Job ID = 6529819 SRX = SRX495202 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:36 17633613 reads; of these: 17633613 (100.00%) were unpaired; of these: 244031 (1.38%) aligned 0 times 11965919 (67.86%) aligned exactly 1 time 5423663 (30.76%) aligned >1 times 98.62% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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 8 files... [bam_rmdupse_core] 4290107 / 17389582 = 0.2467 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 03:12:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.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 03:12:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:31: 1000000 INFO @ Tue, 30 Jun 2020 03:12:38: 2000000 INFO @ Tue, 30 Jun 2020 03:12:46: 3000000 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 03:12:53: 4000000 INFO @ Tue, 30 Jun 2020 03:12:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.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 03:12:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:13:01: 5000000 INFO @ Tue, 30 Jun 2020 03:13:01: 1000000 INFO @ Tue, 30 Jun 2020 03:13:09: 6000000 INFO @ Tue, 30 Jun 2020 03:13:09: 2000000 INFO @ Tue, 30 Jun 2020 03:13:16: 7000000 INFO @ Tue, 30 Jun 2020 03:13:18: 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 03:13:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.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 03:13:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:13:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:13:24: 8000000 INFO @ Tue, 30 Jun 2020 03:13:26: 4000000 INFO @ Tue, 30 Jun 2020 03:13:30: 1000000 INFO @ Tue, 30 Jun 2020 03:13:32: 9000000 INFO @ Tue, 30 Jun 2020 03:13:34: 5000000 INFO @ Tue, 30 Jun 2020 03:13:37: 2000000 INFO @ Tue, 30 Jun 2020 03:13:40: 10000000 INFO @ Tue, 30 Jun 2020 03:13:42: 6000000 INFO @ Tue, 30 Jun 2020 03:13:44: 3000000 INFO @ Tue, 30 Jun 2020 03:13:49: 11000000 INFO @ Tue, 30 Jun 2020 03:13:50: 7000000 INFO @ Tue, 30 Jun 2020 03:13:51: 4000000 INFO @ Tue, 30 Jun 2020 03:13:58: 12000000 INFO @ Tue, 30 Jun 2020 03:13:58: 5000000 INFO @ Tue, 30 Jun 2020 03:13:58: 8000000 INFO @ Tue, 30 Jun 2020 03:14:05: 6000000 INFO @ Tue, 30 Jun 2020 03:14:06: 13000000 INFO @ Tue, 30 Jun 2020 03:14:07: 9000000 INFO @ Tue, 30 Jun 2020 03:14:07: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 03:14:07: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 03:14:07: #1 total tags in treatment: 13099475 INFO @ Tue, 30 Jun 2020 03:14:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:14:07: #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 03:14:08: #1 tags after filtering in treatment: 13099471 INFO @ Tue, 30 Jun 2020 03:14:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:14:08: #1 finished! INFO @ Tue, 30 Jun 2020 03:14:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:14:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:14:09: #2 number of paired peaks: 262 WARNING @ Tue, 30 Jun 2020 03:14:09: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Tue, 30 Jun 2020 03:14:09: start model_add_line... INFO @ Tue, 30 Jun 2020 03:14:09: start X-correlation... INFO @ Tue, 30 Jun 2020 03:14:09: end of X-cor INFO @ Tue, 30 Jun 2020 03:14:09: #2 finished! INFO @ Tue, 30 Jun 2020 03:14:09: #2 predicted fragment length is 29 bps INFO @ Tue, 30 Jun 2020 03:14:09: #2 alternative fragment length(s) may be 3,29,40 bps INFO @ Tue, 30 Jun 2020 03:14:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.05_model.r WARNING @ Tue, 30 Jun 2020 03:14:09: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:14:09: #2 You may need to consider one of the other alternative d(s): 3,29,40 WARNING @ Tue, 30 Jun 2020 03:14:09: #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 03:14:09: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:14:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:14:12: 7000000 INFO @ Tue, 30 Jun 2020 03:14:14: 10000000 INFO @ Tue, 30 Jun 2020 03:14:20: 8000000 INFO @ Tue, 30 Jun 2020 03:14:23: 11000000 INFO @ Tue, 30 Jun 2020 03:14:27: 9000000 INFO @ Tue, 30 Jun 2020 03:14:31: 12000000 INFO @ Tue, 30 Jun 2020 03:14:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:14:34: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:14:39: 13000000 INFO @ Tue, 30 Jun 2020 03:14:40: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 03:14:40: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 03:14:40: #1 total tags in treatment: 13099475 INFO @ Tue, 30 Jun 2020 03:14:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:14:40: #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 03:14:41: #1 tags after filtering in treatment: 13099471 INFO @ Tue, 30 Jun 2020 03:14:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:14:41: #1 finished! INFO @ Tue, 30 Jun 2020 03:14:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:14:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:14:42: 11000000 INFO @ Tue, 30 Jun 2020 03:14:42: #2 number of paired peaks: 262 WARNING @ Tue, 30 Jun 2020 03:14:42: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Tue, 30 Jun 2020 03:14:42: start model_add_line... INFO @ Tue, 30 Jun 2020 03:14:42: start X-correlation... INFO @ Tue, 30 Jun 2020 03:14:42: end of X-cor INFO @ Tue, 30 Jun 2020 03:14:42: #2 finished! INFO @ Tue, 30 Jun 2020 03:14:42: #2 predicted fragment length is 29 bps INFO @ Tue, 30 Jun 2020 03:14:42: #2 alternative fragment length(s) may be 3,29,40 bps INFO @ Tue, 30 Jun 2020 03:14:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.10_model.r WARNING @ Tue, 30 Jun 2020 03:14:42: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:14:42: #2 You may need to consider one of the other alternative d(s): 3,29,40 WARNING @ Tue, 30 Jun 2020 03:14:42: #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 03:14:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:14:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:14:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.05_summits.bed INFO @ Tue, 30 Jun 2020 03:14:45: Done! pass1 - making usageList (516 chroms): 2 millis pass2 - checking and writing primary data (2323 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:14:49: 12000000 INFO @ Tue, 30 Jun 2020 03:14:56: 13000000 INFO @ Tue, 30 Jun 2020 03:14:57: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 03:14:57: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 03:14:57: #1 total tags in treatment: 13099475 INFO @ Tue, 30 Jun 2020 03:14:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:14:57: #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 03:14:57: #1 tags after filtering in treatment: 13099471 INFO @ Tue, 30 Jun 2020 03:14:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:14:57: #1 finished! INFO @ Tue, 30 Jun 2020 03:14:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:14:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:14:58: #2 number of paired peaks: 262 WARNING @ Tue, 30 Jun 2020 03:14:58: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Tue, 30 Jun 2020 03:14:58: start model_add_line... INFO @ Tue, 30 Jun 2020 03:14:58: start X-correlation... INFO @ Tue, 30 Jun 2020 03:14:58: end of X-cor INFO @ Tue, 30 Jun 2020 03:14:58: #2 finished! INFO @ Tue, 30 Jun 2020 03:14:58: #2 predicted fragment length is 29 bps INFO @ Tue, 30 Jun 2020 03:14:58: #2 alternative fragment length(s) may be 3,29,40 bps INFO @ Tue, 30 Jun 2020 03:14:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.20_model.r WARNING @ Tue, 30 Jun 2020 03:14:58: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:14:58: #2 You may need to consider one of the other alternative d(s): 3,29,40 WARNING @ Tue, 30 Jun 2020 03:14:58: #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 03:14:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:14:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:15:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:15:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:15:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:15:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.10_summits.bed INFO @ Tue, 30 Jun 2020 03:15:18: Done! pass1 - making usageList (257 chroms): 1 millis pass2 - checking and writing primary data (532 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:15:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:15:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:15:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:15:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495202/SRX495202.20_summits.bed INFO @ Tue, 30 Jun 2020 03:15:34: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (120 records, 4 fields): 5 millis CompletedMACS2peakCalling