search

tgen / lumosVar2

Calls somatic SNVs, indels, and allelic copy number jointly across multiple samples from the same patient. These can be standard tumor/normal pair, longitudinal samples, primary/met, etc. Can also be used for tumor only calling, ideally with a high tumor content and a low tumor content sample.
MIT License
10 stars 1 forks source link

Running the runNormalMetrics.py error #3

Closed jsonProgram closed 4 years ago

jsonProgram commented 4 years ago

/data/testuser/02_bin/lumosVar2/scripts/runNormalMetrics.py config.yaml 1

<<ERROR [E::hts_open_format] Failed to open file 1.txt.gz [W::fai_get_val] Reference 1 not found in file, returning empty sequence gvm.c:1666: Failed to load reference genome from index. (err code -2) b'' Traceback (most recent call last): File "/data/testuser/02_bin/lumosVar2/scripts/runNormalMetrics.py", line 60, in die("gvm failed:\n" + stderr) TypeError: can only concatenate str (not "NoneType") to str

<<

I can find the fasta.fai in the fasta directory. but gvm cann't read this fai file ?

rhalperin commented 4 years ago

It sounds like it is not finding a contig named "1" in your reference fasta. Does your fasta have it named "chr1". lumosVar does not currently support the "chr" prefix, though intend to add that feature soon.

On Wed, Feb 19, 2020 at 10:19 PM jsonProgram notifications@github.com wrote:

/data/testuser/02_bin/lumosVar2/scripts/runNormalMetrics.py config.yaml 1

<<ERROR [E::hts_open_format] Failed to open file 1.txt.gz [W::fai_get_val] Reference 1 not found in file, returning empty sequence gvm.c:1666: Failed to load reference genome from index. (err code -2) b'' Traceback (most recent call last): File "/data/testuser/02_bin/lumosVar2/scripts/runNormalMetrics.py", line 60, in die("gvm failed:\n" + stderr) TypeError: can only concatenate str (not "NoneType") to str

<<

I can find the fasta.fai in the fasta directory. but gvm cann't read this fai file ?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/tgen/lumosVar2/issues/3?email_source=notifications&email_token=ACSZWCWGXE4HXD6R6CW4NTTRDYHGNA5CNFSM4KYHNZ7KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IO34DBQ, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACSZWCRXVLCEFQLT5IZOO5TRDYHGNANCNFSM4KYHNZ7A .

--

This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

jsonProgram commented 4 years ago

Yes! This reference is ucsc_hg19 .

Thank you！