ERROR: genesPassQC.bed file was not generated correctly. at ExonDel.pl line 217, <REFSEQ> line 1007907

[CCgenetics15]

Hi Shilin,

I tried running the last version of ExonDel and it gave an error:
perl ExonDel.pl -i Bams.list -c ExonDel.cfg -o results
[Tue Sep 1 11:40:43 2015] All genes will be used
[Tue Sep 1 11:40:43 2015] Loading BED file
[Tue Sep 1 11:58:37 2015] Finish BED file (cover 3003680644 base pairs)
[Tue Sep 1 11:58:37 2015] Loading RefSeq file
[Tue Sep 1 11:58:39 2015] Finish RefSeq file
[Tue Sep 1 11:58:39 2015] #####################################################################
[Tue Sep 1 11:58:39 2015] #ERROR: genesPassQC.bed file was not generated correctly.
[Tue Sep 1 11:58:39 2015] #Decrease exon_bp_cover_threshold and overall_exon_count_threshold in configure file.
[Tue Sep 1 11:58:39 2015] #More information at README config file section.
[Tue Sep 1 11:58:39 2015] #####################################################################
ERROR: genesPassQC.bed file was not generated correctly. at ExonDel.pl line 217, line 1007907.

[slzhao]

Hello,

Did you try the example in ExonDel? Does it work?
Based on the error message, the issue is "#Decrease exon_bp_cover_threshold
and overall_exon_count_threshold in configure file." Try to decrease the
following two parameters in configure file and it should work.

#Minimal percent of covered base pairs for each exon
exon_bp_cover_threshold=0.1
#Minimal percent of covered exons for each gene. 1 means 100%
overall_exon_count_threshold=1

2015-09-01 5:22 GMT-05:00 CCgenetics15 notifications@github.com:

Hi Shilin,

I tried running the last version of ExonDel and it gave an error:
perl ExonDel.pl -i Bams.list -c ExonDel.cfg -o results
[Tue Sep 1 11:40:43 2015] All genes will be used
[Tue Sep 1 11:40:43 2015] Loading BED file
[Tue Sep 1 11:58:37 2015] Finish BED file (cover 3003680644 base pairs)
[Tue Sep 1 11:58:37 2015] Loading RefSeq file
[Tue Sep 1 11:58:39 2015] Finish RefSeq file
[Tue Sep 1 11:58:39 2015]
#####################################################################
[Tue Sep 1 11:58:39 2015] #ERROR: genesPassQC.bed file was not generated
correctly.
[Tue Sep 1 11:58:39 2015] #Decrease exon_bp_cover_threshold and
overall_exon_count_threshold in configure file.
[Tue Sep 1 11:58:39 2015] #More information at README config file section.
[Tue Sep 1 11:58:39 2015]
#####################################################################
ERROR: genesPassQC.bed file was not generated correctly. at ExonDel.pl
line 217, line 1007907.

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#8.

[CCgenetics15]

Yes, I tried the example and it worked without problems. I tried also to change the overall_exon_count treshold (0.5) but the error message was always the same.
Thanks,
C.

[slzhao]

The error message means the bed file didn't cover enough length or number
of exons for the genes. Would you please try to set them to very small
values, for example:
#Minimal percent of covered base pairs for each exon
exon_bp_cover_threshold=0.01
#Minimal percent of covered exons for each gene. 1 means 100%
overall_exon_count_threshold=0.01

2015-09-02 2:27 GMT-05:00 CCgenetics15 notifications@github.com:

Yes, I tried the example and it worked without problems. I tried also to
change the overall_exon_count treshold (0.5) but the error message was
always the same.
Thanks,
C.

—
Reply to this email directly or view it on GitHub
#8 (comment).

[CCgenetics15]

Always the same error message:
#ERROR: genesPassQC.bed file was not generated correctly.
[Wed Sep 2 17:16:27 2015] #Decrease exon_bp_cover_threshold and overall_exon_count_threshold in configure file.
[Wed Sep 2 17:16:27 2015] #More information at README config file section.
[Wed Sep 2 17:16:27 2015] #####################################################################
ERROR: genesPassQC.bed file was not generated correctly. at ExonDel.pl line 217, line 1007907.

[slzhao]

Would you please tell me the format of your gtf and bed file?

