errors from evidentialgene pipeline

Question

[HZZ0036]

Hello, Below is the errors that evidentialgene gave me. Does anybody know the reasons? Thanks in advance.

#t2ac: EvidentialGene tr2aacds.pl VERSION 2013.07.27
#t2ac: ERR=256  /opt/asn/apps/cdhit_4.6.1/bin/cd-hit-est  -c 1.00 -T 4 -M 12000 -l 89 -d 0 -i /mnt/homeapps/home/aubhxz/different_elleusine_species/evigene/eg2/velvnr.cds -o /mnt/homeapps/h    ome/aubhxz/different_elleusine_species/evigene/eg2/velvnrcd1.cds 1> /mnt/homeapps/home/aubhxz/different_elleusine_species/evigene/eg2/velvnrcd1.log 2>&1
#t2ac: ERR=256  /opt/asn/apps/cdhit_4.6.1/bin/cd-hit  -T 4 -M 12000 -l 30 -c 0.90 -d 0 -i /mnt/homeapps/home/aubhxz/different_elleusine_species/evigene/eg2/velv.aa -o /mnt/homeapps/home/aub    hxz/different_elleusine_species/evigene/eg2/velv_cd90.aa 1> /mnt/homeapps/home/aubhxz/different_elleusine_species/evigene/eg2/velv_cd90.log 2>&1
#t2ac: ERR=512  /mnt/homeapps/apps/dmc/apps/evidentialgene_05212015/pub/evigene/scripts/prot/..rnaseq/asmrna_dupfilter2.pl  -tinyaln 35 -aasize /mnt/homeapps/home/aubhxz/different_elleusin    e_species/evigene/eg2/velv.aa.qual -CDSALIGN -blastab /mnt/homeapps/home/aubhxz/different_elleusine_species/evigene/eg2/velvnrcd1-self98.blastn   -outeqtab /mnt/homeapps/home/aubhxz/different_elleusine_species/evigene/eg2/velv.alntab -outclass /mnt/homeapps/home/aubhxz/different_elleusine_species/evigene/eg2/velv.trclass >/mnt/homeapps/home/aubhxz/different_elleusine_species/evigene/eg2/velv.adupfilt.log 2>&1
#t2ac: ERR: asmdupclass_sum missing: /mnt/homeapps/home/aubhxz/different_elleusine_species/evigene/eg2/velv.trclass
#t2ac: ERR: asmdupclass_fileset missing: /mnt/homeapps/home/aubhxz/different_elleusine_species/evigene/eg2/velv.trclass

Hui

Answer 1

[Rik Verdonck]

For what it's worth five months later: I came across similar errors, and had a hard time figuring out what was happening because the error message by cd-hit was nothing more than their help page. In the end, I figured it was the multi-threading that went wrong.

If you are running a cd-hit version that does not support multithreading, it does not recognize the parameter -T. The ERR=256 is just a general perl error, which could mean "any error" I think. What actually causes the error is CD-hit simply not executing, but merely dumping it's help page in st.out or st.err.

So, Hui, I think the first thing to do is to try replicating this error with a small test database with cd-hit-est with and without the -T parameter.

Now, for the cd-hit connoisseurs: how do I know which version of cd hit is in my path? It doesn't offer a --version parameter or anything alike. And how do I get evidentialgene to use the "correct" version of cd-hit?

Cheers, Rik

Answer 2

[gilbert.bionet]

Changing the app paths for Evigene's tr2aacds.pl pipeline is a matter of setting Unix paths. See the test drive shell script at arthropods.eugenes.org/EvidentialGene/plants/arabidopsis/evigene_tr2aacds_test/ tr2aacds_test.sh

#t2ac: app=cd-hit-est,  exists in bapps/bin/ path
export PATH=$bapps/bin/:$PATH
#t2ac: app=fastanrdb, path= echo MISSING_fastanrdb
export fastanrdb=$bapps/bin/fastanrdb
#t2ac: app=blastn, path= echo MISSING_blastn
export PATH=$bapps/ncbicpp/bin:$PATH

There is another way, but above should be enough. The other way requires you read the perl code of tr2aacds.pl (or read my as yet unwritten detailed document there-of :), as in 'export cd-hit-est=/full/path/bin/cd-hit-est_versionX'

This is another reason to run this evigene_tr2aacds_test/ case, as it runs or fails quickly, so fiddle with it to get the parts working right before moving on to your real data sets.

Answer 3

[gilbert.bionet]

This is the first error that you need to resolve, others follow from it:

t2ac: ERR=256 /opt/asn/apps/cdhit_4.6.1/bin/cd-hit-est -c 1.00 -T 4 -M 12000 -l 89 -d 0 -i /mnt/homeapps/home/aubhxz/different_elleusine_species/evigene/eg2/velvnr.cds -o /mnt/homeapps/h ome/aubhxz/different_elleusine_species/evigene/eg2/velvnrcd1.cds 1> /mnt/homeapps/home/aubhxz/different_elleusine_species/evigene/eg2/velvnrcd1.log

cd-hit-est failed, but I cant tell why from this. The log file "evigene/eg2/velvnrcd1.log" may give you the answer if you can decipher it. You may want to find a unix/computational person at your location to ask help understanding it. cd-hit has a manual and web page to explain these options, -c 1.00 -T 4 -M 12000 -l 89 -d 0 where -T 4 means use 4 processors, and -M 12000 means use 12 Gigabytes of memory.
If your computer/cluster has limited memory, reduce those two options and try again. That line, "/opt/asn/apps/cdhit_4.6.1/bin/cd-hit-est .. " gives the full unix command, and if you repeat it, it likely will reproduce the error that you or helper can then resolve.

"h ome" may be, but is probably not an error but from wrapping of your text output. - Don Gilbert