majiq builder

[Alicia Smart]

Hi, 

I am trying to run majiq builder and getting the following error: 

(majiq_env)-bash:cga02:/xchip/cga_home/asmart/MAJIQ 1089 $ majiq build /xchip/cga_home/asmart/ensembl.hg19.gff3 -conf /xchip/cga_home/asmart/config.txt --nthreads 4 --output /xchip/cga_home/asmart/MAJIQ/

2016-04-21 15:40:57,853 (PID:49113) - INFO - 

2016-04-21 15:40:57,854 (PID:49113) - INFO - Command: Namespace(conf='/xchip/cga_home/asmart/config.txt', debug=0, func=<function builder at 0x7f4fafc5d578>, gcnorm=True, gff_output='lsvs.gff', logger=None, min_intronic_cov=1.5, minpos=2, minreads=3, non_denovo=False, nthreads=4, only_rna=False, onlygather=False, output='/xchip/cga_home/asmart/MAJIQ/', pcr_filename=None, permissive=False, plotpath=None, silent=False, tmp='/tmp/', transcripts='/xchip/cga_home/asmart/ensembl.hg19.gff3')

2016-04-21 15:40:57,854 (PID:49113) - INFO - ... waiting gff3 parsing

START child, Process-1

Traceback (most recent call last):

  File "/home/unix/asmart/.conda/envs/majiq_env/lib/python2.7/site-packages/majiq-0.9.1-py2.7.egg/majiq/src/builder.py", line 90, in __parallel_gff3

    majiq_io.read_gff(transcripts, pcr_filename, nthreads, logging=tlogger)

  File "/home/unix/asmart/.conda/envs/majiq_env/lib/python2.7/site-packages/majiq-0.9.1-py2.7.egg/majiq/src/io.py", line 689, in read_gff

    for record in __parse_gff3(filename):

  File "/home/unix/asmart/.conda/envs/majiq_env/lib/python2.7/site-packages/majiq-0.9.1-py2.7.egg/majiq/src/io.py", line 555, in __parse_gff3

    assert len(parts) == len(gffInfoFields)

AssertionError

Process Process-1:

Traceback (most recent call last):

  File "/home/unix/asmart/.conda/envs/majiq_env/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap

    self.run()

  File "/home/unix/asmart/.conda/envs/majiq_env/lib/python2.7/multiprocessing/process.py", line 114, in run

    self._target(*self._args, **self._kwargs)

  File "/home/unix/asmart/.conda/envs/majiq_env/lib/python2.7/site-packages/majiq-0.9.1-py2.7.egg/majiq/src/builder.py", line 95, in __parallel_gff3

    raise()

TypeError: exceptions must be old-style classes or derived from BaseException, not tuple

2016-04-21 15:40:57,993 (PID:49113) - INFO - Get samfiles

START child, PoolWorker-2

2016-04-21 15:40:58,239 (PID:49153) - INFO - Building chunk 0

START child, PoolWorker-3

2016-04-21 15:40:58,240 (PID:49154) - INFO - Building chunk 1

START child, PoolWorker-4

START child, PoolWorker-5

END child,  PoolWorker-2

2016-04-21 15:40:58,240 (PID:49155) - INFO - Building chunk 2

2016-04-21 15:40:58,240 (PID:49156) - INFO - Building chunk 3

END child,  PoolWorker-3

END child,  PoolWorker-4

END child,  PoolWorker-5

2016-04-21 15:40:58,267 (PID:49113) - INFO - ... waiting childs

START child, PoolWorker-6

2016-04-21 15:40:58,343 (PID:49160) - INFO - Building chunk 4

END child,  PoolWorker-6

START child, PoolWorker-7

2016-04-21 15:40:58,347 (PID:49161) - INFO - Building chunk 5

END child,  PoolWorker-7

START child, PoolWorker-8

2016-04-21 15:40:58,350 (PID:49162) - INFO - Building chunk 6

END child,  PoolWorker-8

START child, PoolWorker-9

2016-04-21 15:40:58,353 (PID:49163) - INFO - Building chunk 7

END child,  PoolWorker-9

START child, PoolWorker-10

2016-04-21 15:40:58,457 (PID:49164) - INFO - Building chunk 8

END child,  PoolWorker-10

START child, PoolWorker-11

2016-04-21 15:40:58,460 (PID:49165) - INFO - Building chunk 9

END child,  PoolWorker-11

START child, PoolWorker-12

2016-04-21 15:40:58,464 (PID:49166) - INFO - Building chunk 10

END child,  PoolWorker-12

START child, PoolWorker-13

2016-04-21 15:40:58,466 (PID:49167) - INFO - Building chunk 11

END child,  PoolWorker-13

START child, PoolWorker-14

2016-04-21 15:40:58,570 (PID:49168) - INFO - Building chunk 12

START child, PoolWorker-15

2016-04-21 15:40:58,573 (PID:49169) - INFO - Building chunk 13

START child, PoolWorker-16

2016-04-21 15:40:58,577 (PID:49170) - INFO - Building chunk 14

START child, PoolWorker-17

2016-04-21 15:40:58,580 (PID:49171) - INFO - Building chunk 15

END child,  PoolWorker-14

END child,  PoolWorker-15

END child,  PoolWorker-16

END child,  PoolWorker-17

START child, PoolWorker-18

2016-04-21 15:40:58,684 (PID:49172) - INFO - Building chunk 16

START child, PoolWorker-19

2016-04-21 15:40:58,687 (PID:49173) - INFO - Building chunk 17

END child,  PoolWorker-18

END child,  PoolWorker-19

START child, PoolWorker-20

2016-04-21 15:40:58,690 (PID:49174) - INFO - Building chunk 18

END child,  PoolWorker-20

START child, PoolWorker-21

2016-04-21 15:40:58,693 (PID:49175) - INFO - Building chunk 19

END child,  PoolWorker-21

2016-04-21 15:40:58,792 (PID:49113) - INFO - Gather outputs

2016-04-21 15:40:58,966 (PID:49113) - INFO - Gather lsv and generate gff

A3SS [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]

A5SS [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]

SE events [0, 0, 0, 0, 0]

Total SE 0

BOTH 0

2016-04-21 15:40:59,098 (PID:49113) - INFO - End of execution

Configuration file: 

[info]

readlen=76

samdir=/xchip/cga_home/asmart/fh_bams

genome=hg19

genome_path=/xchip/cga_home/asmart/ensembl.hg19.gff3

type=strand-specific

[experiments]

NR=IPI_punch_tumor_Pat03

R=IPI_punch_tumor_Pat02

Please let me know if you have any suggestions. 

Thank you,

Alicia

[Jordi Vaquero]

It looks like there is a problem in your gff3 file, it is like it is truncated or not properly delimited by tabs.

Can you send me the db you are using, so I can take a deeper look?

Thanks

Jordi