List index out of range in "associate_tags_with_regions.py"

[abalter]

I ran:

$ python $chipseq/SICER.py -c /<path>/bam/mock_input_A.bam -t /home/exacloud/lustre1/<path>/bam/mock_BRD4_A.bam -rt 0 > mock_a_peaks.bed 2> sicermocka.log

And got this in my log:

*** Preprocess raw files to remove reduntant reads
cd /<path>/tmp_sicer_EgQ7hT/tmp_mock_BRD4_A.bam_dir
export PYTHONPATH=/<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/lib
/<path>/miniconda2/bin/python /<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/src/remove_redundant_reads_bam.py -t 0 -b /<path>/results/bam/mock_BRD4_A.bam -o /h<path>/tmp_sicer_EgQ7hT/mock_BRD4_A.removed.bam -f 0 -F 4 -q 5

cd /<path>/tmp_sicer_EgQ7hT/tmp_mock_input_A.bam_dir
export PYTHONPATH=/<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/lib
/<path>/miniconda2/bin/python /<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/src/remove_redundant_reads_bam.py -t 0 -b /<path>/results/bam/mock_input_A.bam -o /<path>/tmp_sicer_EgQ7hT/mock_input_A.removed.bam -f 0 -F 4 -q 5

*** Partion the genome in windows
cd /<path>/tmp_sicer_EgQ7hT
export PYTHONPATH=/<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/lib
/<path>/miniconda2/bin/python /<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/src/run-make-graph-file-by-chrom_bam.py -b /<path>/tmp_sicer_EgQ7hT/mock_BRD4_A.removed.bam -w 200 -i 150 -o /<path>/tmp_sicer_EgQ7hT/summary.bedgraph

*** Find candidate islands exhibiting clustering
export PYTHONPATH=/<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/lib
/<path>/miniconda2/bin/python /<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/src/find_islands_in_pr.py --bam /<path>/results/bam/mock_BRD4_A.bam -b /<path>/tmp_sicer_EgQ7hT/summary.bedgraph -w 200 -g 600 -t 0.74 -e 1000  -f /<path>/tmp_sicer_EgQ7hT/scoreisland.bed
Window_size: 200
Gap size: 600
E value is: 1000.0
Total read count: 44053384.0
Genome Length: 3099750718
Effective genome Length: 2293815531
Window average: 3.84105726068
Window pvalue: 0.2
Minimum num of tags in a qualified window: 6
Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows
Determine the score threshold from random background
The score threshold is: 38.137
Make and write islands
    KI270747.1 does not have any islands meeting the required significance
    KI270302.1 does not have any islands meeting the required significance
    KI270710.1 does not have any islands meeting the required significance
    KI270755.1 does not have any islands meeting the required significance
    KI270583.1 does not have any islands meeting the required significance
    KI270322.1 does not have any islands meeting the required significance
    KI270708.1 does not have any islands meeting the required significance
    KI270743.1 does not have any islands meeting the required significance
    KI270510.1 does not have any islands meeting the required significance
    KI270741.1 does not have any islands meeting the required significance
    KI270521.1 does not have any islands meeting the required significance
    KI270587.1 does not have any islands meeting the required significance
    KI270320.1 does not have any islands meeting the required significance
    GL000221.1 does not have any islands meeting the required significance
    KI270310.1 does not have any islands meeting the required significance
    KI270714.1 does not have any islands meeting the required significance
    KI270716.1 does not have any islands meeting the required significance
    KI270737.1 does not have any islands meeting the required significance
    KI270580.1 does not have any islands meeting the required significance
    KI270749.1 does not have any islands meeting the required significance
    KI270423.1 does not have any islands meeting the required significance
    KI270706.1 does not have any islands meeting the required significance
    KI270721.1 does not have any islands meeting the required significance
    KI270753.1 does not have any islands meeting the required significance
    KI270508.1 does not have any islands meeting the required significance
    GL000194.1 does not have any islands meeting the required significance
    KI270582.1 does not have any islands meeting the required significance
    KI270522.1 does not have any islands meeting the required significance
    GL000009.2 does not have any islands meeting the required significance
    GL000226.1 does not have any islands meeting the required significance
    KI270362.1 does not have any islands meeting the required significance
    KI270707.1 does not have any islands meeting the required significance
    KI270734.1 does not have any islands meeting the required significance
    KI270418.1 does not have any islands meeting the required significance
Total number of islands: 19312

*** Calculate significance of candidate islands using the control library
export PYTHONPATH=/<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/lib
/<path>/miniconda2/bin/python /<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/src/associate_tags_with_chip_and_control_w_fc_q_bam.py -a /<path>/tmp_sicer_EgQ7hT/mock_BRD4_A.removed.bam -b /<path>/tmp_sicer_EgQ7hT/mock_input_A.removed.bam -d /<path>/tmp_sicer_EgQ7hT/scoreisland.bed -f 150 -t 0.74 -o /<path>/tmp_sicer_EgQ7hT/island-summary.bed
chip library size  44056150
control library size 48890374
Traceback (most recent call last):
  File "/<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/src/associate_tags_with_chip_and_control_w_fc_q_bam.py", line 204, in <module>
    main(sys.argv)
  File "/<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/src/associate_tags_with_chip_and_control_w_fc_q_bam.py", line 105, in main
    position = associate_tags_with_regions.tag_position(sline, opt.fragment_size)
  File "/<path>/users/balter/chip-seq-analysis/chipseq/SICERpy/SICERpy/lib/associate_tags_with_regions.py", line 37, in tag_position
    if plus.match(sline[5]):
IndexError: list index out of range

[JiangQi1996]

Have you solved this problem?I got this error too,can you tell me the reason,thanks.

[abalter]

Sorry. I never did and moved on to a different peak caller.

[endrebak]

It means that one of the lines in the file has fewer than 6 fields. Why I do not know. Have you tried https://github.com/biocore-ntnu/epic2 ?

On Monday, February 25, 2019, Ariel Balter notifications@github.com wrote:

Sorry. I never did and moved on to a different peak caller.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/dariober/SICERpy/issues/3#issuecomment-466869943, or mute the thread https://github.com/notifications/unsubscribe-auth/AQ9I0otO29f3UA4pcVwZV09f9uSMJPr1ks5vQ2l0gaJpZM4K0V3R .

[abalter]

That's what I ended up using. Worked well for me.

[dariober]

Indeed- use https://github.com/biocore-ntnu/epic2 apologies I haven't updated this issue.