error running concoct test

[madhubioinfo]

Hi I have installed all the dependencies and trying to run concoct in centos 6 while executing test script it is showing following error ..E................

ERROR: test_gen_input_table.TestCMD.test_with_bamfiles

Traceback (most recent call last): File "/shared/programs/miniconda3/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(self.arg) File "/shared/programs/CONCOCT/tests/test_gen_input_table.py", line 87, in test_with_bamfiles sample_names = os.path.join(data_path, 'sample_names')) File "/shared/programs/CONCOCT/tests/test_gen_input_table.py", line 63, in run_command shell=True) File "/shared/programs/miniconda3/lib/python2.7/subprocess.py", line 223, in check_output raise CalledProcessError(retcode, cmd, output=output) CalledProcessError: Command 'python /shared/programs/CONCOCT/tests/../scripts/gen_input_table.py --samplenames /shared/programs/CONCOCT/tests/test_data/map/sample_names /shared/programs/CONCOCT/tests/test_data/map/two_contigs.fa /shared/programs/CONCOCT/tests/test_data/map//*-s.bam > /shared/programs/CONCOCT/tests/nose_tmp_output/inputtable.tsv 2> /dev/null' returned non-zero exit status 1

---

Ran 19 tests in 56.022s

FAILED (errors=1)

Thanks

[alneberg]

Hello @madhubioinfo,

It seems to be some problem when running the script scripts/gen_input_table.py. Perhaps you could get a more informative error message if you run:

python /shared/programs/CONCOCT/tests/../scripts/gen_input_table.py --samplenames /shared/programs/CONCOCT/tests/test_data/map/sample_names /shared/programs/CONCOCT/tests/test_data/map/two_contigs.fa /shared/programs/CONCOCT/tests/test_data/map//*-s.bam > /shared/programs/CONCOCT/tests/nose_tmp_output/inputtable.tsv

[madhubioinfo]

Hi I have provided the csv file with comma separated when i use tab separated file its working fine ! Thanks. I need to know detailed description of output. which file i should be looking ?

[alneberg]

Glad that it worked out, even though I'm not sure I understand what caused your error in the first place?

There are I'm afraid not much documentation on the output files. The clustering file consists of two columns, one with the contig id and the other with the assigned bin id. I'd suggest using the scripts/extract_fasta_bins.py to get fasta bins, after using the merge_cutup_clustering.py script to create a new clustering file that correspond to the original contigs rather than the cutup ones.

[madhubioinfo]

there are multiple files produced here concoct_out_args.txt concoct_out_log.txt concoct_out_PCA_components_data_gt1000.csv concoct_out_clustering_gt1000.csv concoct_out_original_data_gt1000.csv concoct_out_PCA_transformed_data_gt1000.csv

which one I should be looking into ?

Is it especially designed for bacterial metagenomes? or even the fungal metagenomes can also be used ?

[alneberg]

Yes, concoct_out_clustering_gt1000.csv contains the clustering so that's the one you want to use into merge_cutup_clustering.py.

The other files contain information about the run, the data itself or the PCA transformation done on the data.

CONCOCT should be able to handle other than bacterial genomes. Certainly Archaeal genomes but also small Eukaryotes. Good luck!

[madhubioinfo]

thanks