Job ID = 6530060 SRX = SRX6962950 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:19:27 50479123 reads; of these: 50479123 (100.00%) were unpaired; of these: 4680953 (9.27%) aligned 0 times 34203249 (67.76%) aligned exactly 1 time 11594921 (22.97%) aligned >1 times 90.73% overall alignment rate Time searching: 00:19:27 Overall time: 00:19:27 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 20 files... [bam_rmdupse_core] 13306478 / 45798170 = 0.2905 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 03:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.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 03:52:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:52:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:52:26: 1000000 INFO @ Tue, 30 Jun 2020 03:52:31: 2000000 INFO @ Tue, 30 Jun 2020 03:52:38: 3000000 INFO @ Tue, 30 Jun 2020 03:52:44: 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 03:52:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.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 03:52:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:52:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:52:50: 5000000 INFO @ Tue, 30 Jun 2020 03:52:56: 1000000 INFO @ Tue, 30 Jun 2020 03:52:56: 6000000 INFO @ Tue, 30 Jun 2020 03:53:02: 2000000 INFO @ Tue, 30 Jun 2020 03:53:02: 7000000 INFO @ Tue, 30 Jun 2020 03:53:08: 3000000 INFO @ Tue, 30 Jun 2020 03:53:08: 8000000 INFO @ Tue, 30 Jun 2020 03:53:14: 4000000 INFO @ Tue, 30 Jun 2020 03:53:15: 9000000 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 03:53:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.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 03:53:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:53:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:53:20: 5000000 INFO @ Tue, 30 Jun 2020 03:53:21: 10000000 INFO @ Tue, 30 Jun 2020 03:53:26: 1000000 INFO @ Tue, 30 Jun 2020 03:53:26: 6000000 INFO @ Tue, 30 Jun 2020 03:53:28: 11000000 INFO @ Tue, 30 Jun 2020 03:53:33: 7000000 INFO @ Tue, 30 Jun 2020 03:53:33: 2000000 INFO @ Tue, 30 Jun 2020 03:53:35: 12000000 INFO @ Tue, 30 Jun 2020 03:53:39: 8000000 INFO @ Tue, 30 Jun 2020 03:53:40: 3000000 INFO @ Tue, 30 Jun 2020 03:53:42: 13000000 INFO @ Tue, 30 Jun 2020 03:53:45: 9000000 INFO @ Tue, 30 Jun 2020 03:53:47: 4000000 INFO @ Tue, 30 Jun 2020 03:53:49: 14000000 INFO @ Tue, 30 Jun 2020 03:53:51: 10000000 INFO @ Tue, 30 Jun 2020 03:53:54: 5000000 INFO @ Tue, 30 Jun 2020 03:53:56: 15000000 INFO @ Tue, 30 Jun 2020 03:53:57: 11000000 INFO @ Tue, 30 Jun 2020 03:54:01: 6000000 INFO @ Tue, 30 Jun 2020 03:54:03: 16000000 INFO @ Tue, 30 Jun 2020 03:54:03: 12000000 INFO @ Tue, 30 Jun 2020 03:54:08: 7000000 INFO @ Tue, 30 Jun 2020 03:54:09: 17000000 INFO @ Tue, 30 Jun 2020 03:54:10: 13000000 INFO @ Tue, 30 Jun 2020 03:54:15: 8000000 INFO @ Tue, 30 Jun 2020 03:54:16: 14000000 INFO @ Tue, 30 Jun 2020 03:54:16: 18000000 INFO @ Tue, 30 Jun 2020 03:54:22: 9000000 INFO @ Tue, 30 Jun 2020 03:54:22: 15000000 INFO @ Tue, 30 Jun 2020 03:54:23: 19000000 INFO @ Tue, 30 Jun 2020 03:54:28: 16000000 INFO @ Tue, 30 Jun 2020 03:54:28: 10000000 INFO @ Tue, 30 Jun 2020 03:54:30: 20000000 INFO @ Tue, 30 Jun 2020 03:54:34: 17000000 INFO @ Tue, 30 Jun 2020 03:54:35: 11000000 INFO @ Tue, 30 Jun 2020 03:54:37: 21000000 INFO @ Tue, 30 Jun 2020 03:54:40: 18000000 INFO @ Tue, 30 Jun 2020 03:54:42: 12000000 INFO @ Tue, 30 Jun 2020 03:54:44: 22000000 INFO @ Tue, 30 Jun 2020 03:54:46: 19000000 INFO @ Tue, 30 Jun 2020 03:54:49: 13000000 INFO @ Tue, 30 Jun 2020 03:54:51: 23000000 INFO @ Tue, 30 Jun 2020 03:54:52: 20000000 INFO @ Tue, 30 Jun 2020 03:54:56: 14000000 INFO @ Tue, 30 Jun 2020 03:54:58: 24000000 INFO @ Tue, 30 Jun 2020 03:54:58: 21000000 INFO @ Tue, 30 Jun 2020 03:55:03: 15000000 INFO @ Tue, 30 Jun 2020 03:55:04: 22000000 INFO @ Tue, 30 Jun 2020 03:55:04: 25000000 INFO @ Tue, 30 Jun 2020 03:55:10: 16000000 INFO @ Tue, 30 Jun 2020 03:55:10: 23000000 INFO @ Tue, 30 Jun 2020 03:55:12: 26000000 INFO @ Tue, 30 Jun 2020 03:55:16: 24000000 INFO @ Tue, 30 Jun 2020 03:55:16: 17000000 INFO @ Tue, 30 Jun 2020 03:55:19: 27000000 INFO @ Tue, 30 Jun 2020 03:55:22: 25000000 INFO @ Tue, 30 Jun 2020 03:55:23: 18000000 INFO @ Tue, 30 Jun 2020 03:55:26: 28000000 INFO @ Tue, 30 Jun 2020 03:55:28: 26000000 INFO @ Tue, 30 Jun 2020 03:55:30: 19000000 INFO @ Tue, 30 Jun 2020 03:55:33: 29000000 INFO @ Tue, 30 Jun 2020 03:55:35: 27000000 INFO @ Tue, 30 Jun 2020 03:55:37: 20000000 INFO @ Tue, 30 Jun 2020 03:55:40: 30000000 INFO @ Tue, 30 Jun 2020 03:55:41: 28000000 INFO @ Tue, 30 Jun 2020 03:55:43: 21000000 INFO @ Tue, 30 Jun 2020 03:55:46: 31000000 INFO @ Tue, 30 Jun 2020 03:55:47: 29000000 INFO @ Tue, 30 Jun 2020 03:55:50: 22000000 INFO @ Tue, 30 Jun 2020 03:55:53: 30000000 INFO @ Tue, 30 Jun 2020 03:55:54: 32000000 INFO @ Tue, 30 Jun 2020 03:55:57: 23000000 INFO @ Tue, 30 Jun 2020 03:55:57: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:55:57: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:55:57: #1 total tags in treatment: 32491692 INFO @ Tue, 30 Jun 2020 03:55:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:55:57: #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 03:55:58: #1 tags after filtering in treatment: 32491688 INFO @ Tue, 30 Jun 2020 03:55:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:55:58: #1 finished! INFO @ Tue, 30 Jun 2020 03:55:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:56:00: 31000000 INFO @ Tue, 30 Jun 2020 03:56:01: #2 number of paired peaks: 157 WARNING @ Tue, 30 Jun 2020 03:56:01: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 30 Jun 2020 03:56:01: start model_add_line... INFO @ Tue, 30 Jun 2020 03:56:01: start X-correlation... INFO @ Tue, 30 Jun 2020 03:56:01: end of X-cor INFO @ Tue, 30 Jun 2020 03:56:01: #2 finished! INFO @ Tue, 30 Jun 2020 03:56:01: #2 predicted fragment length is 61 bps INFO @ Tue, 30 Jun 2020 03:56:01: #2 alternative fragment length(s) may be 3,61 bps INFO @ Tue, 30 Jun 2020 03:56:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.05_model.r WARNING @ Tue, 30 Jun 2020 03:56:01: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:56:01: #2 You may need to consider one of the other alternative d(s): 3,61 WARNING @ Tue, 30 Jun 2020 03:56:01: #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 03:56:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:56:03: 24000000 INFO @ Tue, 30 Jun 2020 03:56:06: 32000000 INFO @ Tue, 30 Jun 2020 03:56:09: 25000000 INFO @ Tue, 30 Jun 2020 03:56:09: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:56:09: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:56:09: #1 total tags in treatment: 32491692 INFO @ Tue, 30 Jun 2020 03:56:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:56:09: #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 03:56:10: #1 tags after filtering in treatment: 32491688 INFO @ Tue, 30 Jun 2020 03:56:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:56:10: #1 finished! INFO @ Tue, 30 Jun 2020 03:56:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:56:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:56:12: #2 number of paired peaks: 157 WARNING @ Tue, 30 Jun 2020 03:56:12: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 30 Jun 2020 03:56:12: start model_add_line... INFO @ Tue, 30 Jun 2020 03:56:13: start X-correlation... INFO @ Tue, 30 Jun 2020 03:56:13: end of X-cor