Job ID = 6529597 SRX = SRX335500 Genome = dm6 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:23 27086977 reads; of these: 27086977 (100.00%) were unpaired; of these: 3780857 (13.96%) aligned 0 times 20203899 (74.59%) aligned exactly 1 time 3102221 (11.45%) aligned >1 times 86.04% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 7177974 / 23306120 = 0.3080 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 02:50:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.bam'] # control file = None # effective genome size = 1.20e+08 # 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 02:50:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:50:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:50:32: 1000000 INFO @ Tue, 30 Jun 2020 02:50:38: 2000000 INFO @ Tue, 30 Jun 2020 02:50:43: 3000000 INFO @ Tue, 30 Jun 2020 02:50:49: 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 02:50:55: 5000000 INFO @ Tue, 30 Jun 2020 02:50:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.bam'] # control file = None # effective genome size = 1.20e+08 # 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 02:50:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:50:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:01: 6000000 INFO @ Tue, 30 Jun 2020 02:51:03: 1000000 INFO @ Tue, 30 Jun 2020 02:51:07: 7000000 INFO @ Tue, 30 Jun 2020 02:51:09: 2000000 INFO @ Tue, 30 Jun 2020 02:51:13: 8000000 INFO @ Tue, 30 Jun 2020 02:51:15: 3000000 INFO @ Tue, 30 Jun 2020 02:51:20: 9000000 INFO @ Tue, 30 Jun 2020 02:51:22: 4000000 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 02:51:26: 10000000 INFO @ Tue, 30 Jun 2020 02:51:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.bam'] # control file = None # effective genome size = 1.20e+08 # 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 02:51:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:28: 5000000 INFO @ Tue, 30 Jun 2020 02:51:33: 11000000 INFO @ Tue, 30 Jun 2020 02:51:34: 1000000 INFO @ Tue, 30 Jun 2020 02:51:36: 6000000 INFO @ Tue, 30 Jun 2020 02:51:40: 12000000 INFO @ Tue, 30 Jun 2020 02:51:42: 2000000 INFO @ Tue, 30 Jun 2020 02:51:43: 7000000 INFO @ Tue, 30 Jun 2020 02:51:48: 13000000 INFO @ Tue, 30 Jun 2020 02:51:50: 3000000 INFO @ Tue, 30 Jun 2020 02:51:50: 8000000 INFO @ Tue, 30 Jun 2020 02:51:55: 14000000 INFO @ Tue, 30 Jun 2020 02:51:57: 9000000 INFO @ Tue, 30 Jun 2020 02:51:58: 4000000 INFO @ Tue, 30 Jun 2020 02:52:02: 15000000 INFO @ Tue, 30 Jun 2020 02:52:04: 10000000 INFO @ Tue, 30 Jun 2020 02:52:05: 5000000 INFO @ Tue, 30 Jun 2020 02:52:09: 16000000 INFO @ Tue, 30 Jun 2020 02:52:10: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:52:10: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:52:10: #1 total tags in treatment: 16128146 INFO @ Tue, 30 Jun 2020 02:52:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:10: #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 02:52:11: #1 tags after filtering in treatment: 16128045 INFO @ Tue, 30 Jun 2020 02:52:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:11: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:52:11: 11000000 INFO @ Tue, 30 Jun 2020 02:52:12: #2 number of paired peaks: 135 WARNING @ Tue, 30 Jun 2020 02:52:12: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:12: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:12: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:12: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:12: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:12: #2 predicted fragment length is 11 bps INFO @ Tue, 30 Jun 2020 02:52:12: #2 alternative fragment length(s) may be 3,11,49,64,122,405,458,475,535 bps INFO @ Tue, 30 Jun 2020 02:52:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.05_model.r WARNING @ Tue, 30 Jun 2020 02:52:12: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:12: #2 You may need to consider one of the other alternative d(s): 3,11,49,64,122,405,458,475,535 WARNING @ Tue, 30 Jun 2020 02:52:12: #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 02:52:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:13: 6000000 INFO @ Tue, 30 Jun 2020 02:52:18: 12000000 INFO @ Tue, 30 Jun 2020 02:52:20: 7000000 INFO @ Tue, 30 Jun 2020 02:52:25: 13000000 INFO @ Tue, 30 Jun 2020 02:52:28: 8000000 INFO @ Tue, 30 Jun 2020 02:52:32: 14000000 INFO @ Tue, 30 Jun 2020 02:52:35: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:52:39: 15000000 INFO @ Tue, 30 Jun 2020 02:52:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:52:43: 10000000 INFO @ Tue, 30 Jun 2020 02:52:46: 16000000 INFO @ Tue, 30 Jun 2020 02:52:47: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:52:47: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:52:47: #1 total tags in treatment: 16128146 INFO @ Tue, 30 Jun 2020 02:52:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:47: #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 02:52:48: #1 tags after filtering in treatment: 16128045 INFO @ Tue, 30 Jun 2020 02:52:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:48: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:52:49: #2 number of paired peaks: 135 WARNING @ Tue, 30 Jun 2020 02:52:49: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:49: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:49: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:49: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:49: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:49: #2 predicted fragment length is 11 bps INFO @ Tue, 30 Jun 2020 02:52:49: #2 alternative fragment length(s) may be 3,11,49,64,122,405,458,475,535 bps INFO @ Tue, 30 Jun 2020 02:52:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.10_model.r WARNING @ Tue, 30 Jun 2020 02:52:49: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:49: #2 You may need to consider one of the other alternative d(s): 3,11,49,64,122,405,458,475,535 WARNING @ Tue, 30 Jun 2020 02:52:49: #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 02:52:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:50: 11000000 INFO @ Tue, 30 Jun 2020 02:52:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:52:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:52:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.05_summits.bed INFO @ Tue, 30 Jun 2020 02:52:56: Done! pass1 - making usageList (18 chroms): 0 millis pass2 - checking and writing primary data (39 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:52:57: 12000000 INFO @ Tue, 30 Jun 2020 02:53:04: 13000000 INFO @ Tue, 30 Jun 2020 02:53:11: 14000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:53:18: 15000000 INFO @ Tue, 30 Jun 2020 02:53:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:53:25: 16000000 INFO @ Tue, 30 Jun 2020 02:53:26: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:53:26: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:53:26: #1 total tags in treatment: 16128146 INFO @ Tue, 30 Jun 2020 02:53:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:26: #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 02:53:27: #1 tags after filtering in treatment: 16128045 INFO @ Tue, 30 Jun 2020 02:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:27: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:28: #2 number of paired peaks: 135 WARNING @ Tue, 30 Jun 2020 02:53:28: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:28: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:28: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:28: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:28: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:28: #2 predicted fragment length is 11 bps INFO @ Tue, 30 Jun 2020 02:53:28: #2 alternative fragment length(s) may be 3,11,49,64,122,405,458,475,535 bps INFO @ Tue, 30 Jun 2020 02:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.20_model.r WARNING @ Tue, 30 Jun 2020 02:53:28: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:53:28: #2 You may need to consider one of the other alternative d(s): 3,11,49,64,122,405,458,475,535 WARNING @ Tue, 30 Jun 2020 02:53:28: #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 02:53:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.10_summits.bed INFO @ Tue, 30 Jun 2020 02:53:34: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:53:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335500/SRX335500.20_summits.bed INFO @ Tue, 30 Jun 2020 02:54:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling