Error with --nolamda option enabled

[dimkonstanto]

Greetings,

I am facing some troubles when I am using --nolamda option:

macs2 callpeak -t CB9TUACXX_OATAC_TAS_17s005511-1-1_lane6_1_sequence.dup.bed -f BED --nomodel --nolambda --keep-dup all --shift 37 --extsize 73 -n peak_calling/nolambda_out

...

INFO @ Wed, 15 Nov 2017 14:44:10: 50000000 INFO @ Wed, 15 Nov 2017 14:44:12: 51000000 INFO @ Wed, 15 Nov 2017 14:44:14: 52000000 INFO @ Wed, 15 Nov 2017 14:44:16: 53000000 INFO @ Wed, 15 Nov 2017 14:44:19: 54000000 INFO @ Wed, 15 Nov 2017 14:44:21: 55000000 INFO @ Wed, 15 Nov 2017 14:44:23: 56000000 INFO @ Wed, 15 Nov 2017 14:44:26: #1 tag size is determined as 49 bps INFO @ Wed, 15 Nov 2017 14:44:26: #1 tag size = 49 INFO @ Wed, 15 Nov 2017 14:44:26: #1 total tags in treatment: 56122595 INFO @ Wed, 15 Nov 2017 14:44:26: #1 finished! INFO @ Wed, 15 Nov 2017 14:44:26: #2 Build Peak Model... INFO @ Wed, 15 Nov 2017 14:44:26: #2 Skipped... INFO @ Wed, 15 Nov 2017 14:44:26: #2 Sequencing ends will be shifted towards 3' by 37 bp(s) INFO @ Wed, 15 Nov 2017 14:44:26: #2 Use 73 as fragment length INFO @ Wed, 15 Nov 2017 14:44:26: #3 Call peaks... INFO @ Wed, 15 Nov 2017 14:44:26: # local lambda is disabled! INFO @ Wed, 15 Nov 2017 14:44:26: #3 !!!! DYNAMIC LAMBDA IS DISABLED !!!! INFO @ Wed, 15 Nov 2017 14:44:26: #3 Pre-compute pvalue-qvalue table... Traceback (most recent call last): File "/usr/local/bin/macs2", line 614, in main() File "/usr/local/bin/macs2", line 56, in main run( args ) File "/usr/local/lib/python2.7/dist-packages/MACS2/callpeak_cmd.py", line 261, in run peakdetect.call_peaks() File "MACS2/PeakDetect.pyx", line 110, in MACS2.PeakDetect.PeakDetect.call_peaks (MACS2/PeakDetect.c:1665) File "MACS2/PeakDetect.pyx", line 364, in MACS2.PeakDetect.PeakDetect.__call_peaks_wo_control (MACS2/PeakDetect.c:4714) File "MACS2/IO/CallPeakUnit.pyx", line 858, in MACS2.IO.CallPeakUnit.CallerFromAlignments.call_peaks (MACS2/IO/CallPeakUnit.c:12340) File "MACS2/IO/CallPeakUnit.pyx", line 883, in MACS2.IO.CallPeakUnit.CallerFromAlignments.call_peaks (MACS2/IO/CallPeakUnit.c:11717) File "MACS2/IO/CallPeakUnit.pyx", line 653, in MACS2.IO.CallPeakUnit.CallerFromAlignments.__cal_pvalue_qvalue_table (MACS2/IO/CallPeakUnit.c:9065) File "MACS2/IO/CallPeakUnit.pyx", line 496, in MACS2.IO.CallPeakUnit.CallerFromAlignments.__pileup_treat_ctrl_a_chromosome (MACS2/IO/CallPeakUnit.c:7329) TypeError: 'float' object cannot be interpreted as an index

while when I do not enable it, the program is run with no errors.

Any help would be appreciated.

[yuxinghai]

I meet the same problem in MACS2-2.1.0.20150420

[OscarBrock]

I've also encountered this problem. Is there a known solution?

[dimkonstanto]

Not yet from my side..

2018-07-11 23:52 GMT+03:00 OscarBrock [email protected]:

I've also encountered this problem. Is there a known solution?

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[Heroico]

Hi all,

I get the same error on MACS2. From looking around the web, this seems an obscure issue from numpy - many people reported fixing it by changing to different python/numpy/numerical libraries installation.

In my case this happened in a cluster environment with system-installed libraries. I then used conda with python 3.7 and macs2 from bioconda and it worked.

[taoliu]

@Heroico Right. This is one of the major updates in recent macs2 releases -- to test under different environments. To install macs2 from bioconda definitely will make life easier/happier.