Have used NGSEPGUI for 3.3 and 4 in Windows. Taking my data to the mainframe and using NGSEPcore_4.1.0 and first time for NGSEP on the command line. Tried a call like this:
java -Xmx100g -jar NGSEPcore_4.1.0.jar MultisampleVariantsDetector-r GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b_genomic.fna -o vcf/test2.vcf -psp -minMQ 20 -maxAlnsPerStartPos 2 ignore3 3 -h 0.01 -maxBaseQS 30 -minQuality 20 -embeddedSNVs false Csort.bam
but many of the options were treated as input files . I suspect that all those options need to precede all the file declarations . when I look at the examples all the options precede the -r and -o declarations. Also, in the online instructions there is an asterisk at the end, which is present on many of the examples and that makes no sense to me. What is the asterisk for? I note that having an asterisk in the Csort.bam changes the font so it is confusing to have an asterisk in this text box.
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Is that asterisk on the end of line supposed to be there. All the options supposedly are passed correctly. I get the impression that certain options are expected in a specific spot/order.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Have used NGSEPGUI for 3.3 and 4 in Windows. Taking my data to the mainframe and using NGSEPcore_4.1.0 and first time for NGSEP on the command line. Tried a call like this:
java -Xmx100g -jar NGSEPcore_4.1.0.jar MultisampleVariantsDetector-r GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b_genomic.fna -o vcf/test2.vcf -psp -minMQ 20 -maxAlnsPerStartPos 2 ignore3 3 -h 0.01 -maxBaseQS 30 -minQuality 20 -embeddedSNVs false Csort.bam
but many of the options were treated as input files . I suspect that all those options need to precede all the file declarations . when I look at the examples all the options precede the -r and -o declarations. Also, in the online instructions there is an asterisk at the end, which is present on many of the examples and that makes no sense to me. What is the asterisk for? I note that having an asterisk in the Csort.bam changes the font so it is confusing to have an asterisk in this text box.
Well, I am at a loss. My call to the program:
java -Xmx100g -jar NGSEPcore_4.1.0.jar MultisampleVariantsDetector -psp -minMQ 20 -maxAlnsPerStartPos 2 ignore3 3 -h 0.01 -maxBaseQS 30 -minQuality 20 -embeddedSNVs false -r GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b_genomic.fna -o vcf/test2.vcf C*sort.bam
Output in err file:
an 08, 2022 7:54:09 AM ngsep.discovery.MultisampleVariantsDetector logParameters
INFO: Input files: [ignore3, 3, -h, 0.01, -maxBaseQS, 30, -minQuality, 20, -embeddedSNVs, false, -r, GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b_genomic.fna, -o, vcf/testC1all.vcf, C10Esort.bam, C10Fsort.bam, C11Asort.bam, C11Bsort.bam, C11Gsort.bam, C11Hsort.bam, C12Bsort.bam, C12Csort.bam]
so everything is being treated as an input file. the instructions say:
USAGE:
java -jar NGSEPcore.jar MultisampleVariantsDetector <options> <alignments_file>*</alignments_file></options>
Is that asterisk on the end of line supposed to be there. All the options supposedly are passed correctly. I get the impression that certain options are expected in a specific spot/order.
Never mind; missing the '-' before ignore3.
Hi Douglas
No problem. Let me know if you have any other issue running the command line of NGSEP.
Best regards
Jorge