Hi,
When running cuffmerge, I only got very implicit error messages. It seemed that the gtf files were converted into sam files, but then stuck.
I tried to troubleshot in several aspects: checking the name of chromosome(with chr or not); sorting the gtf files (chr name then coordinate); with larger memories. But none of them helped. I'm wondering if any of you might also meet this.
Any suggestion will be helpful, thanks.
=============command and message====================
$ cuffmerge -g dmel-all-r6.09.gtf -s dmel_chr_r609.fa assemblies.txt
[Sun Feb 21 17:29:11 2016] Beginning transcriptome assembly merge
-------------------------------------------
[Sun Feb 21 17:29:11 2016] Preparing output location ./merged_asm/
[Sun Feb 21 17:29:14 2016] Converting GTF files to SAM
[17:29:14] Loading reference annotation.
[17:29:16] Loading reference annotation.
[17:29:17] Loading reference annotation.
[17:29:18] Loading reference annotation.
[Sun Feb 21 17:29:19 2016] Quantitating transcripts
You are using Cufflinks v2.2.1, which is the most recent release.
Command line:
cufflinks -o ./merged_asm/ -F 0.05 -g
../../../dmelGenomes/dmel-all-r6.09.gtf -q --overhang-tolerance 200
--library-type=transfrags -A 0.0 --min-frags-per-transfr
ag 0 --no-5-extend -p 1
./merged_asm/tmp/mergeSam_fileTqiEXC
[17:29:19] Loading reference annotation.
[17:29:23] Inspecting reads and determining fragment length distribution.
[FAILED]
Error: could not execute cufflinks
When running cuffmerge, I only got very implicit error messages. It seemed that the gtf files were converted into sam files, but then stuck.
I tried to troubleshot in several aspects: checking the name of chromosome(with chr or not); sorting the gtf files (chr name then coordinate); with larger memories. But none of them helped. I'm wondering if any of you might also meet this.
Any suggestion will be helpful, thanks.
=============command and message====================
$ cuffmerge -g dmel-all-r6.09.gtf -s dmel_chr_r609.fa assemblies.txt
[Sun Feb 21 17:29:11 2016] Beginning transcriptome assembly merge
-------------------------------------------
[Sun Feb 21 17:29:11 2016] Preparing output location ./merged_asm/
[Sun Feb 21 17:29:14 2016] Converting GTF files to SAM
[17:29:14] Loading reference annotation.
[17:29:16] Loading reference annotation.
[17:29:17] Loading reference annotation.
[17:29:18] Loading reference annotation.
[Sun Feb 21 17:29:19 2016] Quantitating transcripts
You are using Cufflinks v2.2.1, which is the most recent release.
Command line:
cufflinks -o ./merged_asm/ -F 0.05 -g
../../../dmelGenomes/dmel-all-r6.09.gtf -q --overhang-tolerance 200
--library-type=transfrags -A 0.0 --min-frags-per-transfr
ag 0 --no-5-extend -p 1
./merged_asm/tmp/mergeSam_fileTqiEXC
[17:29:19] Loading reference annotation.
[17:29:23] Inspecting reads and determining fragment length distribution.
[FAILED]
Error: could not execute cufflinks
Comment