Merge problem

[bioinfo-dirty-jobs]

I have centos 5.5 I need to try to merge my vcf and then I would like to use ensembl.
I call my variant using mutect1,mutect2,varscan and vardict.
`

`/jdk1.8.0_121/bin/java -jar bcbio-variation-recall-0.1.7 merge 411_merge_prova.vcf.gz hg19_primary.fa 411.mutect1.pass.vcf.gz 411.varscan.pass.vcf.gz 411.vardict.pass.vcf.gz 411.mutect2.pass.vcf.gz

I have this error:

`2017-05-10 18:01:18 compute-00-01.ilmn INFO [bcbio.run.itx] - view: invalid option -- f
2017-05-10 18:01:18 compute-00-01.ilmn INFO [bcbio.run.itx] - open: No such file or directory
2017-05-10 18:01:18 compute-00-01.ilmn INFO [bcbio.run.itx] - JOIN_variant/411/inprep/txtmp3431699226313172048/run.sh: line 3:  6847 Segmentation fault      bcftools view -f 'PASS,.' 411.mutect1.pass.vcf.gz
2017-05-10 18:01:18 compute-00-01.ilmn INFO [bcbio.run.itx] -       6848 Done                    | bgzip -c > JOIN_variant/411/inprep/txtmp3431699226313172048/411.mutect1.pass-qprep-passonly.vcf.gz
2017-05-10 18:01:18 compute-00-01.ilmn ERROR [bcbio.run.itx] - 
java.lang.Exception: Shell command failed: bcftools view -f 'PASS,.' 411.mutect1.pass.vcf.gz | bgzip -c > JOIN_variant/411/inprep/txtmp3431699226313172048/411.mutect1.pass-qprep-passonly.vcf.gz
                           6848 Done                    | bgzip -c > JOIN_variant/411/inprep/txtmp3431699226313172048/411.mutect1.pass-qprep-passonly.vcf.gz
                    JOIN_variant/411/inprep/txtmp3431699226313172048/run.sh: line 3:  6847 Segmentation fault      bcftools view -f 'PASS,.' 411.mutect1.pass.vcf.gz
                     open: No such file or directory
                     view: invalid option -- f
                         bcbio.run.itx/check-run       itx.clj:  168
bcbio.variation.ensemble.prep/bgzip-index-vcf/fn      prep.clj:   47
   bcbio.variation.ensemble.prep/bgzip-index-vcf      prep.clj:   47
                      clojure.lang.RestFn.invoke   RestFn.java:  559
  bcbio.variation.recall.merge/prep-by-region/fn     merge.clj:  135
                             clojure.core/map/fn      core.clj: 2622
                       clojure.lang.LazySeq.sval  LazySeq.java:   40
                        clojure.lang.LazySeq.seq  LazySeq.java:   49
                             clojure.lang.RT.seq       RT.java:  507
                                clojure.core/seq      core.clj:  137
                             clojure.core/map/fn      core.clj: 2616
                       clojure.lang.LazySeq.sval  LazySeq.java:   40
                        clojure.lang.LazySeq.seq  LazySeq.java:   49
                             clojure.lang.RT.seq       RT.java:  507
                                clojure.core/seq      core.clj:  137
                              clojure.core/apply      core.clj:  630
                             clojure.core/mapcat      core.clj: 2660
                      clojure.lang.RestFn.invoke   RestFn.java:  423
  bcbio.variation.recall.split/group-breakpoints     split.clj:   67
     bcbio.variation.recall.split/group-pregions     split.clj:   87
     bcbio.variation.recall.merge/prep-by-region     merge.clj:  138
       bcbio.variation.recall.merge/combine-vcfs     merge.clj:  152
              bcbio.variation.recall.merge/-main     merge.clj:  193
                     clojure.lang.RestFn.applyTo   RestFn.java:  137
                              clojure.core/apply      core.clj:  630
            bcbio.variation.recall.main/-main/fn      main.clj:   34
               bcbio.variation.recall.main/-main      main.clj:   33
                     clojure.lang.RestFn.applyTo   RestFn.java:  137
                bcbio.variation.recall.main.main              :     

