to /tmp/1311070026218/NGSrich_genome_s-ngs-client-linux.10819.txt
TARGET REGIONS FILE:
/tmp/1311070026218/baits_chr17_brca1.target reduced to /tmp/1311070026218/NGSrich_target_s-ngs-client-linux.10819.txt
Reduced file /tmp/1311070026218/NGSrich_target_s-ngs-client-linux.10819.txt sorted
STEP 1 successfully completed
=====================2=========================
>>> STEP 2: computing target coverage data
Target BED coverage file created (/stockage/ngs-client-01/tools/samtools/test_target/sam/enrichment/data/align_LBC03_enrichment.bed)
Per-base coverage file created (/tmp/1311070026218/coverage_s-ngs-client-linux.10819.txt)
Summary statistics file created (/stockage/ngs-client-01/tools/samtools/test_target/sam/enrichment/data/align_LBC03_enrichment.xml)
STEP 2 successfully completed
=====================3=========================
>>> STEP 3: evaluating enrichment files
java.io.IOException: Cannot run program "Rscript": java.io.IOException: error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:475)
at java.lang.Runtime.exec(Runtime.java:610)
at java.lang.Runtime.exec(Runtime.java:448)
at java.lang.Runtime.exec(Runtime.java:345)
at Enrichment.evaluate(Enrichment.java:179)
at NGSrichEvaluate.main(NGSrichEvaluate.java:122)
at NGSrich.main(NGSrich.java:26)
Caused by: java.io.IOException: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.<init>(UNIXProcess.java:164)
at java.lang.ProcessImpl.start(ProcessImpl.java:81)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:468)
... 6 more
=====================4=========================
>>> STEP 4: computing targets wiggle data
Computing wiggle file for on-target reads
Wiggle file for on-target reads created
Output written to /stockage/ngs-client-01/tools/samtools/test_target/sam/enrichment/data/align_LBC03_onTarget.wig
STEP 4 successfully completed.
=====================5=========================
>>> STEP 5: computing overall wiggle data
Computing wiggle file for all reads
Wiggle file for all reads created
Output written to /stockage/ngs-client-01/tools/samtools/test_target/sam/enrichment/data/align_LBC03.wig
STEP 5 successfully completed.
It's normal ?
I hold you informed of progress!
Regards
Antoine
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