GRIT-1.1.3 - TypeError: object of type 'generator' has no len()

[Vikas Bansal]

Dear Nathan,

I am running GRIT on the test data you provided. Command line used-

run_grit.py --control AdMatedF_Ecl_20days_Heads.control.txt --reference flybase-r5.45.chr4.gtf -t 20

I am getting an error. Please see below some part of error. In the end I do not get any transcripts in gtf file.

Thanks in advance and best wishes,

Vikas

Waiting for gene to process (1)

FINISHED Finding Exons in Chrm 4 Strand + Pos 1085081-1099332

Waiting for gene to process (1)

Waiting for gene to process (1)

Waiting for gene to process (1)

Waiting for gene to process (1)

Waiting for gene to process (1)

Loading discovered.AdMatedF_Ecl_20days_Heads.elements.bed

Finished Loading discovered.AdMatedF_Ecl_20days_Heads.elements.bed

Estimating the fragment length distribution

Finished estimating the fragment length distribution

Initializing processing data

Clustering elements into genes for 4:-

Clustering elements into genes for 4:+

Finished initializing processing data

Spawning new worker child

Initializing background writer

Spawning new worker child

Spawning new worker child

Building transcript and ORFs for Gene 4_p_34

Spawning new worker child

Building transcript and ORFs for Gene 4_p_33

FINISHED Building transcript and ORFs for Gene 4_p_34

Spawning new worker child

FINISHED Building transcript and ORFs for Gene 4_p_33

Finding design matrix for Gene 4_p_34

Spawning new worker child

Building transcript and ORFs for Gene 4_p_32

Finding design matrix for Gene 4_p_34(4:+:1219475-1226882) - 2 transcripts

Finding design matrix for Gene 4_p_33

Spawning new worker child

Building transcript and ORFs for Gene 4_p_31

FINISHED Building transcript and ORFs for Gene 4_p_32

Finding design matrix for Gene 4_p_33(4:+:1206428-1213165) - 4 transcripts

Building transcript and ORFs for Gene 4_p_30

Spawning new worker child

Finding design matrix for Gene 4_p_32

FINISHED Building transcript and ORFs for Gene 4_p_30

Building transcript and ORFs for Gene 4_p_29

Spawning new worker child

Finding design matrix for Gene 4_p_32(4:+:1168076-1190969) - 12 transcripts

Waiting for write queue to fill.

FINISHED Building transcript and ORFs for Gene 4_p_29

Finding design matrix for Gene 4_p_30

Spawning new worker child

Building transcript and ORFs for Gene 4_p_28

Building transcript and ORFs for Gene 4_p_27

Finding design matrix for Gene 4_p_30(4:+:1144789-1145888) - 2 transcripts

Spawning new worker child

Finding design matrix for Gene 4_p_29

FINISHED Building transcript and ORFs for Gene 4_p_28

FINISHED Building transcript and ORFs for Gene 4_p_27

Building transcript and ORFs for Gene 4_p_26

Spawning new worker child

Finding design matrix for Gene 4_p_27

FINISHED Building transcript and ORFs for Gene 4_p_26

Finding design matrix for Gene 4_p_28

Process Process-131:

Traceback (most recent call last):

  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap

    self.run()

  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run

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

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py", line 754, in worker

    (rnaseq_reads, promoter_reads, polya_reads) )

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py", line 472, in build_design_matrices_worker

    config.MAX_NUM_TRANSCRIPTS)

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py", line 834, in __init__

    self._build_rnaseq_arrays(gene, rnaseq_reads, fl_dists)

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py", line 693, in _build_rnaseq_arrays

    expected_rnaseq_array, observed_rnaseq_array)

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py", line 600, in cluster_rows

    (len(clusters), expected_rnaseq_array.shape[1]) )

TypeError: object of type 'generator' has no len()

Building transcript and ORFs for Gene 4_p_25

Spawning new worker child

FINISHED Building transcript and ORFs for Gene 4_p_31

Finding design matrix for Gene 4_p_27(4:+:1052488-1055186) - 1 transcripts

Finding design matrix for Gene 4_p_28(4:+:1081591-1081888) - 1 transcripts

Finding design matrix for Gene 4_p_26

FINISHED Building transcript and ORFs for Gene 4_p_25

Building transcript and ORFs for Gene 4_p_24

Spawning new worker child

Building transcript and ORFs for Gene 4_p_23

Finding design matrix for Gene 4_p_26(4:+:1010344-1028353) - 8 transcripts

Process Process-133:

Traceback (most recent call last):

  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap

    self.run()

  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run

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

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py", line 754, in worker

    (rnaseq_reads, promoter_reads, polya_reads) )

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py", line 472, in build_design_matrices_worker

    config.MAX_NUM_TRANSCRIPTS)

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py", line 834, in __init__

FINISHED Building transcript and ORFs for Gene 4_p_24

    self._build_rnaseq_arrays(gene, rnaseq_reads, fl_dists)

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py", line 693, in _build_rnaseq_arrays

    expected_rnaseq_array, observed_rnaseq_array)

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py", line 600, in cluster_rows

    (len(clusters), expected_rnaseq_array.shape[1]) )

TypeError: object of type 'generator' has no len()

Waiting for write queue to fill.

Process Process-247:

Traceback (most recent call last):

  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap

    self.run()

  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run

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

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py", line 754, in worker

    (rnaseq_reads, promoter_reads, polya_reads) )

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py", line 472, in build_design_matrices_worker

    config.MAX_NUM_TRANSCRIPTS)

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py", line 834, in __init__

    self._build_rnaseq_arrays(gene, rnaseq_reads, fl_dists)

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py", line 693, in _build_rnaseq_arrays

    expected_rnaseq_array, observed_rnaseq_array)

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py", line 600, in cluster_rows

    (len(clusters), expected_rnaseq_array.shape[1]) )

TypeError: object of type 'generator' has no len()

Process Process-205:

Traceback (most recent call last):

  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap

    self.run()

  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run

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

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py", line 754, in worker

    (rnaseq_reads, promoter_reads, polya_reads) )

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py", line 472, in build_design_matrices_worker

    config.MAX_NUM_TRANSCRIPTS)

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py", line 834, in __init__

    self._build_rnaseq_arrays(gene, rnaseq_reads, fl_dists)

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py", line 693, in _build_rnaseq_arrays

    expected_rnaseq_array, observed_rnaseq_array)

  File "/usr/local/lib/python2.7/dist-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py", line 600, in cluster_rows

    (len(clusters), expected_rnaseq_array.shape[1]) )

TypeError: object of type 'generator' has no len()

Finished building transcripts

[Vikas Bansal]

Bingo! Thanks to Mikael (see below). It works like a charm.

 

Hi Vikas,

I recently installed GRIT, and i've got a similar problem.

"Error: object of type 'generator' has no len()"

Please check the python module version of python-networkx it must be 1.7.

rm -rf /lib/python2.7/site-packages/networkx-1.9-py2.7.egg (or where ever the networkx-1.9-py2.7.egg is located)
pip install networkx==1.7

After downgrading this module version it seems to work for me.

Regards,

Mikael

[njster]

Hi! 

I just wonder if there is another way to solve this problem? I work on our company's cluster and there is no way I can do this. I tried to install networkx-1.7 under my user folder and still got a bunch of error messages.

I use python-2.7.7 and networkx on our cluster is 1.9. I tried python-2.7.4 with networkx-1.7, but got the error with cython and gcc versions.

Thanks a lot,

Ying