2015-09-03 1:54 GMT-05:00 CCgenetics15 notifications@github.com:

Always the same error message:
#ERROR: genesPassQC.bed file was not generated correctly.
[Wed Sep 2 17:16:27 2015] #Decrease exon_bp_cover_threshold and
overall_exon_count_threshold in configure file.
[Wed Sep 2 17:16:27 2015] #More information at README config file section.
[Wed Sep 2 17:16:27 2015]
#####################################################################
ERROR: genesPassQC.bed file was not generated correctly. at ExonDel.pl
line 217, line 1007907.

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#8 (comment).

[CCgenetics15]

Bed file (downloaded from UCSC table browser)
chr1 16767166 16786584 NM_001145278 0 + 16767256 16785385 0 8 104,101,105,82,109,178,76,1248, 0,2960,7198,7388,8421,11166,15146,18170,
chr1 16767166 16786584 NM_001145277 0 + 16767256 16785491 0 7 182,101,105,82,109,178,1248, 0,2960,7198,7388,8421,11166,18170,
chr1 33547778 33567493 NR_126031 0 + 33567493 33567493 0 8 177,174,173,172,166,163,113,60, 0,1776,9872,11067,12370,14529,15889,19655,
chr1 16767166 16786584 NM_018090 0 + 16767256 16785385 0 8 182,101,105,82,109,178,76,1248, 0,2960,7198,7388,8421,11166,15146,18170,

Gtf file
chr1 hg19_refGene start_codon 67000042 67000044 0.000000 + . gene_id "NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene CDS 67000042 67000051 0.000000 + 0 gene_id "NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene exon 66999639 67000051 0.000000 + . gene_id "NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene CDS 67091530 67091593 0.000000 + 2 gene_id "NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene exon 67091530 67091593 0.000000 + . gene_id "NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene CDS 67098753 67098777 0.000000 + 1 gene_id "NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene exon 67098753 67098777 0.000000 + . gene_id "NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene CDS 67101627 67101698 0.000000 + 0 gene_id "NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene exon 67101627 67101698 0.000000 + . gene_id "NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene CDS 67105460 67105516 0.000000 + 0 gene_id "NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene exon 67105460 67105516 0.000000 + . gene_id "NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene CDS 67108493 67108547 0.000000 + 0 gene_id "NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene exon 67108493 67108547 0.000000 + . gene_id "NM_032291"; transcript_id "NM_032291";

[slzhao]

To download a gtf file with correct format, please select track as RefSeq
Genes in UCSC table browser. Its format should be
#gtf file (with header):

#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount
exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames
23 NM_005509 chr5 + 118407083 118584822
118407264 118582914 3
118407083,118433673,1184376292, 118407351,118433799,118437701, 0
DMXL1 cmpl cmpl 0,0,0,

2015-09-07 2:30 GMT-05:00 CCgenetics15 notifications@github.com:

Bed file (downloaded from UCSC table browser)
chr1 16767166 16786584 NM_001145278 0 + 16767256 16785385 0 8
104,101,105,82,109,178,76,1248, 0,2960,7198,7388,8421,11166,15146,18170,
chr1 16767166 16786584 NM_001145277 0 + 16767256 16785491 0 7
182,101,105,82,109,178,1248, 0,2960,7198,7388,8421,11166,18170,
chr1 33547778 33567493 NR_126031 0 + 33567493 33567493 0 8
177,174,173,172,166,163,113,60, 0,1776,9872,11067,12370,14529,15889,19655,
chr1 16767166 16786584 NM_018090 0 + 16767256 16785385 0 8
182,101,105,82,109,178,76,1248, 0,2960,7198,7388,8421,11166,15146,18170,

