Job ID = 6529097 SRX = SRX2350726 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:03:54 15764843 reads; of these: 15764843 (100.00%) were unpaired; of these: 221791 (1.41%) aligned 0 times 12763791 (80.96%) aligned exactly 1 time 2779261 (17.63%) aligned >1 times 98.59% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1722736 / 15543052 = 0.1108 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 01:17:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 30 Jun 2020 01:17:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:17:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:17:09: 1000000 INFO @ Tue, 30 Jun 2020 01:17:16: 2000000 INFO @ Tue, 30 Jun 2020 01:17:23: 3000000 INFO @ Tue, 30 Jun 2020 01:17:30: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 01:17:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 30 Jun 2020 01:17:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:17:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:17:37: 5000000 INFO @ Tue, 30 Jun 2020 01:17:40: 1000000 INFO @ Tue, 30 Jun 2020 01:17:45: 6000000 INFO @ Tue, 30 Jun 2020 01:17:47: 2000000 INFO @ Tue, 30 Jun 2020 01:17:53: 7000000 INFO @ Tue, 30 Jun 2020 01:17:55: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 01:18:01: 8000000 INFO @ Tue, 30 Jun 2020 01:18:02: 4000000 INFO @ Tue, 30 Jun 2020 01:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 30 Jun 2020 01:18:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:18:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:18:09: 9000000 INFO @ Tue, 30 Jun 2020 01:18:10: 5000000 INFO @ Tue, 30 Jun 2020 01:18:10: 1000000 INFO @ Tue, 30 Jun 2020 01:18:17: 10000000 INFO @ Tue, 30 Jun 2020 01:18:17: 6000000 INFO @ Tue, 30 Jun 2020 01:18:17: 2000000 INFO @ Tue, 30 Jun 2020 01:18:25: 11000000 INFO @ Tue, 30 Jun 2020 01:18:25: 7000000 INFO @ Tue, 30 Jun 2020 01:18:25: 3000000 INFO @ Tue, 30 Jun 2020 01:18:32: 8000000 INFO @ Tue, 30 Jun 2020 01:18:32: 4000000 INFO @ Tue, 30 Jun 2020 01:18:33: 12000000 INFO @ Tue, 30 Jun 2020 01:18:40: 9000000 INFO @ Tue, 30 Jun 2020 01:18:40: 5000000 INFO @ Tue, 30 Jun 2020 01:18:41: 13000000 INFO @ Tue, 30 Jun 2020 01:18:47: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:18:47: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:18:47: #1 total tags in treatment: 13820316 INFO @ Tue, 30 Jun 2020 01:18:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:18:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:18:48: #1 tags after filtering in treatment: 13820316 INFO @ Tue, 30 Jun 2020 01:18:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:18:48: #1 finished! INFO @ Tue, 30 Jun 2020 01:18:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:18:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:18:48: 10000000 INFO @ Tue, 30 Jun 2020 01:18:48: 6000000 INFO @ Tue, 30 Jun 2020 01:18:49: #2 number of paired peaks: 286 WARNING @ Tue, 30 Jun 2020 01:18:49: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 30 Jun 2020 01:18:49: start model_add_line... INFO @ Tue, 30 Jun 2020 01:18:49: start X-correlation... INFO @ Tue, 30 Jun 2020 01:18:49: end of X-cor INFO @ Tue, 30 Jun 2020 01:18:49: #2 finished! INFO @ Tue, 30 Jun 2020 01:18:49: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:18:49: #2 alternative fragment length(s) may be 1,39 bps INFO @ Tue, 30 Jun 2020 01:18:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.05_model.r WARNING @ Tue, 30 Jun 2020 01:18:49: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:18:49: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Tue, 30 Jun 2020 01:18:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:18:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:18:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:18:55: 11000000 INFO @ Tue, 30 Jun 2020 01:18:56: 7000000 INFO @ Tue, 30 Jun 2020 01:19:03: 12000000 INFO @ Tue, 30 Jun 2020 01:19:04: 8000000 INFO @ Tue, 30 Jun 2020 01:19:11: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:19:13: 9000000 INFO @ Tue, 30 Jun 2020 01:19:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:19:17: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:19:17: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:19:17: #1 total tags in treatment: 13820316 INFO @ Tue, 30 Jun 2020 01:19:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:19:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:19:18: #1 tags after filtering in treatment: 13820316 INFO @ Tue, 30 Jun 2020 01:19:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:19:18: #1 finished! INFO @ Tue, 30 Jun 2020 01:19:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:19:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:19:19: #2 number of paired peaks: 286 WARNING @ Tue, 30 Jun 2020 01:19:19: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 30 Jun 2020 01:19:19: start model_add_line... INFO @ Tue, 30 Jun 2020 01:19:19: start X-correlation... INFO @ Tue, 30 Jun 2020 01:19:19: end of X-cor INFO @ Tue, 30 Jun 2020 01:19:19: #2 finished! INFO @ Tue, 30 Jun 2020 01:19:19: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:19:19: #2 alternative fragment length(s) may be 1,39 bps INFO @ Tue, 30 Jun 2020 01:19:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.10_model.r WARNING @ Tue, 30 Jun 2020 01:19:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:19:19: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Tue, 30 Jun 2020 01:19:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:19:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:19:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:19:21: 10000000 INFO @ Tue, 30 Jun 2020 01:19:28: 11000000 INFO @ Tue, 30 Jun 2020 01:19:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:19:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:19:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.05_summits.bed INFO @ Tue, 30 Jun 2020 01:19:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:19:36: 12000000 INFO @ Tue, 30 Jun 2020 01:19:44: 13000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:19:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:19:50: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:19:50: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:19:50: #1 total tags in treatment: 13820316 INFO @ Tue, 30 Jun 2020 01:19:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:19:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:19:50: #1 tags after filtering in treatment: 13820316 INFO @ Tue, 30 Jun 2020 01:19:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:19:50: #1 finished! INFO @ Tue, 30 Jun 2020 01:19:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:19:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:19:52: #2 number of paired peaks: 286 WARNING @ Tue, 30 Jun 2020 01:19:52: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 30 Jun 2020 01:19:52: start model_add_line... INFO @ Tue, 30 Jun 2020 01:19:52: start X-correlation... INFO @ Tue, 30 Jun 2020 01:19:52: end of X-cor INFO @ Tue, 30 Jun 2020 01:19:52: #2 finished! INFO @ Tue, 30 Jun 2020 01:19:52: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:19:52: #2 alternative fragment length(s) may be 1,39 bps INFO @ Tue, 30 Jun 2020 01:19:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.20_model.r WARNING @ Tue, 30 Jun 2020 01:19:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:19:52: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Tue, 30 Jun 2020 01:19:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:19:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:19:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:20:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:20:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:20:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.10_summits.bed INFO @ Tue, 30 Jun 2020 01:20:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:20:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350726/SRX2350726.20_summits.bed INFO @ Tue, 30 Jun 2020 01:20:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling