Bridger assembly error!

[mitul-patel]

Hello,

I wanted to perform assembly on paired-end RNAseq data.

Here is the command I used: perl ~/software/Bridger_r2014-12-01/Bridger.pl --seqType fq --left Sample1_R1_fastq.gz --right Sample1_R2_fastq.gz --CPU 4 --SS_lib_type FR --output bridger_out

But I am getting following error:

Splicing Graphs Reconstruction

CMD: ~/software/Bridger_r2014-12-01/src/Assemble --reads both.fa -k 25 --pair_end --fr_strand 2 2>Assemble.log Error, cmd: ~/software/Bridger_r2014-12-01/src/Assemble --reads both.fa -k 25 --pair_end --fr_strand 2 2>Assemble.log died with ret 256 !

Assemble.log: [Error] Cannot create directory ./RawGraphs/ !

Any idea why I am getting this error. I tried with changing the permission of output folder but still getting this error.

Many thanks.

[fei0810]

I got the same error , but when I checked the directory I find ./RawGraphs/ has been created indeed

[gufernandezn]

Hi , im getting the same issue, as well as the previous comment the ./RawGraphs/ has been created but empty. i have changed too the permission in all the directory with chmod. Im working in debian jessi 8 operative system, 8processors 32GB ram.

[Onejrussell-Zymergen]

If this is a fix available, could someone please provide instructions?

[melissawhitaker]

I'm having the same issue - are there any updates?

[xiekunwhy]

Add one line before my $assemble_cmd = "$SRC_DIR/Assemble --reads $target_fa -k $kmer_length ";(Line 255 in Bridger.pl): 255: &process_cmd("mkdir RawGraphs"); 256: my $assemble_cmd = "$SRC_DIR/Assemble --reads $target_fa -k $kmer_length "; RawGraphs can be replace by your own directory. I think there is a bug in Assemble when creating output directory

[zsalvet]

The root cause of the bug is wrong handling of return code from boost::filesystem::create_directories(), it does not return error indication but whether new directory has been create or not (it already existed). assemble.txt