Running igblast returns an error

[ghost]

Hi, I'm going to testing TraCer by runing tracer test.But everytime it returns an error after printing runing IgBlast,fully copy as follows: `##Running IgBLAST## CMD failed:

Traceback (most recent call last): File "/share/apps/anaconda3/bin/tracer", line 9, in load_entry_point('tracer==0.5', 'console_scripts', 'tracer')() File "/share/apps/anaconda3/lib/python3.5/site-packages/tracer-0.5-py3.5.egg/tracerlib/launcher.py", line 43, in launch Task().run() File "/share/apps/anaconda3/lib/python3.5/site-packages/tracer-0.5-py3.5.egg/tracerlib/tasks.py", line 1206, in run loci=['A', 'B'], max_junc_len=50).run() File "/share/apps/anaconda3/lib/python3.5/site-packages/tracer-0.5-py3.5.egg/tracerlib/tasks.py", line 371, in run cell = self.ig_blast() File "/share/apps/anaconda3/lib/python3.5/site-packages/tracer-0.5-py3.5.egg/tracerlib/tasks.py", line 502, in ig_blast self.resume_with_existing_files, fmt) File "/share/apps/anaconda3/lib/python3.5/site-packages/tracer-0.5-py3.5.egg/tracerlib/tracer_func.py", line 1265, in run_IgBlast print(" ").join(pipes.quote(s) for s in command) AttributeError: 'NoneType' object has no attribute 'join' I followed the installation to install igblast,the tree ofigblast/binis as follows: |-- igblastn |-- igblastp |-- internal_data | -- human | |-- human.ndm.imgt | |-- human.ndm.kabat | |-- human.pdm.imgt | |-- human.pdm.kabat | |-- human_TR_V.nhr | |-- human_TR_V.nin | |-- human_TR_V.nog | |-- human_TR_V.nsd | |-- human_TR_V.nsi | |-- human_TR_V.nsq | |-- human_TR_V.phr | |-- human_TR_V.pin | |-- human_TR_V.pog | |-- human_TR_V.psd | |-- human_TR_V.psi | |-- human_TR_V.psq | |-- human_V.nhr | |-- human_V.nin | |-- human_V.nog | |-- human_V.nsd | |-- human_V.nsi | |-- human_V.nsq | |-- human_V.phr | |-- human_V.pin | |-- human_V.pog | |-- human_V.psd | |-- human_V.psi |-- human_V.psq -- makeblastdb And I set $IGDATA to ~/tool/igblast-1.9.0/bin

I got a file under test_data/results/cell1/IgBLAST_output/ named cell1_TCR_A_fmt3.IgBLASTOut,but it's empty,so I tried to run igblast with cell1_TCR_A.Trinity.fasta under test_data/results/cell1/Trinity_output/ by igblastn -germline_db_V /home/user/tool/tracer-master/resources/Hsap/igblast_dbs/TCR_V.fa \ -germline_db_D /home/user/tool/tracer-master/resources/Hsap/igblast_dbs/TCR_D.fa \ -germline_db_J /home/user/tool/tracer-master/resources/Hsap/igblast_dbs/TCR_J.fa \ -domain_system imgt \ -organism human \ -ig_seqtype TCR \ -num_alignments_V 5 \ -num_alignments_D 5 \ -num_alignments_J 5 \ -outfmt 3 \ -query cell1_TCR_A.Trinity.fasta It looks like everything is fine,but there is a warning message above:Warning: Auxilary data file could not be found. I don't know which step is going to be a problem.

[mstubb]

Hi,

Thanks for this.

This specific crash is happening because of a bug in the way that TraCeR tries to report an error if IgBlast fails. I've just pushed a fix for this to the master branch. Please can you update to the latest commit to and then try running tracer test again - you should now get more informative output that will report the IgBLAST error. Let me know what that is and I'll see if I can help.

Very best,

Mike

[SeadonXing]

Running IgBLAST

CMD failed:

Traceback (most recent call last): File "/Bailab5/xingxudong/Software/anaconda2/bin/tracer", line 11, in load_entry_point('tracer==0.5', 'console_scripts', 'tracer')() File "/home/xingxudong/.local/lib/python2.7/site-packages/tracer-0.5-py2.7.egg/tracerlib/launcher.py", line 43, in launch Task().run() File "/home/xingxudong/.local/lib/python2.7/site-packages/tracer-0.5-py2.7.egg/tracerlib/tasks.py", line 1206, in run loci=['A', 'B'], max_junc_len=50).run() File "/home/xingxudong/.local/lib/python2.7/site-packages/tracer-0.5-py2.7.egg/tracerlib/tasks.py", line 371, in run cell = self.ig_blast() File "/home/xingxudong/.local/lib/python2.7/site-packages/tracer-0.5-py2.7.egg/tracerlib/tasks.py", line 502, in ig_blast self.resume_with_existing_files, fmt) File "/home/xingxudong/.local/lib/python2.7/site-packages/tracer-0.5-py2.7.egg/tracerlib/tracer_func.py", line 1265, in run_IgBlast print(" ").join(pipes.quote(s) for s in command) AttributeError: 'NoneType' object has no attribute 'join'

I got the same errors by using tracer-0.6.0. Have you fixed the bug ? How to solve this problems ?

Best Xudong

[SeadonXing]

Running IgBLAST

CMD failed: /Bailab5/xingxudong/Software/ncbi-igblast-1.10.0/bin/igblastn -germline_db_V /Bailab5/xingxudong/Software/tracer-master/resources/Mmus/igblast_dbs/TCR_V.fa -germline_db_D /Bailab5/xingxudong/Software/tracer-master/resources/Mmus/igblast_dbs/TCR_D.fa -germline_db_J /Bailab5/xingxudong/Software/tracer-master/resources/Mmus/igblast_dbs/TCR_J.fa -domain_system imgt -organism mouse -ig_seqtype TCR -show_translation -num_alignments_V 5 -num_alignments_D 5 -num_alignments_J 5 -outfmt 3 -auxiliary_data optional_file/mouse_gl.aux -query /Bailab5/xingxudong/Test/TraCeR/results/cell1/Trinity_output/cell1_TCR_A.Trinity.fasta

BLAST query/options error: Germline annotation database mouse/mouse_TR_V could not be found in [internal_data] directory Please refer to the BLAST+ user manual.

When I update to the latest commit to and then try running tracer test again - I got the IgBLAST error

[mstubb]

Have you got a working version of IgBlast as per the instructions here? https://github.com/Teichlab/tracer/blob/master/README.md#installing-igblast

Make sure you've downloaded the internal_data directory to the correct place and set your $IGDATA environment variable.

[SeadonXing]

Cheers , I solve the problems by run "export IGDATA=/Bailab5/xingxudong/Software/ncbi-igblast-1.10.0/bin" straightly. But I still confused that I add the IGDATA path by vim and source /home/.bash_profile file. command is : IGDATA=/Bailab5/xingxudong/Software/ncbi-igblast-1.10.0/bin:$IGDATA

But somehow It cant be found by the systems. Anyway, thanks borther !

Best Xudong