Job ID = 6626712 SRX = ERX088869 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: 00:27:31 149789918 reads; of these: 149789918 (100.00%) were unpaired; of these: 26908001 (17.96%) aligned 0 times 102712665 (68.57%) aligned exactly 1 time 20169252 (13.47%) aligned >1 times 82.04% overall alignment rate Time searching: 00:27:31 Overall time: 00:27:31 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 52 files... [bam_rmdupse_core] 82241356 / 122881917 = 0.6693 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, 14 Jul 2020 09:14:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.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, 14 Jul 2020 09:14:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:14:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:14:04: 1000000 INFO @ Tue, 14 Jul 2020 09:14:09: 2000000 INFO @ Tue, 14 Jul 2020 09:14:14: 3000000 INFO @ Tue, 14 Jul 2020 09:14:19: 4000000 INFO @ Tue, 14 Jul 2020 09:14:24: 5000000 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, 14 Jul 2020 09:14:29: 6000000 INFO @ Tue, 14 Jul 2020 09:14:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.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, 14 Jul 2020 09:14:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:14:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:14:34: 7000000 INFO @ Tue, 14 Jul 2020 09:14:35: 1000000 INFO @ Tue, 14 Jul 2020 09:14:39: 8000000 INFO @ Tue, 14 Jul 2020 09:14:40: 2000000 INFO @ Tue, 14 Jul 2020 09:14:44: 9000000 INFO @ Tue, 14 Jul 2020 09:14:45: 3000000 INFO @ Tue, 14 Jul 2020 09:14:49: 10000000 INFO @ Tue, 14 Jul 2020 09:14:50: 4000000 INFO @ Tue, 14 Jul 2020 09:14:54: 11000000 INFO @ Tue, 14 Jul 2020 09:14:55: 5000000 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, 14 Jul 2020 09:14:59: 12000000 INFO @ Tue, 14 Jul 2020 09:15:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.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, 14 Jul 2020 09:15:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:15:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:15:00: 6000000 INFO @ Tue, 14 Jul 2020 09:15:04: 13000000 INFO @ Tue, 14 Jul 2020 09:15:05: 7000000 INFO @ Tue, 14 Jul 2020 09:15:06: 1000000 INFO @ Tue, 14 Jul 2020 09:15:09: 14000000 INFO @ Tue, 14 Jul 2020 09:15:11: 8000000 INFO @ Tue, 14 Jul 2020 09:15:12: 2000000 INFO @ Tue, 14 Jul 2020 09:15:14: 15000000 INFO @ Tue, 14 Jul 2020 09:15:16: 9000000 INFO @ Tue, 14 Jul 2020 09:15:18: 3000000 INFO @ Tue, 14 Jul 2020 09:15:19: 16000000 INFO @ Tue, 14 Jul 2020 09:15:21: 10000000 INFO @ Tue, 14 Jul 2020 09:15:24: 4000000 INFO @ Tue, 14 Jul 2020 09:15:25: 17000000 INFO @ Tue, 14 Jul 2020 09:15:26: 11000000 INFO @ Tue, 14 Jul 2020 09:15:29: 5000000 INFO @ Tue, 14 Jul 2020 09:15:30: 18000000 INFO @ Tue, 14 Jul 2020 09:15:31: 12000000 INFO @ Tue, 14 Jul 2020 09:15:35: 19000000 INFO @ Tue, 14 Jul 2020 09:15:35: 6000000 INFO @ Tue, 14 Jul 2020 09:15:37: 13000000 INFO @ Tue, 14 Jul 2020 09:15:40: 20000000 INFO @ Tue, 14 Jul 2020 09:15:41: 7000000 INFO @ Tue, 14 Jul 2020 09:15:42: 14000000 INFO @ Tue, 14 Jul 2020 09:15:45: 21000000 INFO @ Tue, 14 Jul 2020 09:15:47: 15000000 INFO @ Tue, 14 Jul 2020 09:15:47: 8000000 INFO @ Tue, 14 Jul 2020 09:15:50: 22000000 INFO @ Tue, 14 Jul 2020 09:15:52: 16000000 INFO @ Tue, 14 Jul 2020 09:15:53: 9000000 INFO @ Tue, 14 Jul 2020 09:15:56: 23000000 INFO @ Tue, 14 Jul 2020 09:15:57: 17000000 INFO @ Tue, 14 Jul 2020 09:15:59: 10000000 INFO @ Tue, 14 Jul 2020 09:16:01: 24000000 INFO @ Tue, 14 Jul 2020 09:16:02: 18000000 INFO @ Tue, 14 Jul 2020 09:16:05: 11000000 INFO @ Tue, 14 Jul 2020 09:16:06: 25000000 INFO @ Tue, 14 Jul 2020 09:16:08: 19000000 INFO @ Tue, 14 Jul 2020 09:16:11: 26000000 INFO @ Tue, 14 Jul 2020 09:16:11: 12000000 INFO @ Tue, 14 Jul 2020 09:16:13: 20000000 INFO @ Tue, 14 Jul 2020 09:16:16: 27000000 INFO @ Tue, 14 Jul 2020 09:16:17: 13000000 INFO @ Tue, 14 Jul 2020 09:16:18: 21000000 INFO @ Tue, 14 Jul 2020 09:16:21: 28000000 INFO @ Tue, 14 Jul 2020 09:16:23: 22000000 INFO @ Tue, 14 Jul 2020 09:16:23: 14000000 INFO @ Tue, 14 Jul 2020 09:16:27: 29000000 INFO @ Tue, 14 Jul 2020 09:16:28: 23000000 INFO @ Tue, 14 Jul 2020 09:16:29: 15000000 INFO @ Tue, 14 Jul 2020 09:16:32: 30000000 INFO @ Tue, 14 Jul 2020 09:16:34: 24000000 INFO @ Tue, 14 Jul 2020 09:16:35: 16000000 INFO @ Tue, 14 Jul 2020 09:16:37: 31000000 INFO @ Tue, 14 Jul 2020 09:16:39: 25000000 INFO @ Tue, 14 Jul 2020 09:16:41: 17000000 INFO @ Tue, 14 Jul 2020 09:16:42: 32000000 INFO @ Tue, 14 Jul 2020 09:16:44: 26000000 INFO @ Tue, 14 Jul 2020 09:16:47: 18000000 INFO @ Tue, 14 Jul 2020 09:16:47: 33000000 INFO @ Tue, 14 Jul 2020 09:16:49: 27000000 INFO @ Tue, 14 Jul 2020 09:16:53: 34000000 INFO @ Tue, 14 Jul 2020 09:16:53: 19000000 INFO @ Tue, 14 Jul 2020 09:16:54: 28000000 INFO @ Tue, 14 Jul 2020 09:16:58: 35000000 INFO @ Tue, 14 Jul 2020 09:16:59: 20000000 INFO @ Tue, 14 Jul 2020 09:16:59: 29000000 INFO @ Tue, 14 Jul 2020 09:17:03: 36000000 INFO @ Tue, 14 Jul 2020 09:17:05: 30000000 INFO @ Tue, 14 Jul 2020 09:17:05: 21000000 INFO @ Tue, 14 Jul 2020 09:17:08: 37000000 INFO @ Tue, 14 Jul 2020 09:17:10: 31000000 INFO @ Tue, 14 Jul 2020 09:17:11: 22000000 INFO @ Tue, 14 Jul 2020 09:17:14: 38000000 INFO @ Tue, 14 Jul 2020 09:17:15: 32000000 INFO @ Tue, 14 Jul 2020 09:17:17: 23000000 INFO @ Tue, 14 Jul 2020 09:17:19: 39000000 INFO @ Tue, 14 Jul 2020 09:17:20: 33000000 INFO @ Tue, 14 Jul 2020 09:17:23: 24000000 INFO @ Tue, 14 Jul 2020 09:17:24: 40000000 INFO @ Tue, 14 Jul 2020 09:17:26: 34000000 INFO @ Tue, 14 Jul 2020 09:17:28: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 09:17:28: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 09:17:28: #1 total tags in treatment: 40640561 INFO @ Tue, 14 Jul 2020 09:17:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:17:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:17:29: #1 tags after filtering in treatment: 40640488 INFO @ Tue, 14 Jul 2020 09:17:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:17:29: #1 finished! INFO @ Tue, 14 Jul 2020 09:17:29: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:17:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:17:29: 25000000 INFO @ Tue, 14 Jul 2020 09:17:31: #2 number of paired peaks: 479 WARNING @ Tue, 14 Jul 2020 09:17:31: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Tue, 14 Jul 2020 09:17:31: start model_add_line... INFO @ Tue, 14 Jul 2020 09:17:32: start X-correlation... INFO @ Tue, 14 Jul 2020 09:17:32: end of X-cor INFO @ Tue, 14 Jul 2020 09:17:32: #2 finished! INFO @ Tue, 14 Jul 2020 09:17:32: #2 predicted fragment length is 40 bps INFO @ Tue, 14 Jul 2020 09:17:32: #2 alternative fragment length(s) may be 3,40 bps INFO @ Tue, 14 Jul 2020 09:17:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.05_model.r WARNING @ Tue, 14 Jul 2020 09:17:32: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:17:32: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Tue, 14 Jul 2020 09:17:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:17:32: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:17:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:17:32: 35000000 INFO @ Tue, 14 Jul 2020 09:17:35: 26000000 INFO @ Tue, 14 Jul 2020 09:17:38: 36000000 INFO @ Tue, 14 Jul 2020 09:17:41: 27000000 INFO @ Tue, 14 Jul 2020 09:17:44: 37000000 INFO @ Tue, 14 Jul 2020 09:17:47: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:17:50: 38000000 INFO @ Tue, 14 Jul 2020 09:17:53: 29000000 INFO @ Tue, 14 Jul 2020 09:17:56: 39000000 INFO @ Tue, 14 Jul 2020 09:17:59: 30000000 INFO @ Tue, 14 Jul 2020 09:18:01: 40000000 INFO @ Tue, 14 Jul 2020 09:18:05: 31000000 INFO @ Tue, 14 Jul 2020 09:18:05: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 09:18:05: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 09:18:05: #1 total tags in treatment: 40640561 INFO @ Tue, 14 Jul 2020 09:18:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:18:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:18:06: #1 tags after filtering in treatment: 40640488 INFO @ Tue, 14 Jul 2020 09:18:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:18:06: #1 finished! INFO @ Tue, 14 Jul 2020 09:18:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:18:09: #2 number of paired peaks: 479 WARNING @ Tue, 14 Jul 2020 09:18:09: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Tue, 14 Jul 2020 09:18:09: start model_add_line... INFO @ Tue, 14 Jul 2020 09:18:09: start X-correlation... INFO @ Tue, 14 Jul 2020 09:18:09: end of X-cor INFO @ Tue, 14 Jul 2020 09:18:09: #2 finished! INFO @ Tue, 14 Jul 2020 09:18:09: #2 predicted fragment length is 40 bps INFO @ Tue, 14 Jul 2020 09:18:09: #2 alternative fragment length(s) may be 3,40 bps INFO @ Tue, 14 Jul 2020 09:18:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.10_model.r WARNING @ Tue, 14 Jul 2020 09:18:09: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:18:09: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Tue, 14 Jul 2020 09:18:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:18:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:18:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:18:11: 32000000 INFO @ Tue, 14 Jul 2020 09:18:17: 33000000 INFO @ Tue, 14 Jul 2020 09:18:23: 34000000 INFO @ Tue, 14 Jul 2020 09:18:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:18:29: 35000000 INFO @ Tue, 14 Jul 2020 09:18:35: 36000000 INFO @ Tue, 14 Jul 2020 09:18:41: 37000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:18:47: 38000000 INFO @ Tue, 14 Jul 2020 09:18:53: 39000000 INFO @ Tue, 14 Jul 2020 09:18:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:18:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:18:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.05_summits.bed INFO @ Tue, 14 Jul 2020 09:18:58: Done! pass1 - making usageList (531 chroms): 6 millis INFO @ Tue, 14 Jul 2020 09:18:59: 40000000 pass2 - checking and writing primary data (37739 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:19:03: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 09:19:03: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 09:19:03: #1 total tags in treatment: 40640561 INFO @ Tue, 14 Jul 2020 09:19:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:19:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:19:03: #1 tags after filtering in treatment: 40640488 INFO @ Tue, 14 Jul 2020 09:19:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:19:03: #1 finished! INFO @ Tue, 14 Jul 2020 09:19:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:19:06: #2 number of paired peaks: 479 WARNING @ Tue, 14 Jul 2020 09:19:06: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Tue, 14 Jul 2020 09:19:06: start model_add_line... INFO @ Tue, 14 Jul 2020 09:19:06: start X-correlation... INFO @ Tue, 14 Jul 2020 09:19:06: end of X-cor INFO @ Tue, 14 Jul 2020 09:19:06: #2 finished! INFO @ Tue, 14 Jul 2020 09:19:06: #2 predicted fragment length is 40 bps INFO @ Tue, 14 Jul 2020 09:19:06: #2 alternative fragment length(s) may be 3,40 bps INFO @ Tue, 14 Jul 2020 09:19:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.20_model.r WARNING @ Tue, 14 Jul 2020 09:19:06: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:19:06: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Tue, 14 Jul 2020 09:19:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:19:06: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:19:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:19:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:19:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:19:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:19:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.10_summits.bed INFO @ Tue, 14 Jul 2020 09:19:37: Done! pass1 - making usageList (408 chroms): 2 millis pass2 - checking and writing primary data (17174 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:20:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:20:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:20:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:20:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX088869/ERX088869.20_summits.bed INFO @ Tue, 14 Jul 2020 09:20:29: Done! pass1 - making usageList (179 chroms): 1 millis pass2 - checking and writing primary data (4536 records, 4 fields): 9 millis CompletedMACS2peakCalling