genomeParameters.txt missing

Eran Eyal

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Nov 3, 2017, 12:11:28 PM11/3/17

to STAR-Fusion

Hi,

I am trying to run STAR-Fusion with GRCh37 libraries. I am getting an error message that genomeParameters.txt is missing. Indeed I can not find the file in both large resources directory (26GB) or the small one. What do I miss here?

EXITING because of FATAL ERROR: could not open genome file /data/genomedata/annotations/hg19/GRCh37_gencode_v19_CTAT_lib_July192017/ctat_genome_lib_build_dir//ref_genome.fa.star.idx/genomeParameters.txt

SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions

Brian Haas

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Nov 3, 2017, 12:27:57 PM11/3/17

to Eran Eyal, STAR-Fusion

Hi Eran,

Does this file not exist?

/data/genomedata/annotations/hg19/GRCh37_gencode_v19_CTAT_lib_July192017/ctat_genome_lib_build_dir//ref_genome.fa.star.idx/genomeParameters.txt

Can you send me a list of the files that are in that directory?

best,

~b

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Brian Haas

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Nov 3, 2017, 12:48:09 PM11/3/17

to Eran Eyal, STAR-Fusion

Was this from a plug-n-play or a source tar.gz file that you then built yourself?

Brian Haas

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Nov 3, 2017, 1:17:34 PM11/3/17

to Eran Eyal, STAR-Fusion

I'm not sure why it's not showing up. I'd suggest trying a new version. I've just prepared new plug-n-play versions here:

https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/

and the plug-n-play version should have the following contents:

-rw-rw-r-- 1 bhaas regev_lab 933 Jul 19 13:27 genomeParameters.txt
-rw-rw-r-- 1 bhaas regev_lab 273 Jul 19 13:28 chrStart.txt
-rw-rw-r-- 1 bhaas regev_lab 376 Jul 19 13:28 chrNameLength.txt
-rw-rw-r-- 1 bhaas regev_lab 138 Jul 19 13:28 chrName.txt
-rw-rw-r-- 1 bhaas regev_lab 238 Jul 19 13:28 chrLength.txt
-rw-rw-r-- 1 bhaas regev_lab 1046532 Jul 19 15:12 geneInfo.tab
-rw-rw-r-- 1 bhaas regev_lab 42486994 Jul 19 15:12 exonGeTrInfo.tab
-rw-rw-r-- 1 bhaas regev_lab 12030020 Jul 19 15:12 transcriptInfo.tab
-rw-rw-r-- 1 bhaas regev_lab 17221630 Jul 19 15:12 exonInfo.tab
-rw-rw-r-- 1 bhaas regev_lab 8921492 Jul 19 15:12 sjdbList.fromGTF.out.tab
-rw-rw-r-- 1 bhaas regev_lab 8915033 Jul 19 15:12 sjdbList.out.tab
-rw-rw-r-- 1 bhaas regev_lab 10098713 Jul 19 15:12 sjdbInfo.txt
-rw-rw-r-- 1 bhaas regev_lab 3200284647 Jul 19 15:22 Genome
-rw-rw-r-- 1 bhaas regev_lab 24458836614 Jul 19 15:27 SA
-rw-rw-r-- 1 bhaas regev_lab 1565873619 Jul 19 15:27 SAindex
-rw-rw-r-- 1 bhaas regev_lab 0 Jul 19 15:27 build.ok

Eran Eyal

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Nov 4, 2017, 2:06:06 PM11/4/17

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Just to close this thread,

I now believe I worked with a truncated library archive, so it was my fault and nothing wrong with STAR-Fusion resource packages.

On any case, Brian posted yesterday a new version for the resource packages.
Thanks,

Eran

On Friday, November 3, 2017 at 6:27:57 PM UTC+2, Brian Haas wrote:

Hi Eran,

Does this file not exist?
/data/genomedata/annotations/hg19/GRCh37_gencode_v19_CTAT_lib_July192017/ctat_genome_lib_build_dir//ref_genome.fa.star.idx/genomeParameters.txt

Can you send me a list of the files that are in that directory?

best,

~b

On Fri, Nov 3, 2017 at 12:11 PM, Eran Eyal <eyal...@gmail.com> wrote:

Hi,
I am trying to run STAR-Fusion with GRCh37 libraries. I am getting an error message that genomeParameters.txt is missing. Indeed I can not find the file in both large resources directory (26GB) or the small one. What do I miss here?

EXITING because of FATAL ERROR: could not open genome file /data/genomedata/annotations/hg19/GRCh37_gencode_v19_CTAT_lib_July192017/ctat_genome_lib_build_dir//ref_genome.fa.star.idx/genomeParameters.txt
SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions

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Laura Hilton

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Feb 23, 2018, 1:57:40 PM2/23/18

to STAR-Fusion

Hi Brian,

I'm now having the same problem. I checked my ctat_genome_lib_build_dir and it has all the files you listed below. I just downloaded the reference two days ago.

The error I get is:

Feb 23 10:27:31 ..... started STAR run

Feb 23 10:27:31 ..... loading genome

EXITING because of FATAL ERROR: could not open genome file ./GenomeDir//genomeParameters.txt

SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions

My command is:

STAR-Fusion --genome_lib_dir /path/to/ctat_genome_lib_build_dir/ \

--left_fq $fq1 \

--right_fq $fq2 \

--output_dir $outDir/$rootName \

--FusionInspector inspect \

--denovo_reconstruct \

--CPU $threads \

--max_promiscuity 5 \

--tmpdir $outdir/tmp

Any suggestions?

Brian Haas

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Feb 23, 2018, 2:03:01 PM2/23/18

to Laura Hilton, STAR-Fusion

Hi Laura,

I wonder if the full .tar.gz file ended up getting downloaded, or if the connection broke early...

Were you able to match up the md5 value? I'm running tar -tvf on the .tar.gz file right now to get the file listing.

best,

~b

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Brian Haas

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Feb 23, 2018, 2:08:39 PM2/23/18

to Laura Hilton, STAR-Fusion

I added this file:

https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh37_gencode_v19_CTAT_lib_Nov012017.plug-n-play.tar.file_listing

which lists the contents of the v19 archive.

I'll do this for the others too.

best,

~b

Laura Hilton

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Feb 23, 2018, 5:06:22 PM2/23/18

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It would appear that the problem is resolved without downloading the library again, but I still don't know what was wrong with my command before.

Anyway, thanks for your quick response.

Laura

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Brian Haas

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Feb 23, 2018, 5:44:18 PM2/23/18

to Laura Hilton, STAR-Fusion

Hi Luara,

If you could share your insights on how it might have fixed itself, that would be helpful in case it should happen again to someone else.

best,

~b

Laura Hilton

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Feb 23, 2018, 6:00:09 PM2/23/18

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I honestly think it must have been a typo in the file path to the library, but I can't spot it myself. If I had something more insightful to share, I would definitely share it!

Brian Haas

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Feb 23, 2018, 6:09:15 PM2/23/18

to Laura Hilton, STAR-Fusion

no worries. many thanks. :-)

~b

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