search

hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
314 stars 117 forks source link

question about variat calling #71

Open sunyanling opened 8 years ago

sunyanling commented 8 years ago

First step, I succesd in alignment, but the second step ,I don' know why it is failed . The running time still relapsed ,but actual expending CPU time is immobile. there're no writing in the results file. The code as below "speedseq var \ -o V9\ -t 23 \ annotations/human_g1k_v37.fasta \ V9.bam" I use 150G mem and 30 thread. There is no error , just no results . who can tell me why

sunyanling commented 8 years ago

``

cc2qe commented 8 years ago

do you need to change "V9\" to "V9 \" (with a space)?

also, maybe try running it with "-v" for verbose output

sunyanling commented 8 years ago

I use "- v" it finished ,but still have no results. speedseq var \ -o V9 \ -t 23 \ -v \ speedseq/annotations/human_g1k_v37.fasta \ V9.bam

also when I use "-w" ,it stopped quickly. I am sure I put it on the options position. what should I do?

cc2qe commented 8 years ago

Did the command print anything out to the screen while it was running? It might help diagnose the problem

cc2qe commented 8 years ago

also, it should have created a temp directory while it was working. Did it?

sunyanling commented 8 years ago

it create a temp directory and print some results like"V9.GL000249.1:0..38502.vcf,V9.GL000248.1:0..39786.vcf,V9.GL000247.1:0..36422.vcf,V9.GL000246.1:0..38154.vcf,V9.9:0..141213431.vcf......windows.bed,var_command.txt" But there 're nothing in the vcf files .anything wrong?

cc2qe commented 8 years ago

First, you should ensure that your BAM file is not corrupt. Also, speedseq -v will print out its internal commands while it is running. Use that information to diagnose the step that is causing the problem.