"IndexError: list index out of range" in plot_1d_clusters

[SebastianHollizeck]

Hi,

I seem to have run into an issue when generating the plots with the command

~/bin/PhylogicNDT/PhylogicNDT.py Cluster -i CA99 -sif /dawson_genomics/Projects/CASCADE/CA99/analysis/phylogicNDT/samples.sif -rb --maf_input_type calc_ccf

There were file produced

total 904M
drwxrwsr-x 2 shollizeck res_dawsongenomics  512 Oct 14 23:36 CA99_1d_cluster_plots
-rw-r--r-- 1 shollizeck res_dawsongenomics 549K Oct 14 23:34 CA99.cluster_ccfs.txt
-rw-rw-r-- 1 shollizeck res_dawsongenomics 1.7K Oct 14 23:36 CA99.cnvs.txt
-rw-r--r-- 1 shollizeck res_dawsongenomics 903M Oct 14 23:36 CA99.mut_ccfs.txt
-rw-rw-r-- 1 shollizeck res_dawsongenomics 111K Oct 14 23:36 CA99.unclustered.txt

but the 1d cluster plots folder is empty and the log file displays the following error at the end

Traceback (most recent call last):
  File "/home/shollizeck/bin/PhylogicNDT/PhylogicNDT.py", line 515, in <module>
    args.func(args)
  File "/home/shollizeck/bin/PhylogicNDT/Cluster/Cluster.py", line 100, in run_tool
    phylogicoutput.plot_1d_clusters('{}.cluster_ccfs.txt'.format(patient_data.indiv_name))
  File "/home/shollizeck/bin/PhylogicNDT/output/PhylogicOutput.py", line 703, in plot_1d_clusters
    dist.setAttribute('fill', ClusterColors.get_rgb_string(c))
  File "/home/shollizeck/bin/PhylogicNDT/output/PhylogicOutput.py", line 1456, in get_rgb_string
    return 'rgb({},{},{})'.format(*cls.color_list[c])
IndexError: list index out of range

Could it be, that the program ran out of colours to use, as the CA99.cluster_ccfs.txt says there are 81 clusters to be considered?

Cheers,
Sebastian

[jcha40]

Your intuition is correct, PhylogicNDT is limited to 58 colors for clusters. If there are any clusters with very few events (maybe less than 5), there is a high possibility that they are artifactual, and I would try blacklisting them.

[SebastianHollizeck]

Hi,

sorry I was occupied with another project, so now that i am coming back I would like to fix this problem.

I ran PhylogicNDT again but without -rb, because i thought then i can blacklist the clusters which have low support, however the program still fails with the same error, so i cannot really blacklist clusters, before they are created.

nevertheless I then had a look at the cluster assignment you can see, that the smallest cluster is still 6 variants.
I could remove everything under 10 supporting variants, which seems arbitraty, but if thats the only way to get it to run I will try that. Is there an option for the clustering to supply a minimum amount of required support?

[shollizeck@vmpr-res-cluster1 ~]$ cut -f 14 PhylogicNDT/CA80.mut_ccfs.txt | sort | uniq -c | sort -n
      1 Cluster_Assignment
      6 55
      8 38
     11 42
     12 12
     12 22
     15 34
     18 37
     18 43
     21 23
     24 41
     24 48
     24 5
     30 36
     34 11
     34 45
     35 30
     36 16
     36 4
     36 9
     42 2
     42 20
     42 26
     42 52
     48 10
     48 33
     60 28
     62 6
     72 24
     72 49
     78 17
     90 32
     92 27
     93 18
     94 53
     99 13
     99 15
    100 25
    108 46
    113 29
    117 31
    126 54
    129 50
    132 14
    132 7
    136 3
    136 35
    138 58
    159 21
    170 39
    174 40
    188 51
    202 56
    216 47
    264 19
    264 44
    434 8
   7817 57
   8779 1