Index out of range error

[Alan Wong]

Hi all,

I have this error when running Binsanity-wf and it won't proceed to check bin quality with checkM:

Traceback (most recent call last):

  File "/srv/scratch/z3336178/anaconda/envs/binsanity/bin/checkm", line 36, in <module>

    from checkm import main

  File "/srv/scratch/z3336178/anaconda/envs/binsanity/lib/python2.7/site-packages/checkm/main.py", line 25, in <module>

    from checkm.defaultValues import DefaultValues

  File "/srv/scratch/z3336178/anaconda/envs/binsanity/lib/python2.7/site-packages/checkm/defaultValues.py", line 26, in <module>

    class DefaultValues():

  File "/srv/scratch/z3336178/anaconda/envs/binsanity/lib/python2.7/site-packages/checkm/defaultValues.py", line 29, in DefaultValues

    __DBM = DBManager()

  File "/srv/scratch/z3336178/anaconda/envs/binsanity/lib/python2.7/site-packages/checkm/checkmData.py", line 114, in __init__

    if not self.setRoot():

  File "/srv/scratch/z3336178/anaconda/envs/binsanity/lib/python2.7/site-packages/checkm/checkmData.py", line 140, in setRoot

    path = self.confirmPath(path=path)

  File "/srv/scratch/z3336178/anaconda/envs/binsanity/lib/python2.7/site-packages/checkm/checkmData.py", line 162, in confirmPath

    path = raw_input("Where should CheckM store it's data?\n" \

EOFError: EOF when reading a line

        ******************************************************

        **********************BinSanity***********************

        |____________________________________________________|

        |                                                    | 

        |             Computing Coverage Array               | 

        |____________________________________________________|

        

          Preference: -3

          Maximum Iterations: 4000

          Convergence Iterations: 400

          Contig Cut-Off: 2000

          Damping Factor: 0.95

          Coverage File: coverage.cov.x100.lognorm

          Fasta File: contig1000.fa

          Output Directory: Bins

          (25901, 1)

         ______________________________________________________   

        |                                                      |

        |                 Clustering Contigs                   |

        |______________________________________________________|

        

        

          Cluster 0: 752

          Cluster 1: 2794

          Cluster 2: 1823

          Cluster 3: 1254

          Cluster 4: 922

          Cluster 5: 2992

          Cluster 6: 3689

          Cluster 7: 3771

          Cluster 8: 1883

          Cluster 9: 3115

          Cluster 10: 1491

          Cluster 11: 1415

          Total Number of Bins: 12

         _____________________________________________________

                                                               

                       Putative Bins Computed                 

                       in 17044.510591 seconds                          

         _____________________________________________________

         _____________________________________________________

        |                                                     |

        |       Evaluating Genome With CheckM Lineage_wf      |

        |_____________________________________________________|

        

Traceback (most recent call last):

  File "/srv/scratch/z3336178/anaconda/envs/binsanity/bin/Binsanity-wf", line 408, in <module>

    checkm_analysis(os.path.join(args.outputdir,str(args.prefix)+"_checkm_lineagewf-results.txt"),".fna",str(out_1))

  File "/srv/scratch/z3336178/anaconda/envs/binsanity/bin/Binsanity-wf", line 241, in checkm_analysis

    del new_2[0]

IndexError: list assignment index out of range

My command line is:

cd $dir/binsanity

module add python/2.7.12

module add checkm/1.0.7

source activate binsanity

Binsanity-wf -f $dir/binsanity -l contig1000.fa -c coverage.cov.x100.lognorm -x 2000 -o Bins

I installed binsanity through anaconda, but checkM was already installed in the global environment in the HPC.

Is it a problem of failing to locate checkM? If so, how could I specify the path of checkM in the script?

Cheers and many thanks

Alan

[Elaina]

My initial inclination would be to check if you have properly set the checkM data folders. So once you install CheckM you need to download the data files and then run the command `checkm data setRoot`. It will then prompt you to identify where the checkM data folder is.