Job ID = 6529653 SRX = SRX3723041 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: 00:19:27 51245602 reads; of these: 51245602 (100.00%) were unpaired; of these: 4932607 (9.63%) aligned 0 times 34769491 (67.85%) aligned exactly 1 time 11543504 (22.53%) aligned >1 times 90.37% overall alignment rate Time searching: 00:19:28 Overall time: 00:19:28 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] 13950918 / 46312995 = 0.3012 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 03:44:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.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 03:44:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:44:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:45:05: 1000000 INFO @ Tue, 30 Jun 2020 03:45:15: 2000000 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 03:45:25: 3000000 INFO @ Tue, 30 Jun 2020 03:45:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.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 03:45:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:45:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:45:34: 4000000 INFO @ Tue, 30 Jun 2020 03:45:35: 1000000 INFO @ Tue, 30 Jun 2020 03:45:44: 2000000 INFO @ Tue, 30 Jun 2020 03:45:44: 5000000 INFO @ Tue, 30 Jun 2020 03:45:52: 3000000 INFO @ Tue, 30 Jun 2020 03:45:53: 6000000 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 03:45:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.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 03:45:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:45:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:46:01: 4000000 INFO @ Tue, 30 Jun 2020 03:46:03: 7000000 INFO @ Tue, 30 Jun 2020 03:46:05: 1000000 INFO @ Tue, 30 Jun 2020 03:46:10: 5000000 INFO @ Tue, 30 Jun 2020 03:46:13: 8000000 INFO @ Tue, 30 Jun 2020 03:46:15: 2000000 INFO @ Tue, 30 Jun 2020 03:46:19: 6000000 INFO @ Tue, 30 Jun 2020 03:46:22: 9000000 INFO @ Tue, 30 Jun 2020 03:46:25: 3000000 INFO @ Tue, 30 Jun 2020 03:46:28: 7000000 INFO @ Tue, 30 Jun 2020 03:46:32: 10000000 INFO @ Tue, 30 Jun 2020 03:46:35: 4000000 INFO @ Tue, 30 Jun 2020 03:46:36: 8000000 INFO @ Tue, 30 Jun 2020 03:46:42: 11000000 INFO @ Tue, 30 Jun 2020 03:46:44: 5000000 INFO @ Tue, 30 Jun 2020 03:46:45: 9000000 INFO @ Tue, 30 Jun 2020 03:46:51: 12000000 INFO @ Tue, 30 Jun 2020 03:46:53: 10000000 INFO @ Tue, 30 Jun 2020 03:46:53: 6000000 INFO @ Tue, 30 Jun 2020 03:47:00: 13000000 INFO @ Tue, 30 Jun 2020 03:47:02: 11000000 INFO @ Tue, 30 Jun 2020 03:47:02: 7000000 INFO @ Tue, 30 Jun 2020 03:47:09: 14000000 INFO @ Tue, 30 Jun 2020 03:47:09: 12000000 INFO @ Tue, 30 Jun 2020 03:47:12: 8000000 INFO @ Tue, 30 Jun 2020 03:47:17: 13000000 INFO @ Tue, 30 Jun 2020 03:47:18: 15000000 INFO @ Tue, 30 Jun 2020 03:47:21: 9000000 INFO @ Tue, 30 Jun 2020 03:47:25: 14000000 INFO @ Tue, 30 Jun 2020 03:47:27: 16000000 INFO @ Tue, 30 Jun 2020 03:47:30: 10000000 INFO @ Tue, 30 Jun 2020 03:47:33: 15000000 INFO @ Tue, 30 Jun 2020 03:47:35: 17000000 INFO @ Tue, 30 Jun 2020 03:47:38: 11000000 INFO @ Tue, 30 Jun 2020 03:47:41: 16000000 INFO @ Tue, 30 Jun 2020 03:47:44: 18000000 INFO @ Tue, 30 Jun 2020 03:47:47: 12000000 INFO @ Tue, 30 Jun 2020 03:47:49: 17000000 INFO @ Tue, 30 Jun 2020 03:47:52: 19000000 INFO @ Tue, 30 Jun 2020 03:47:55: 13000000 INFO @ Tue, 30 Jun 2020 03:47:57: 18000000 INFO @ Tue, 30 Jun 2020 03:48:01: 20000000 INFO @ Tue, 30 Jun 2020 03:48:04: 14000000 INFO @ Tue, 30 Jun 2020 03:48:05: 19000000 INFO @ Tue, 30 Jun 2020 03:48:09: 21000000 INFO @ Tue, 30 Jun 2020 03:48:12: 15000000 INFO @ Tue, 30 Jun 2020 03:48:13: 20000000 INFO @ Tue, 30 Jun 2020 03:48:18: 22000000 INFO @ Tue, 30 