2017-05-10 18:01:18 compute-00-01.ilmn ERROR [bcbio.variation.recall.main] - 
java.lang.Exception: Shell command failed: bcftools view -f 'PASS,.' 411.mutect1.pass.vcf.gz | bgzip -c > JOIN_variant/411/inprep/txtmp3431699226313172048/411.mutect1.pass-qprep-passonly.vcf.gz
                           6848 Done                    | bgzip -c > JOIN_variant/411/inprep/txtmp3431699226313172048/411.mutect1.pass-qprep-passonly.vcf.gz
                     JOIN_variant/411/inprep/txtmp3431699226313172048/run.sh: line 3:  6847 Segmentation fault      bcftools view -f 'PASS,.' 411.mutect1.pass.vcf.gz
                     open: No such file or directory
                     view: invalid option -- f
                         bcbio.run.itx/check-run       itx.clj:  168
bcbio.variation.ensemble.prep/bgzip-index-vcf/fn      prep.clj:   47
   bcbio.variation.ensemble.prep/bgzip-index-vcf      prep.clj:   47
                      clojure.lang.RestFn.invoke   RestFn.java:  559
  bcbio.variation.recall.merge/prep-by-region/fn     merge.clj:  135
                             clojure.core/map/fn      core.clj: 2622
                       clojure.lang.LazySeq.sval  LazySeq.java:   40
                        clojure.lang.LazySeq.seq  LazySeq.java:   49
                             clojure.lang.RT.seq       RT.java:  507
                                clojure.core/seq      core.clj:  137
                             clojure.core/map/fn      core.clj: 2616
                       clojure.lang.LazySeq.sval  LazySeq.java:   40
                        clojure.lang.LazySeq.seq  LazySeq.java:   49
                             clojure.lang.RT.seq       RT.java:  507
                                clojure.core/seq      core.clj:  137
                              clojure.core/apply      core.clj:  630
                             clojure.core/mapcat      core.clj: 2660
                      clojure.lang.RestFn.invoke   RestFn.java:  423
  bcbio.variation.recall.split/group-breakpoints     split.clj:   67
     bcbio.variation.recall.split/group-pregions     split.clj:   87
     bcbio.variation.recall.merge/prep-by-region     merge.clj:  138
       bcbio.variation.recall.merge/combine-vcfs     merge.clj:  152
              bcbio.variation.recall.merge/-main     merge.clj:  193
                     clojure.lang.RestFn.applyTo   RestFn.java:  137
                              clojure.core/apply      core.clj:  630
            bcbio.variation.recall.main/-main/fn      main.clj:   34
               bcbio.variation.recall.main/-main      main.clj:   33
                     clojure.lang.RestFn.applyTo   RestFn.java:  137
                bcbio.variation.recall.main.main `

If I change with the last version of  samtools 1.3.1 I have this error:
017-05-10 18:22:01 compute-00-01.ilmn ERROR [bcbio.variation.recall.main] - 
java.lang.Exception: Shell command failed: bcftools tabix -p vcf JOIN_variant/411/inprep/txtmp4490758790926506175/411.vardict.pass-qprep-passonly.vcf.gz
                     tbx_index_build failed: Is the file bgzip-compressed? Was wrong -p [type] option used?
                     [E::hts_idx_push] chromosome blocks not continuous
                         bcbio.run.itx/check-run       itx.clj:  168
                         bcbio.run.itx/check-run       itx.clj:  172
bcbio.variation.ensemble.prep/tabix-index-vcf/fn      prep.clj:   33
   bcbio.variation.ensemble.prep/tabix-index-vcf      prep.clj:   28
   bcbio.variation.ensemble.prep/bgzip-index-vcf      prep.clj:   51
                      clojure.lang.RestFn.invoke   RestFn.java:  559
  bcbio.variation.recall.merge/prep-by-region/fn     merge.clj:  135
                             clojure.core/map/fn      core.clj: 2622
                       clojure.lang.LazySeq.sval  LazySeq.java:   40
                        clojure.lang.LazySeq.seq  LazySeq.java:   49
                             clojure.lang.RT.seq       RT.java:  507
                                clojure.core/seq      core.clj:  137
                             clojure.core/map/fn      core.clj: 2616
                       clojure.lang.LazySeq.sval  LazySeq.java:   40
                        clojure.lang.LazySeq.seq  LazySeq.java:   49
                             clojure.lang.RT.seq       RT.java:  507
                                clojure.core/seq      core.clj:  137
                              clojure.core/apply      core.clj:  630
                             clojure.core/mapcat      core.clj: 2660
                      clojure.lang.RestFn.invoke   RestFn.java:  423
  bcbio.variation.recall.split/group-breakpoints     split.clj:   67
     bcbio.variation.recall.split/group-pregions     split.clj:   87
     bcbio.variation.recall.merge/prep-by-region     merge.clj:  138
       bcbio.variation.recall.merge/combine-vcfs     merge.clj:  152
              bcbio.variation.recall.merge/-main     merge.clj:  193
                     clojure.lang.RestFn.applyTo   RestFn.java:  137
                              clojure.core/apply      core.clj:  630
            bcbio.variation.recall.main/-main/fn      main.clj:   34
               bcbio.variation.recall.main/-main      main.clj:   33
                     clojure.lang.RestFn.applyTo   RestFn.java:  137
                bcbio.variation.recall.main.main              :     

Could you please help me?

[chapmanb]

Thanks for using the ensemble method and for the detailed report. It looks like you might have an older incompatible version of bcftools. What does:

bcftools --version

report? The error is that bcftools view does not have a -f option which is present in recent versions (1.3.x or 1.4.x). Hopefully upgrading bcftools to one of those will resolve the problem.

[bioinfo-dirty-jobs]

Thanks so much for your quick help

[sbsuser@compute-00-01 411]$ bcftools -v
bcftools 1.3.1
Using htslib 1.3.1
Copyright (C) 2016 Genome Research Ltd.
License Expat: The MIT/Expat license
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Unfortunately I have RHEL 5.5 I can't upgrade...

[chapmanb]

Thanks for following up, 1.3.1 has the -f option for view so now I'm confused as to what is going on. Is it possible you have multiple bcftools versions installed on the machine and the bcbio-variation-recall command was run with a different PATH? Sorry, I'm not sure what else to suggest beyond that, the error message seems to indicate that it's the source of the error. Hope this helps some.

[bioinfo-dirty-jobs]

I set the PATh again.. I will send you any errors. I need to open a new threads for ensemble...