The GTF file might be corrupted! Stop at line : 1

[hackerzone85]

I have encountered a bug while preparing reference sequence of Arabidopsis_thaliana using RSEM (latest developer version). The fasta and gtf files were downloaded from ftp://ftp.ensemblgenomes.org/pub/release-30/plants/. Here is the cmd output:

blab@blab: rsem-prepare-reference -gtf filtered.gtf --bowtie2 --bowtie-path /usr/bin/bowtie2 Arabidopsis_thaliana.TAIR10.30.dna.toplevel.fa at.tair10.30
Warning: If Bowtie is not used, no need to set --bowtie-path option!
rsem-extract-reference-transcripts at.tair10.30 0 filtered.gtf None 0 Arabidopsis_thaliana.TAIR10.30.dna.toplevel.fa
The GTF file might be corrupted!
Stop at line : 1    tair    exon    4810488 4811109 .   +   .   gene_id "AT1G14040"; gene_version "1"; transcript_id "AT1G14040.1"; transcript_version "1"; exon_number "1"; gene_name "PHO1;H3"; gene_source "tair"; gene_biotype "protein_coding"; transcript_name "PHO1;H3"; transcript_source "tair"; transcript_biotype "protein_coding"; exon_id "AT1G14040.1.exon1"; exon_version "1";
Error Message: Cannot separate the identifier from the value for attribute H3"!
"rsem-extract-reference-transcripts at.tair10.30 0 filtered.gtf None 0 Arabidopsis_thaliana.TAIR10.30.dna.toplevel.fa" failed! Plase check if you provide correct parameters/options for the pipeline!

What is correct format of gtf file?

[bli25wisc]

Hi Mahendra Gaur,

Thanks for reporting this bug to us. We have already fixed it. Please update your RSEM to v1.2.27 and everything should work smoothly.

Best, Bo

On 2016-01-29 06:41, Mahendra Gaur wrote:

I have encountered a bug while preparing reference sequence of Arabidopsis_thaliana using RSEM (latest developer version) The fasta and gtf files were downloaded from ftp://ftpensemblgenomesorg/pub/release-30/plants/ Here is the cmd output:

blab@blab: rsem-prepare-reference -gtf filteredgtf --bowtie2 --bowtie-path /usr/bin/bowtie2 Arabidopsis_thalianaTAIR1030dnatoplevelfa attair1030 Warning: If Bowtie is not used, no need to set --bowtie-path option! rsem-extract-reference-transcripts attair1030 0 filteredgtf None 0 Arabidopsis_thalianaTAIR1030dnatoplevelfa The GTF file might be corrupted! Stop at line : 1 tair exon 4810488 4811109 + gene_id "AT1G14040"; gene_version "1"; transcript_id "AT1G140401"; transcript_version "1"; exon_number "1"; gene_name "PHO1;H3"; gene_source "tair"; gene_biotype "protein_coding"; transcript_name "PHO1;H3"; transcript_source "tair"; transcript_biotype "protein_coding"; exon_id "AT1G140401exon1"; exon_version "1"; Error Message: Cannot separate the identifier from the value for attribute H3"! "rsem-extract-reference-transcripts attair1030 0 filteredgtf None 0 Arabidopsis_thalianaTAIR1030dnatoplevelfa" failed! Plase check if you provide correct parameters/options for the pipeline!

What is correct format of gtf file?

Reply to this email directly or view it on GitHub [1].

*

Links:

[1] https://github.com/deweylab/RSEM/issues/17

[rtewhey]

Hi Bo, This could be unrelated but I have been receiving the same error with rsem-prepare-reference despite updating to v1.1.27. I have verified the error with the GTF files linked on the RSEM website.

/idi/sabeti-data/rtewhey/bin/RSEM-1.2.27/rsem-prepare-reference --gtf gencode.v19.annotation.gtf -p 8 GRCh37.p13.genome.fa GRCh37.gencode_v19.RSEM
rsem-extract-reference-transcripts GRCh37.gencode_v19.RSEM 0 gencode.v19.annotation.gtf None 0 GRCh37.p13.genome.fa
The GTF file might be corrupted!
Stop at line : chr1 HAVANA  exon    11869   12227   .   +   .   gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1;  exon_id "ENSE00002234944.1";  level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
Error Message: Cannot locate the identifier from attribute gene_id "ENSG00000223972.4";!
"rsem-extract-reference-transcripts GRCh37.gencode_v19.RSEM 0 gencode.v19.annotation.gtf None 0 GRCh37.p13.genome.fa" failed! Plase check if you provide correct parameters/options for the pipeline!

btw, I can confirm dropping down to 1.1.25 resolves the issue.

[bli25wisc]

Hi rtewhey,

Sorry for the bugs. I just fixed them and released a new version.

Best, Bo

On 2016-02-02 06:50, rtewhey wrote:

Hi Bo, This could be unrelated but I have been receiving the same error with rsem-prepare-reference despite updating to v1.1.27. I have verified the error with the GTF files linked on the RSEM website.

/idi/sabeti-data/rtewhey/bin/RSEM-1.2.27/rsem-prepare-reference --gtf gencode.v19.annotation.gtf -p 8 GRCh37.p13.genome.fa GRCh37.gencode_v19.RSEM rsem-extract-reference-transcripts GRCh37.gencode_v19.RSEM 0 gencode.v19.annotation.gtf None 0 GRCh37.p13.genome.fa The GTF file might be corrupted! Stop at line : chr1 HAVANA exon 11869 12227 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1"; Error Message: Cannot locate the identifier from attribute gene_id "ENSG00000223972.4";! "rsem-extract-reference-transcripts GRCh37.gencode_v19.RSEM 0 gencode.v19.annotation.gtf None 0 GRCh37.p13.genome.fa" failed! Plase check if you provide correct parameters/options for the pipeline!

Reply to this email directly or view it on GitHub [1].

*

Links:

[1] https://github.com/deweylab/RSEM/issues/17#issuecomment-178610788

[hackerzone85]

Hi Bo Li Thanks for fixing bug. Its works now, my reference is prepared now. Very Very thanks Bo.

[bamankwa]

Hi, It appears this, ftp://ftp.ensembl.org/pub/release-98/gtf/drosophila_melanogaster/ file in Ensemble is corrupted could help uploading a fixed version for me? Thank you.

Bright