issue with bowtie completing

[angelajmcd]

Hi Michael,

I've been trying to assemble some plastomes with Fast-Plast today but haven't been able to get past step 2. I installed it via your instructions, with all the dependencies in the bin folder. I've also verified that fast-plast.pl paths to dependency directories are also set (though they could be wrong, I suppose. I'll paste them here:

directories

my $FPROOT = "$FindBin::RealBin"; my $AFIN_DIR = "$FPROOT/afin"; my $COVERAGE_DIR = "$FPROOT/Coverage_Analysis"; my $FPBIN = "$FPROOT/bin"; my $TRIMMOMATIC="/Applications/Fast-Plast/bin/Trimmomatic-0.36//trimmomatic-0.36.jar"; #path to trimmomatic executable my $BOWTIE2="/Applications/Fast-Plast/bin/bowtie2-2.2.9/bowtie2"; #path to bowtie2 executable my $SPADES="/Applications/Fast-Plast/bin/SPAdes-3.11.1-Linux/bin/spades.py"; #path to spades executable my $BLAST="/Applications/Fast-Plast/bin/ncbi-blast-2.6.0+/bin/"; #path to blast executable my $SSPACE="/Applications/Fast-Plast/bin/sspace_basic-2.1.1//SSPACE_Basic.pl"; #path to sspace exectuable my $BOWTIE1="/Applications/Fast-Plast/bin/bowtie-1.1.2/"; #path to bowtie1 executable my $JELLYFISH="/Applications/Fast-Plast/bin/jellyfish-2.2.6/bin/jellyfish"; #path to jellyfish2 excecutable

Anyway. The error I get looks like this (after trimmomatic completes successfully): Use of uninitialized value $temp_order in exists at fast-plast.pl line 1130, <$default_gb> line 2041. Use of uninitialized value $temp_order in hash element at fast-plast.pl line 1132, <$default_gb> line 2041. Traceback (most recent call last): File "/Applications/Fast-Plast/bin/bowtie2-2.2.9/bowtie2-build", line 95, in main() File "/Applications/Fast-Plast/bin/bowtie2-2.2.9/bowtie2-build", line 92, in main os.execv(build_bin_spec, argv) OSError: [Errno 8] Exec format error sh: /Applications/Fast-Plast/bin/bowtie2-2.2.9/bowtie2-align-s: cannot execute binary file (ERR): Description of arguments failed! Exiting now ... No mapped reads files were identified to run SPAdes. Please check 2_Bowtie_Mapping.

I've tried manually setting the paths to executables, letting the install script set paths, used zipped and unzipped reads, used options for --coverage_analysis and not, set full paths to reads and included reads in the folder with the script... I'm hoping I just am (repeatedly) making a silly error.

Thoughts on what I might be doing wrong? Thanks a ton, Angela

[mrmckain]

Hi Angela,

Are you running with a specific order for the mapping? If not, Fast-Plast is using each represented order in the database. One entry had an order missing, which is why you see the error at 1130/1132. That might be throwing the bowtie2 error. I have updated the GenBank_Plastomes file in bin to fix this.

Implement that new file and give it a go. Let me know how things progress.

Best, Michael

[angelajmcd]

Hi Michael, I tried it using Gentianales originally, but then I switched to using all orders. Both tries had the same result/errors. I updated this morning and have tried running with all orders and am getting stuck the same point. The lines about line 1130/1132 are gone but I get this now after TrimmomaticPE completes: Traceback (most recent call last): File "/Applications/Fast-Plast/bin/bowtie2-2.2.9/bowtie2-build", line 95, in main() File "/Applications/Fast-Plast/bin/bowtie2-2.2.9/bowtie2-build", line 92, in main os.execv(build_bin_spec, argv) OSError: [Errno 8] Exec format error sh: /Applications/Fast-Plast/bin/bowtie2-2.2.9/bowtie2-align-s: cannot execute binary file (ERR): Description of arguments failed! Exiting now ... No mapped reads files were identified to run SPAdes. Please check 2_Bowtie_Mapping.

Perhaps its a problem with how bowtie2 installs? I can't really tell.

[mrmckain]

Are you running on a Linux system? Mac's have a different Bowtie2 installation.

[angelajmcd]

Wow. I am not... :)

I installed proper dependencies and edited the .pl file. It's runnin! Sorry & thanks!