Question about CREST

Question

[mangfu100]

Hi.

I encounter a problem during process of CREST test. So I am writing here of my problem.

I think it's just a test case of program so I expect somebody can fix my problem.

Below is command input and my error message.

./CREST.pl -f tumor.bam.cover -d tumor.bam -g germline.bam --ref_genome /DATA1/AITL/hg19/ucsc.hg19.fasta -t ./hg19.2bit

4       125893227       +       5
Output is in /tmp/Si39yJ93qh/UGsHsdVrnm.fa.cap.contigs.clip.fa.psl
[bam_parse_region] fail to determine the sequence name.
10      66301865        -       9
Output is in /tmp/Si39yJ93qh/urwTNUR_7U.fa.cap.contigs.clip.fa.psl
[bam_parse_region] fail to determine the sequence name.
10      66301858        +       4
Output is in /tmp/Si39yJ93qh/tmzP5LgNVK.fa.cap.contigs.clip.fa.psl
SV filter starting....
low compexity filter
sh: ptrfinder: command not found
Type distance filter
Germline sclip filter
Can't call method "dna" on an undefined value at StructVar.pm line 931.

As you also see above, there have two problems.

First is [bam_parse_region] fail to determine the sequence name.

I think that this error can be fixed by matching bam files and reference files regarding chr string.

(ex. 4 -> chr4)

And, I think the second problem is important and I don't know how to solve.

The second problem is Can't call method "dna" on an undefined value at StructVar.pm line 931.

I didn't understand why this error message occur.

I hope this can also be fixed through solving first problem, but It's my guess.

Does anybody who use CREST before exist? If so, I need your help sincerely.

Thank you.

[Sean Davis]

I'd suggest making sure that your sequence names match first. Nothing will work as expected without that prerequisite being met. Ideally, you should use the same fasta file that you used for alignment.

[Kasthuri]

Hi Mangfu100,

Were you able to fix this error? I get the same error too and I am not what is causing it. I am using the same genomic build I used for aligning this genomes. Any help? Thanks.

[mangfu100]

Hi Kasthuri

Yes. I have already fixed my problems.

you need to take a look at how you set your 2bit or fasta files.

If all of your 2bit or fasta files are setting equally, there may be no problems anymore.

[13180854865]

Hi Mangfu100,

My reference fasta is ucsc.hg19.fasta, i used faToTwoBit tool to get the ucsc.hg19.2bit file, but there are two errors like yours, do you know how to fix it ? what' your meaning of setting 2bit and fasta files equally? thank you.

Below is command input and my error message.

./CREST.pl -f tumor.bam.cover -d tumor.bam -g germline.bam --ref_genome ucsc.hg19.fasta -t ucsc.hg19.2bit --cap3 ./CAP3/cap3 --blatclient ./gfClient --blat ./blat --blatserver 127.0.0.1 --blatport 9967 --nopaired --norm_tandem_repeat
4       125893227       +       5
Output is in /tmp/1pJs5Frz6L/bgybXjaOps.fa.cap.contigs.clip.fa.psl
[bam_parse_region] fail to determine the sequence name.
10      66301865        -       9
Output is in /tmp/1pJs5Frz6L/zGpQSACqy4.fa.cap.contigs.clip.fa.psl
[bam_parse_region] fail to determine the sequence name.
10      66301858        +       4
Output is in /tmp/1pJs5Frz6L/yEm8338uXu.fa.cap.contigs.clip.fa.psl
SV filter starting....
Type distance filter
Germline sclip filter
Can't call method "dna" on an undefined value at /home/wangqw/perl5/lib/perl5/5.16.3/x86_64-linux-thread-multi/StructVar.pm line 931.