Input/output error

[gmachaj]

Hi, I have a problem with index building for TE.gtf.

TEtranscripts --sortByPos --format BAM --mode multi -t /media/gabi/Maxtor/Marchew_Kallus_RNAseq/bam/DH-P-1_sorted.bam /media/gabi/Maxtor/Marchew_Kallus_RNAseq/bam/DH-P-2_sorted.bam /media/gabi/Maxtor/Marchew_Kallus_RNAseq/bam/DH-P-3_sorted.bam -c /media/gabi/Maxtor/Marchew_Kallus_RNAseq/bam/DH-B-1_sorted.bam /media/gabi/Maxtor/Marchew_Kallus_RNAseq/bam/DH-B-2_sorted.bam /media/gabi/Maxtor/Marchew_Kallus_RNAseq/bam/DH-B-3_sorted.bam --GTF /media/gabi/Maxtor/Marchew_Kallus_RNAseq/TEtool/genes_input3.gtf --TE /media/gabi/Maxtor/Marchew_Kallus_RNAseq/TEtool/rep3.gtf --project DH INFO @ Tue, 06 Mar 2018 16:30:41:

ARGUMENTS LIST:

name = DH

treatment files = ['/media/gabi/Maxtor/Marchew_Kallus_RNAseq/bam/DH-P-1_sorted.bam', '/media/gabi/Maxtor/Marchew_Kallus_RNAseq/bam/DH-P-2_sorted.bam', '/media/gabi/Maxtor/Marchew_Kallus_RNAseq/bam/DH-P-3_sorted.bam']

control files = ['/media/gabi/Maxtor/Marchew_Kallus_RNAseq/bam/DH-B-1_sorted.bam', '/media/gabi/Maxtor/Marchew_Kallus_RNAseq/bam/DH-B-2_sorted.bam', '/media/gabi/Maxtor/Marchew_Kallus_RNAseq/bam/DH-B-3_sorted.bam']

GTF file = /media/gabi/Maxtor/Marchew_Kallus_RNAseq/TEtool/genes_input3.gtf

TE file = /media/gabi/Maxtor/Marchew_Kallus_RNAseq/TEtool/rep3.gtf

multi-mapper mode = multi

stranded = yes

normalization = DESeq_default (rpm: Reads Per Million mapped; quant: Quantile normalization)

FDR cutoff = 5.00e-02

fold-change cutoff = 1.00

read count cutoff = 1

number of iteration = 10

Alignments grouped by read ID = False

INFO @ Tue, 06 Mar 2018 16:30:41: Processing GTF files ...

INFO @ Tue, 06 Mar 2018 16:30:41: Building gene index .......

100000 GTF lines processed. 200000 GTF lines processed. 300000 GTF lines processed. 400000 GTF lines processed. INFO @ Tue, 06 Mar 2018 16:41:09: Done building gene index ......

INFO @ Tue, 06 Mar 2018 16:41:09: Building TE index .......

chr1 blastn exon 1 240 783.80 + . gene_id "CL8*"; transcript_id "173870"; family_id "Copia"; class_id "LTR"; TE GTF format error! There is no annotation at line 1. Error in building gene/TE index

[olivertam]

Hi, Could you double-check that the first 9 columns in the TE GTF file are separated by tabs, and the values in column 9 are separated by spaces? Thanks.

[gmachaj]

Hi, Thank you for reply. Yes they are tab separated and spaces are in 9 column. So there is be some other problem... Actually I had problems with my TE file from very beginning - starting from gff3 to gtf conversion. I will be very grateful if you could help me to process my TE gff files to adjust them to the Tetranscripts tool requirements. Best,

https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail Wolny od wirusów. www.avast.com https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2018-03-06 18:14 GMT+01:00 Oliver Tam notifications@github.com:

Hi, Could you double-check that the first 9 columns in the TE GTF file are separated by tabs, and the values in column 9 are separated by spaces? Thanks.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/mhammell-laboratory/tetoolkit/issues/19#issuecomment-370856570, or mute the thread https://github.com/notifications/unsubscribe-auth/AjY-2cd4-q0cTMwMvmpKiN4ZDvU5Q6ieks5tbsQSgaJpZM4SeoBi .

[olivertam]

Hi, If you would like to send me the TE GFF/GTF file that you have generated, I can certainly take a look. You can contact me directly at tam at cshl dot edu. Thanks.

[gmachaj]

OK, Thanks