Problem with BESST in the pipeline

[xbarvazx]

Hi,

I get the following error at the BESST part of the script, any ideas why?

(2018-05-30 06:24:22) Execution of 'python BESST/runBESST'. Command line: /storage/raz/gatb-minia-pipeline/tools/memused python /storage/raz/gatb-minia-pipeline/BESST/runBESST -c assembly_k121.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000 Number of initial contigs: 54117 Estimating insert size from 1000001 mappings with quality over --min_mapq 11. Choosing mode: 470 mu_adjusted:562.118735931, sigma_adjusted:191.434136248, skewness_adjusted:0.825079377678 mode adj: 470 median adj 531 Creating contig graph with library: assembly.lib_0.bam Traceback (most recent call last): File "/storage/raz/gatb-minia-pipeline/BESST/runBESST", line 431, in main(args) File "/storage/raz/gatb-minia-pipeline/BESST/runBESST", line 182, in main (G, G_prime) = CG.PE(Contigs, Scaffolds, Information, C_dict, param, small_contigs, small_scaffolds, bam_file) #Create graph, single out too short contigs/scaffolds and store them in F File "/storage/raz/gatb-minia-pipeline/BESST/BESST/CreateGraph.py", line 202, in PE CreateEdge(cont_obj1, cont_obj2, scaf_obj1, scaf_obj2, G_prime, param, alignedread, counter, contig1, contig2, save_obs=False) File "/storage/raz/gatb-minia-pipeline/BESST/BESST/CreateGraph.py", line 844, in CreateEdge G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)]['obs_sq'] = (obs1 + obs2) ** 2 AttributeError: 'Graph' object has no attribute 'edge' maximal memory used: 285 MB (2018-05-30 06:24:40) Execution of 'python BESST/runBESST' failed. Command line: /storage/raz/gatb-minia-pipeline/tools/memused python /storage/raz/gatb-minia-pipeline/BESST/runBESST -c assembly_k121.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000

Thanks,

[rchikhi]

Hmm on top of my head, not really, but @ksahlin might know!

[ksahlin]

Probably you have networkx >=2.0 installed, see https://github.com/ksahlin/BESST/issues/64 . Installing a lower version of networkx should fix this, e.g., with pip install 'networkx==1.9' --force-reinstall.

[xbarvazx]

Thanks, I will try that. I also changed the hardcode to sspace and it work.

Cheers,

[rchikhi]

Thanks Kristoffer!

[Shirley-Q]

I also have this error, but I didn't solve it according to your tips(pip install 'networkx==1.9' --force-reinstall). And I can't understand "changed the hardcode to sspace and it work." Could you help me? Best wishes, Shirley

[rchikhi]

The last part refers to changing line https://github.com/GATB/gatb-minia-pipeline/blob/master/gatb#L64 manually. With BESST, do you get the exact same error message as above after installing networkx 1.9?

[ksahlin]

If you get the exact same error after running pip install 'networkx==1.9' --force-reinstall it is likely that the pipeline still are using a networkx version >=2.0, maybe from another python installation.

[mkweskin]

I was having this problem and saw the networkx <2.0 recommendation in this thread and an issue on the BESST github Issues list.

Could the gatb-minia-pipeline Readme.md install instructions be updated to include networkx==1.9? 😸

[Krannich479]

I am running scaffolding successfully with networkx 1.6. See time stamp for reference.

[rchikhi]

Readme has been updated to install BESST directly, without installing any prerequisites manually

[silviajusti]

I've been getting this error for 3 out of 14 similar samples. All running at the same time, on the same server, under the same conditions...

[rchikhi]

for the failing samples, can you try uninstalling besst and networkx and reinstall them through python2 -m pip install --user BESST?