Is tgicl not able to work with some certain sequence quantities of fast
From zengxi.hada@gmail.com@21:1/5 to All on Wed Oct 7 06:48:26 2015
I was running TGICL using fasta file to do sequence cluster and assembly. I encountered some rediculous problems. It is that tgicl did work in some certain sequence quantities, but cannot work for some other certain sequence quantities. I don't know why.
I will describe the problem in detail at following.
I ran tgicl with a fasta file with 239635 sequences.
$ tgicl -F Trinity_all_in_one_3.fasta
Use of :locked is deprecated at /usr/share/perl5/TGI/DBDrv.pm line 36.
tgicl (Trinity_all_in_one_3.fasta) encountered an error at step ASSEMBLE
Working directory was /media/zengxi/ffc280cc-f4ce-455b-888d-43dcbb2ff4c3/ubuntu/project/sanqi/filter_contig/all_in_one.
When I extracted the 10000 header line of the Trinity_all_in_one_3.fasta, it worked !
$ head -10000 Trinity_all_in_one_3.fasta > Trinity_all_in_one_3.fasta.head10000 $ tgicl -F Trinity_all_in_one_3.fasta.head10000
Use of :locked is deprecated at /usr/share/perl5/TGI/DBDrv.pm line 36.
tgicl (Trinity_all_in_one_3.fasta.head10000) finished on machine
in /media/zengxi/ffc280cc-f4ce-455b-888d-43dcbb2ff4c3/ubuntu/project/sanqi/filter_contig/all_in_one, without a detectable error.
However, when I extracted the 100 header line of Trinity_all_in_one_3.fasta, I didn't work. Sounds rediculous.
$ head -100 Trinity_all_in_one_3.fasta > Trinity_all_in_one_3.fasta.head100
$ tgicl -F Trinity_all_in_one_3.fasta.head100
Use of :locked is deprecated at /usr/share/perl5/TGI/DBDrv.pm line 36.
tgicl (Trinity_all_in_one_3.fasta.head100) encountered an error at step ASSEMBLE
Working directory was /media/zengxi/ffc280cc-f4ce-455b-888d-43dcbb2ff4c3/ubuntu/project/sanqi/filter_contig/all_in_one.
All above mentioned input files are in correct fasta format.
I also try another two fasta files with 215933 and 215933 sequences respectively. They all work well using tgicl.
I don't know why. Did Anyone encounter this kind of case before? How can I make the Trinity_all_in_one_3.fasta with 239635 sequences work well using tgicl? I really appreciate it if anyone can help me to solve the problem.