IndexError: list index out of range

[JiaZhibo123]

When I run "ALLHiC_plot sample.clean.bam groups.agp chrn.list 500k pdf", I met the mistake Traceback (most recent call last): File "/public/home/zbjia/soft/ALLHiC/bin/ALLHiC_plot", line 249, in read_count_per_chr, read_count_whole_genome = calc_read_count_per_bin(chr_len_db, chr_order, read_on_chr, bin_size) File "/public/home/zbjia/soft/ALLHiC/bin/ALLHiC_plot", line 112, in calc_read_count_per_bin read_count_per_chr[chr1][pos1_index][pos2_index] += 1 IndexError: list index out of range

[sc-zhang]

If you run this script with python3, the result of round function may be unexpected, I've already fix this problem, you can update it, and try again to check if it works or not.

[JiaZhibo123]

My python vision is 3.83, which vision should I update?

[sc-zhang]

I mean I have made some changes in the script, so you can update the ALLHiC_plot and check if it works or not.

[JiaZhibo123]

ok,I copy "https://github.com/tangerzhang/ALLHiC/blob/master/bin/ALLHiC_plot" to my allhic/bin , met the same error

[sc-zhang]

Can you paste your list file and bin size here?

[JiaZhibo123]

list file is ?

[sc-zhang]

chrn.list

[JiaZhibo123]

chrn.list group1 1010788464 group10 607078 group11 309303 group12 285840 group13 282637 group14 215647 group15 203962 group16 173060 group17 106304 group18 47972 group19 45951 group2 1104409 group3 639707 group4 626453 group5 514609 group6 434432 group7 377685 group8 354765 group9 347690 HiC_scaffold_1624 35015 HiC_scaffold_1443 112163 HiC_scaffold_785 181000 HiC_scaffold_1629 30275 HiC_scaffold_1078 445135 HiC_scaffold_1623 36113 HiC_scaffold_845 28000 HiC_scaffold_1628 32157 HiC_scaffold_1617 40664 HiC_scaffold_1622 37003 HiC_scaffold_1625 34558 HiC_scaffold_1636 15454 HiC_scaffold_52 16259 HiC_scaffold_1444 59064 HiC_scaffold_436 35591 HiC_scaffold_515 1000 HiC_scaffold_1074 32000 HiC_scaffold_1260 10946 HiC_scaffold_1630 26609 HiC_scaffold_1631 24996 HiC_scaffold_1618 40482 HiC_scaffold_1627 6040 HiC_scaffold_779 43000 HiC_scaffold_1619 38618 HiC_scaffold_173 31891 HiC_scaffold_135 25000 HiC_scaffold_965 1633033 HiC_scaffold_1620 38325 HiC_scaffold_1364 80066 HiC_scaffold_1621 37372 HiC_scaffold_180 34570 HiC_scaffold_1341 322749 HiC_scaffold_676 109592 HiC_scaffold_1363 88681 HiC_scaffold_546 85385 HiC_scaffold_1634 20763 HiC_scaffold_677 254408 HiC_scaffold_1626 2000 HiC_scaffold_1635 16644 HiC_scaffold_1632 22433 HiC_scaffold_1374 11522 HiC_scaffold_475 27468 HiC_scaffold_1633 21249 HiC_scaffold_540 17022 bin size 500k Thank you

[sc-zhang]

I added the exception check in the new version of script, and you can try it again, and check the log which printed by ALLHiC_plot and paste the lines with "Index error" here.

[JiaZhibo123]

23826017.txt 23826017 (2).txt

[sc-zhang]

1. you need install python module matplotlib
2. the bin size is too large for almost all chromosomes, and the first group is too large than others, maybe you need check if the assembly result is appropriated.
3. you can use different chrn.list files contain different groups, and run ALLHiC_plot with different bin size for them.

[JiaZhibo123]

1. I remove the group 1 from chrn list , no error report . The log file is python /public/home/zbjia/soft/ALLHiC/bin/ALLHiC_plot /public/home/zbjia/allhic/3008clean.bam /public/home/zbjia/allhic/hic/exgroup1/chrn.list 500k pdf "Successfully completed.

Resource usage summary:

CPU time :                                   0.17 sec.
Max Memory :                                 14 MB
Average Memory :                             14.00 MB
Total Requested Memory :                     -
Delta Memory :                               -
Max Swap :                                   -
Max Processes :                              4
Max Threads :                                5
Run time :                                   2 sec.
Turnaround time :                            3 sec.

The output (if any) follows:

This script is used to plot chromatin matrix for ALLHiC results Usage: python /public/home/zbjia/soft/ALLHiC/bin/ALLHiC_plot <sam/bam file> <agp_file> <chr_list> <bin_size> <sam/bam_file> is the sam or bam file of mapping <agp_file> is the file created by allhic <chr_list> is the file containing chromosome ID and length <bin_size> is the bin size of heatmap, it can be a list splited by comma is the extention of plot, e.g. pdf

PS:

Read file <23826072.err> for stderr output of this job." But I don't get any file.

2.I just run group 1, changing the bin size 1m, the output pdf is terrible .

[sc-zhang]

You should remove HiC_scaffolds from chrn.list, and the heatmap of group1 may illustrate that the assembly of it is inappropriate. For other groups, the second parameter of the script is agp file, and you did not provided it, so there is no any output, and the bin size 500k is too large for these groups, so you should use lower bin size and try again.