Gtf file
chr1 hg19_refGene start_codon 67000042 67000044 0.000000 + . gene_id
"NM_032291"; transcript_id "NM_032291";
chr1 hg19_refGene CDS 67000042 67000051 0.000000 + 0 gene_id "NM_032291";
transcript_id "NM_032291";
chr1 hg19_refGene exon 66999639 67000051 0.000000 + . gene_id "NM_032291";
transcript_id "NM_032291";
chr1 hg19_refGene CDS 67091530 67091593 0.000000 + 2 gene_id "NM_032291";
transcript_id "NM_032291";
chr1 hg19_refGene exon 67091530 67091593 0.000000 + . gene_id "NM_032291";
transcript_id "NM_032291";
chr1 hg19_refGene CDS 67098753 67098777 0.000000 + 1 gene_id "NM_032291";
transcript_id "NM_032291";
chr1 hg19_refGene exon 67098753 67098777 0.000000 + . gene_id "NM_032291";
transcript_id "NM_032291";
chr1 hg19_refGene CDS 67101627 67101698 0.000000 + 0 gene_id "NM_032291";
transcript_id "NM_032291";
chr1 hg19_refGene exon 67101627 67101698 0.000000 + . gene_id "NM_032291";
transcript_id "NM_032291";
chr1 hg19_refGene CDS 67105460 67105516 0.000000 + 0 gene_id "NM_032291";
transcript_id "NM_032291";
chr1 hg19_refGene exon 67105460 67105516 0.000000 + . gene_id "NM_032291";
transcript_id "NM_032291";
chr1 hg19_refGene CDS 67108493 67108547 0.000000 + 0 gene_id "NM_032291";
transcript_id "NM_032291";
chr1 hg19_refGene exon 67108493 67108547 0.000000 + . gene_id "NM_032291";
transcript_id "NM_032291";

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#8 (comment).

[CCgenetics15]

Hello,
I downloaded the gtf file with correct format. The analysis started, I had only the following message:

Processing bam files
Use of uninitialized value $fileName in -e at ExonDel.pl line 539, line 5.
Use of uninitialized value $fileName in concatenation (.) or string at ExonDel.pl line 540, line 5.
[Wed Sep 9 10:13:05 2015] doesn't exist

I analysed 5 bam files and I found no deletions. I would to know if it is normal or if there could been some errors.
I report you Exondel.rlog:
[1] "Quantile 0.01 and 0.1 of all reads for each sample will be used as cutoff in exon deletion detection"
[1] "Can't find any exon deletions with 1 windows length\n"
[1] "Can't find any exon deletions with 2 windows length\n"
[1] "Can't find any exon deletions with 3 windows length\n"
[1] "Can't find any exon deletions with 4 windows length\n"
[1] "Can't find any exon deletions with 5 windows length\n"
[1] "Can't find any exon deletions with 6 windows length\n"
[1] "Can't find any exon deletions with 7 windows length\n"
[1] "Can't find any exon deletions with 8 windows length\n"
[1] "Can't find any exon deletions with 9 windows length\n"

Thanks for your help

[slzhao]

"Processing bam files
Use of uninitialized value $fileName in -e at ExonDel.pl line 539, line 5.
Use of uninitialized value $fileName in concatenation (.) or string at
ExonDel.pl line 540, line 5.
[Wed Sep 9 10:13:05 2015] doesn't exist"

This means the format of bam list file is not correct. It should be:
YourBamFile1
YourBamFile2
YourBamFile3

or
YourBamFile1(Tab)SampleName1
YourBamFile2(Tab)SampleName2
YourBamFile3(Tab)SampleName3

2015-09-09 4:13 GMT-05:00 CCgenetics15 notifications@github.com:

Hello,
I downloaded the gtf file with correct format. The analysis started, I had
only the following message:

Processing bam files
Use of uninitialized value $fileName in -e at ExonDel.pl line 539, line 5.
Use of uninitialized value $fileName in concatenation (.) or string at
ExonDel.pl line 540, line 5.
[Wed Sep 9 10:13:05 2015] doesn't exist

I analysed 5 bam files and I found no deletions. I would to know if it is
normal or if there could been some errors.
I report you Exondel.rlog:
[1] "Quantile 0.01 and 0.1 of all reads for each sample will be used as
cutoff in exon deletion detection"
[1] "Can't find any exon deletions with 1 windows length\n"
[1] "Can't find any exon deletions with 2 windows length\n"
[1] "Can't find any exon deletions with 3 windows length\n"
[1] "Can't find any exon deletions with 4 windows length\n"
[1] "Can't find any exon deletions with 5 windows length\n"
[1] "Can't find any exon deletions with 6 windows length\n"
[1] "Can't find any exon deletions with 7 windows length\n"
[1] "Can't find any exon deletions with 8 windows length\n"
[1] "Can't find any exon deletions with 9 windows length\n"

Thanks for your help

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#8 (comment).