svm-zhang/AGOUTI

Empty line in the GFF crashes AGOUTI

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svm-zhang commented

Paste Hannah's problem here:

Dear Mr. Zhang,
I want to use AGOUTI to complete my genome assembly and the job broke down because of some reason that I don't know. Would you please help me to solve the problem ?
Thank you so much!
yours,
hannah.

The command I used is :
python agouti.py scaffold
-assembly monkfruit.contigs.fasta
-bam monkfruit_total.bam
-gff evm_monkfruit_mask.gff3
-outdir ./agouti1
-minMQ 20 -maxFracMM 0.05
-p monkfruit_agouti

And the log file is :

2017-05-03 18:50:41,425 - INFO - PARSE_ARGS PROGRESS - Assembly: /lustre1/deng_pkuhpc/hanxue/mecat/test_with_falcon_long_reads/monkfruit/monkfruit.contigs.fasta
2017-05-03 18:50:41,426 - INFO - PARSE_ARGS PROGRESS - Gene Model: /lustre1/deng_pkuhpc/hanxue/genome_annotation/EVM/do_evm_mask/evm_monkfruit_mask.gff3
2017-05-03 18:50:41,426 - INFO - PARSE_ARGS PROGRESS - Output directory: /lustre1/deng_pkuhpc/hanxue/scaffold/AGOUTI/agouti1
2017-05-03 18:50:41,426 - INFO - PARSE_ARGS PROGRESS - Output prefix: monkfruit_agouti
2017-05-03 18:50:41,427 - INFO - PARSE_ARGS PROGRESS - Minimum number of supports: 5
2017-05-03 18:50:41,427 - INFO - PARSE_ARGS PROGRESS - Length of gaps to fill between contigs: 1000
2017-05-03 18:50:41,429 - INFO - AGOUTI_SEQUENCE PROGRESS - [BEGIN] Reading the initial assembly
2017-05-03 18:50:43,520 - INFO - AGOUTI_SEQUENCE PROGRESS - 4128 sequences parsed
2017-05-03 18:50:43,520 - INFO - AGOUTI_SEQUENCE PROGRESS - The given assembly N50: 433684
2017-05-03 18:50:43,520 - INFO - AGOUTI_SEQUENCE PROGRESS - [DONE]
2017-05-03 18:50:43,546 - INFO - AGOUTI_GFF PROGRESS - [BEGIN] Getting gene models
Traceback (most recent call last):
File "/lustre1/deng_pkuhpc/hanxue/bin/AGOUTI/agouti.py", line 288, in
main()
File "/lustre1/deng_pkuhpc/hanxue/bin/AGOUTI/agouti.py", line 285, in main
args.func(args)
File "/lustre1/deng_pkuhpc/hanxue/bin/AGOUTI/agouti.py", line 201, in run_scaffolder
dGFFs = agGFF.get_gene_models(gffFile, outDir, prefix, args.debug)
File "/lustre1/deng_pkuhpc/hanxue/bin/AGOUTI/lib/agouti_gff.py", line 80, in get_gene_models
if tmp_line[2] == "gene":
IndexError: list index out of range