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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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tRNA scan issue #74

Closed el42008 closed 7 years ago

el42008 commented 7 years ago

Hi Jon,

EVM finished properly, but now the scripts complains about the tRNA scan. I guess is someting about compilation but I am not sure

2017-04-29 06:11:13,499: 126,950 total gene models from EVM
2017-04-29 06:11:13,536: Predicting tRNAs
2017-04-29 06:11:13,539: tRNAscan-SE -o fun_out/predict_misc/tRNAscan.out /mnt/shared/users/el42208/RNA_data/funannotate/fun_out/predict_misc/genome.softmasked.fa
2017-04-29 06:11:13,616: Number found where operator expected at /mnt/apps/tRNAscan-SE/1.23/bin/tRNAscan-SE line 647, near ""/mnt/apps/tRNAscan-SE/"1.23"
        (Missing operator before 1.23?)
String found where operator expected at /mnt/apps/tRNAscan-SE/1.23/bin/tRNAscan-SE line 647, near "1.23"/lib/""
        (Missing operator before "/lib/"?)
Number found where operator expected at /mnt/apps/tRNAscan-SE/1.23/bin/tRNAscan-SE line 649, near ""/mnt/apps/tRNAscan-SE/"1.23"
        (Missing operator before 1.23?)
String found where operator expected at /mnt/apps/tRNAscan-SE/1.23/bin/tRNAscan-SE line 649, near "1.23"/bin/""
        (Missing operator before "/bin/"?)
Number found where operator expected at /mnt/apps/tRNAscan-SE/1.23/bin/tRNAscan-SE line 1441, near ""/mnt/apps/tRNAscan-SE/"1.23"
        (Missing operator before 1.23?)
String found where operator expected at /mnt/apps/tRNAscan-SE/1.23/bin/tRNAscan-SE line 1441, near "1.23"/lib/""
        (Missing operator before "/lib/"?)
Number found where operator expected at /mnt/apps/tRNAscan-SE/1.23/bin/tRNAscan-SE line 1442, near ""/mnt/apps/tRNAscan-SE/"1.23"
        (Missing operator before 1.23?)
String found where operator expected at /mnt/apps/tRNAscan-SE/1.23/bin/tRNAscan-SE line 1442, near "1.23"/lib/""
        (Missing operator before "/lib/"?)
syntax error at /mnt/apps/tRNAscan-SE/1.23/bin/tRNAscan-SE line 647, near ""/mnt/apps/tRNAscan-SE/"1.23"
syntax error at /mnt/apps/tRNAscan-SE/1.23/bin/tRNAscan-SE line 649, near ""/mnt/apps/tRNAscan-SE/"1.23"

Thanks a lot

Elena

nextgenusfs commented 7 years ago

Yes, looks like tRNAscan is not installed properly. Funannotate tries to determine if you have dependencies installed, however it currently does not check if they are working. That is it just checks with essentially a which command to see if program is available in $PATH.

el42008 commented 7 years ago

Hi Jon,

It went further in teh pipeline this time, but now I get the following:

ESC[92m[04:17:43 PM]ESC[0m: OS: linux2, 32 cores, ~ 264 GB RAM. Python: 2.7.13 ESC[92m[04:17:43 PM]ESC[0m: Running funannotate v0.6.0 ESC[92m[04:17:44 PM]ESC[0m: Augustus training set for potato1 already exists, thus funannotate will use those parameters. If you want to re-train, provide a unique name for the --augustus_species argument ESC[92m[04:17:45 PM]ESC[0m: AUGUSTUS (3.2.3) detected, version seems to be compatible with BRAKER1 and BUSCO ESC[92m[04:18:11 PM]ESC[0m: Masked genome: 224,092 scaffolds; 730,142,347 bp ESC[92m[04:18:20 PM]ESC[0m: Using existing transcript evidence alignments ESC[92m[04:18:39 PM]ESC[0m: Using existing protein evidence alignments ESC[92m[04:18:45 PM]ESC[0m: potato1 as already been trained, using existing parameters ESC[92m[04:18:45 PM]ESC[0m: Now launching BRAKER to train GeneMark and Augustus ESC[92m[04:19:48 PM]ESC[0m: 225,157 total gene models from all sources ESC[92m[04:19:54 PM]ESC[0m: Setting up EVM partitions ESC[92m[07:02:04 PM]ESC[0m: Generating EVM command list ESC[92m[07:03:07 PM]ESC[0m: Running EVM commands with 23 CPUs ESC[92m[02:25:36 AM]ESC[0m: Combining partitioned EVM outputs ESC[92m[02:30:08 AM]ESC[0m: Converting EVM output to GFF3 ESC[92m[08:23:48 AM]ESC[0m: Collecting all EVM results ESC[92m[08:54:50 AM]ESC[0m: 127,036 total gene models from EVM ESC[92m[09:58:53 AM]ESC[0m: Predicting tRNAs ESC[92m[09:58:53 AM]ESC[0m: Merging EVM output with tRNAscan output ESC[92m[09:58:53 AM]ESC[0m: Reformatting GFF file using GAG ESC[92m[10:47:45 AM]ESC[0m: 126,826 total gene models ESC[92m[10:47:45 AM]ESC[0m: Filtering out bad gene models (< 50 aa in length, transposable elements, etc). ESC[92m[11:36:25 AM]ESC[0m: 50,977 gene models remaining ESC[92m[11:36:25 AM]ESC[0m: Converting to preliminary Genbank format ESC[92m[12:00:16 PM]ESC[0m: Cleaning models flagged by tbl2asn Traceback (most recent call last): File "/mnt/apps/funannotate/bin/funannotate-predict.py", line 1004, in

lib.ParseErrorReport(DirtyGFF, ErrSum, Val, discrep, NCBIcleanGFF, keep_stops=False) File "/mnt/apps/funannotate/lib/library.py", line 1287, in ParseErrorReport with open(Errsummary) as summary: IOError: [Errno 2] No such file or directory: 'fun_out/predict_misc/gag2/errorsummary.val' Thanks a lot 2017-04-30 20:02 GMT+01:00 Jon Palmer : > Yes, looks like tRNAscan is not installed properly. Funannotate tries to > determine if you have dependencies installed, however it currently does not > check if they are working. That is it just checks with essentially a which > command to see if program is available in $PATH. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > > . >