Issue with tracer test

[Edenapple]

The input command is: tracer test -p 3 -c /home/temp/binaries/tracer-master/tracer.conf -o tracer_test

The error message is (in Trinity): CMD: /home/temp/binaries/trinityrnaseq-Trinity-v2.5.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /home/temp/disk1/@home/edenapple/Desktop/Practice/Mouse/tracer/tracer_test/results/cell1/Trinity_output/Trinity_cell1_TCR_B.Trinity.fasta > /home/temp/disk1/@home/edenapple/Desktop/Practice/Mouse/tracer/tracer_test/results/cell1/Trinity_output/Trinity_cell1_TCR_B.Trinity.fasta.gene_trans_map shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory

The error message is (in IGBlast): Traceback (most recent call last): File "/home/temp/anaconda2/bin/tracer", line 11, in load_entry_point('tracer==0.5', 'console_scripts', 'tracer')() File "/home/temp/anaconda2/lib/python2.7/site-packages/tracer-0.5-py2.7.egg/tracerlib/launcher.py", line 43, in launch Task().run() File "/home/temp/anaconda2/lib/python2.7/site-packages/tracer-0.5-py2.7.egg/tracerlib/tasks.py", line 1201, in run loci=['A', 'B'], max_junc_len=50).run() File "/home/temp/anaconda2/lib/python2.7/site-packages/tracer-0.5-py2.7.egg/tracerlib/tasks.py", line 372, in run self.quantify(cell) File "/home/temp/anaconda2/lib/python2.7/site-packages/tracer-0.5-py2.7.egg/tracerlib/tasks.py", line 638, in quantify tpm = counts[receptor][locus][rec.contig_name] KeyError: 'TRINITY_DN1_c0_g1_i3'

[mstubb]

Hi,

Please have a look at Issue #55 and see if any of the suggestions there help here. If not, please let me know.

Best,

Mike