Jun 2020 03:48:21: 21000000 INFO @ Tue, 30 Jun 2020 03:48:21: 16000000 INFO @ Tue, 30 Jun 2020 03:48:27: 23000000 INFO @ Tue, 30 Jun 2020 03:48:28: 22000000 INFO @ Tue, 30 Jun 2020 03:48:29: 17000000 INFO @ Tue, 30 Jun 2020 03:48:35: 24000000 INFO @ Tue, 30 Jun 2020 03:48:36: 23000000 INFO @ Tue, 30 Jun 2020 03:48:38: 18000000 INFO @ Tue, 30 Jun 2020 03:48:43: 25000000 INFO @ Tue, 30 Jun 2020 03:48:43: 24000000 INFO @ Tue, 30 Jun 2020 03:48:46: 19000000 INFO @ Tue, 30 Jun 2020 03:48:51: 25000000 INFO @ Tue, 30 Jun 2020 03:48:52: 26000000 INFO @ Tue, 30 Jun 2020 03:48:54: 20000000 INFO @ Tue, 30 Jun 2020 03:48:59: 26000000 INFO @ Tue, 30 Jun 2020 03:49:01: 27000000 INFO @ Tue, 30 Jun 2020 03:49:03: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:49:08: 27000000 INFO @ Tue, 30 Jun 2020 03:49:09: 28000000 INFO @ Tue, 30 Jun 2020 03:49:11: 22000000 INFO @ Tue, 30 Jun 2020 03:49:16: 28000000 INFO @ Tue, 30 Jun 2020 03:49:18: 29000000 INFO @ Tue, 30 Jun 2020 03:49:20: 23000000 INFO @ Tue, 30 Jun 2020 03:49:24: 29000000 INFO @ Tue, 30 Jun 2020 03:49:27: 30000000 INFO @ Tue, 30 Jun 2020 03:49:28: 24000000 INFO @ Tue, 30 Jun 2020 03:49:31: 30000000 INFO @ Tue, 30 Jun 2020 03:49:35: 31000000 INFO @ Tue, 30 Jun 2020 03:49:37: 25000000 INFO @ Tue, 30 Jun 2020 03:49:39: 31000000 INFO @ Tue, 30 Jun 2020 03:49:44: 32000000 INFO @ Tue, 30 Jun 2020 03:49:46: 26000000 INFO @ Tue, 30 Jun 2020 03:49:47: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 03:49:47: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 03:49:47: #1 total tags in treatment: 32362077 INFO @ Tue, 30 Jun 2020 03:49:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:49:47: #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 03:49:48: 32000000 INFO @ Tue, 30 Jun 2020 03:49:48: #1 tags after filtering in treatment: 32362077 INFO @ Tue, 30 Jun 2020 03:49:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:49:48: #1 finished! INFO @ Tue, 30 Jun 2020 03:49:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:49:50: #2 number of paired peaks: 166 WARNING @ Tue, 30 Jun 2020 03:49:50: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 30 Jun 2020 03:49:50: start model_add_line... INFO @ Tue, 30 Jun 2020 03:49:51: start X-correlation... INFO @ Tue, 30 Jun 2020 03:49:51: end of X-cor INFO @ Tue, 30 Jun 2020 03:49:51: #2 finished! INFO @ Tue, 30 Jun 2020 03:49:51: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 03:49:51: #2 alternative fragment length(s) may be 3,67 bps INFO @ Tue, 30 Jun 2020 03:49:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.05_model.r WARNING @ Tue, 30 Jun 2020 03:49:51: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:49:51: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Tue, 30 Jun 2020 03:49:51: #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 03:49:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:49:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:49:51: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 03:49:51: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 03:49:51: #1 total tags in treatment: 32362077 INFO @ Tue, 30 Jun 2020 03:49:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:49:51: #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 03:49:52: #1 tags after filtering in treatment: 32362077 INFO @ Tue, 30 Jun 2020 03:49:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:49:52: #1 finished! INFO @ Tue, 30 Jun 2020 03:49:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:49:54: 27000000 INFO @ Tue, 30 Jun 2020 03:49:54: #2 number of paired peaks: 166 WARNING @ Tue, 30 Jun 2020 03:49:54: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 30 Jun 2020 03:49:54: start model_add_line... INFO @ Tue, 30 Jun 2020 03:49:54: start X-correlation... INFO @ Tue, 30 Jun 2020 03:49:54: end of X-cor INFO @ Tue, 30 Jun 2020 03:49:54: #2 finished! INFO @ Tue, 30 Jun 2020 03:49:54: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 03:49:54: #2 alternative fragment length(s) may be 3,67 bps INFO @ Tue, 30 Jun 2020 03:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.10_model.r WARNING @ Tue, 30 Jun 2020 03:49:54: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:49:54: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Tue, 30 Jun 2020 03:49:54: #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 03:49:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:50:02: 28000000 INFO @ Tue, 30 Jun 2020 03:50:10: 29000000 INFO @ Tue, 30 Jun 2020 03:50:18: 30000000 INFO @ Tue, 30 Jun 2020 03:50:25: 31000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:50:34: 32000000 INFO @ Tue, 30 Jun 2020 03:50:37: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 03:50:37: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 03:50:37: #1 total tags in treatment: 32362077 INFO @ Tue, 30 Jun 2020 03:50:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:50:37: #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 03:50:38: #1 tags after filtering in treatment: 32362077 INFO @ Tue, 30 Jun 2020 03:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:50:38: #1 finished! INFO @ Tue, 30 Jun 2020 03:50:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:50:40: #2 number of paired peaks: 166 WARNING @ Tue, 30 Jun 2020 03:50:40: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 30 Jun 2020 03:50:40: start model_add_line... INFO @ Tue, 30 Jun 2020 03:50:40: start X-correlation... INFO @ Tue, 30 Jun 2020 03:50:40: end of X-cor INFO @ Tue, 30 Jun 2020 03:50:40: #2 finished! INFO @ Tue, 30 Jun 2020 03:50:40: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 03:50:40: #2 alternative fragment length(s) may be 3,67 bps INFO @ Tue, 30 Jun 2020 03:50:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.20_model.r WARNING @ Tue, 30 Jun 2020 03:50:40: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:50:40: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Tue, 30 Jun 2020 03:50:40: #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 03:50:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:50:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:50:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:51:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:51:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.05_summits.bed INFO @ Tue, 30 Jun 2020 03:51:07: Done! pass1 - making usageList (858 chroms): 2 millis pass2 - checking and writing primary data (3778 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:51:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:51:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:51:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.10_summits.bed INFO @ Tue, 30 Jun 2020 03:51:10: Done! pass1 - making usageList (743 chroms): 1 millis pass2 - checking and writing primary data (2468 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:51:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:51:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:51:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:51:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3723041/SRX3723041.20_summits.bed INFO @ Tue, 30 Jun 2020 03:51:56: Done! pass1 - making usageList (576 chroms): 1 millis pass2 - checking and writing primary data (1634 records, 4 fields): 33 millis CompletedMACS2peakCalling