INFO @ Tue, 30 Jun 2020 03:56:13: #2 finished! INFO @ Tue, 30 Jun 2020 03:56:13: #2 predicted fragment length is 61 bps INFO @ Tue, 30 Jun 2020 03:56:13: #2 alternative fragment length(s) may be 3,61 bps INFO @ Tue, 30 Jun 2020 03:56:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.10_model.r WARNING @ Tue, 30 Jun 2020 03:56:13: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:56:13: #2 You may need to consider one of the other alternative d(s): 3,61 WARNING @ Tue, 30 Jun 2020 03:56:13: #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 03:56:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:56:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:56:15: 26000000 INFO @ Tue, 30 Jun 2020 03:56:22: 27000000 INFO @ Tue, 30 Jun 2020 03:56:28: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:56:34: 29000000 INFO @ Tue, 30 Jun 2020 03:56:40: 30000000 INFO @ Tue, 30 Jun 2020 03:56:46: 31000000 INFO @ Tue, 30 Jun 2020 03:56:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:56:52: 32000000 INFO @ Tue, 30 Jun 2020 03:56:55: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:56:55: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:56:55: #1 total tags in treatment: 32491692 INFO @ Tue, 30 Jun 2020 03:56:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:56:55: #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 03:56:56: #1 tags after filtering in treatment: 32491688 INFO @ Tue, 30 Jun 2020 03:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:56:56: #1 finished! INFO @ Tue, 30 Jun 2020 03:56:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:56:58: #2 number of paired peaks: 157 WARNING @ Tue, 30 Jun 2020 03:56:58: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 30 Jun 2020 03:56:58: start model_add_line... INFO @ Tue, 30 Jun 2020 03:56:59: start X-correlation... INFO @ Tue, 30 Jun 2020 03:56:59: end of X-cor INFO @ Tue, 30 Jun 2020 03:56:59: #2 finished! INFO @ Tue, 30 Jun 2020 03:56:59: #2 predicted fragment length is 61 bps INFO @ Tue, 30 Jun 2020 03:56:59: #2 alternative fragment length(s) may be 3,61 bps INFO @ Tue, 30 Jun 2020 03:56:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.20_model.r WARNING @ Tue, 30 Jun 2020 03:56:59: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:56:59: #2 You may need to consider one of the other alternative d(s): 3,61 WARNING @ Tue, 30 Jun 2020 03:56:59: #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 03:56:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:56:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:57:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:57:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.05_summits.bed INFO @ Tue, 30 Jun 2020 03:57:15: Done! pass1 - making usageList (834 chroms): 2 millis pass2 - checking and writing primary data (3598 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:57:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:57:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:57:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.10_summits.bed INFO @ Tue, 30 Jun 2020 03:57:24: Done! pass1 - making usageList (739 chroms): 2 millis pass2 - checking and writing primary data (2455 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:57:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:58:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:58:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:58:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6962950/SRX6962950.20_summits.bed INFO @ Tue, 30 Jun 2020 03:58:13: Done! pass1 - making usageList (562 chroms): 2 millis pass2 - checking and writing primary data (1553 records, 4 fields): 38 millis CompletedMACS2peakCalling