Job ID = 6498671 SRX = SRX685463 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:03:11 prefetch.2.10.7: 1) Downloading 'SRR1556385'... 2020-06-26T00:03:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:08:06 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:08:06 prefetch.2.10.7: 1) 'SRR1556385' was downloaded successfully Read 45898739 spots for SRR1556385/SRR1556385.sra Written 45898739 spots for SRR1556385/SRR1556385.sra 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: 00:19:06 45898739 reads; of these: 45898739 (100.00%) were unpaired; of these: 2326106 (5.07%) aligned 0 times 29067163 (63.33%) aligned exactly 1 time 14505470 (31.60%) aligned >1 times 94.93% overall alignment rate Time searching: 00:19:06 Overall time: 00:19:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 11612413 / 43572633 = 0.2665 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 @ Fri, 26 Jun 2020 09:39:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.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 @ Fri, 26 Jun 2020 09:39:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:39:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:39:59: 1000000 INFO @ Fri, 26 Jun 2020 09:40:05: 2000000 INFO @ Fri, 26 Jun 2020 09:40:12: 3000000 INFO @ Fri, 26 Jun 2020 09:40:18: 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 @ Fri, 26 Jun 2020 09:40:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.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 @ Fri, 26 Jun 2020 09:40:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:40:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:40:24: 5000000 INFO @ Fri, 26 Jun 2020 09:40:30: 1000000 INFO @ Fri, 26 Jun 2020 09:40:31: 6000000 INFO @ Fri, 26 Jun 2020 09:40:37: 2000000 INFO @ Fri, 26 Jun 2020 09:40:37: 7000000 INFO @ Fri, 26 Jun 2020 09:40:44: 3000000 INFO @ Fri, 26 Jun 2020 09:40:44: 8000000 INFO @ Fri, 26 Jun 2020 09:40:51: 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 @ Fri, 26 Jun 2020 09:40:51: 9000000 INFO @ Fri, 26 Jun 2020 09:40:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.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 @ Fri, 26 Jun 2020 09:40:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:40:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:40:58: 5000000 INFO @ Fri, 26 Jun 2020 09:40:58: 10000000 INFO @ Fri, 26 Jun 2020 09:41:01: 1000000 INFO @ Fri, 26 Jun 2020 09:41:06: 11000000 INFO @ Fri, 26 Jun 2020 09:41:06: 6000000 INFO @ Fri, 26 Jun 2020 09:41:10: 2000000 INFO @ Fri, 26 Jun 2020 09:41:13: 12000000 INFO @ Fri, 26 Jun 2020 09:41:13: 7000000 INFO @ Fri, 26 Jun 2020 09:41:18: 3000000 INFO @ Fri, 26 Jun 2020 09:41:20: 13000000 INFO @ Fri, 26 Jun 2020 09:41:21: 8000000 INFO @ Fri, 26 Jun 2020 09:41:25: 4000000 INFO @ Fri, 26 Jun 2020 09:41:28: 14000000 INFO @ Fri, 26 Jun 2020 09:41:29: 9000000 INFO @ Fri, 26 Jun 2020 09:41:33: 5000000 INFO @ Fri, 26 Jun 2020 09:41:35: 15000000 INFO @ Fri, 26 Jun 2020 09:41:37: 10000000 INFO @ Fri, 26 Jun 2020 09:41:41: 6000000 INFO @ Fri, 26 Jun 2020 09:41:42: 16000000 INFO @ Fri, 26 Jun 2020 09:41:44: 11000000 INFO @ Fri, 26 Jun 2020 09:41:49: 7000000 INFO @ Fri, 26 Jun 2020 09:41:50: 17000000 INFO @ Fri, 26 Jun 2020 09:41:52: 12000000 INFO @ Fri, 26 Jun 2020 09:41:57: 18000000 INFO @ Fri, 26 Jun 2020 09:41:57: 8000000 INFO @ Fri, 26 Jun 2020 09:41:59: 13000000 INFO @ Fri, 26 Jun 2020 09:42:05: 19000000 INFO @ Fri, 26 Jun 2020 09:42:06: 9000000 INFO @ Fri, 26 Jun 2020 09:42:06: 14000000 INFO @ Fri, 26 Jun 2020 09:42:12: 20000000 INFO @ Fri, 26 Jun 2020 09:42:14: 10000000 INFO @ Fri, 26 Jun 2020 09:42:14: 15000000 INFO @ Fri, 26 Jun 2020 09:42:20: 21000000 INFO @ Fri, 26 Jun 2020 09:42:21: 16000000 INFO @ Fri, 26 Jun 2020 09:42:22: 11000000 INFO @ Fri, 26 Jun 2020 09:42:27: 22000000 INFO @ Fri, 26 Jun 2020 09:42:29: 17000000 INFO @ Fri, 26 Jun 2020 09:42:30: 12000000 INFO @ Fri, 26 Jun 2020 09:42:34: 23000000 INFO @ Fri, 26 Jun 2020 09:42:36: 18000000 INFO @ Fri, 26 Jun 2020 09:42:38: 13000000 INFO @ Fri, 26 Jun 2020 09:42:41: 24000000 INFO @ Fri, 26 Jun 2020 09:42:43: 19000000 INFO @ Fri, 26 Jun 2020 09:42:46: 14000000 INFO @ Fri, 26 Jun 2020 09:42:48: 25000000 INFO @ Fri, 26 Jun 2020 09:42:51: 20000000 INFO @ Fri, 26 Jun 2020 09:42:54: 15000000 INFO @ Fri, 26 Jun 2020 09:42:56: 26000000 INFO @ Fri, 26 Jun 2020 09:42:58: 21000000 INFO @ Fri, 26 Jun 2020 09:43:03: 16000000 INFO @ Fri, 26 Jun 2020 09:43:03: 27000000 INFO @ Fri, 26 Jun 2020 09:43:05: 22000000 INFO @ Fri, 26 Jun 2020 09:43:10: 28000000 INFO @ Fri, 26 Jun 2020 09:43:11: 17000000 INFO @ Fri, 26 Jun 2020 09:43:13: 23000000 INFO @ Fri, 26 Jun 2020 09:43:17: 29000000 INFO @ Fri, 26 Jun 2020 09:43:19: 18000000 INFO @ Fri, 26 Jun 2020 09:43:20: 24000000 INFO @ Fri, 26 Jun 2020 09:43:24: 30000000 INFO @ Fri, 26 Jun 2020 09:43:27: 19000000 INFO @ Fri, 26 Jun 2020 09:43:28: 25000000 INFO @ Fri, 26 Jun 2020 09:43:31: 31000000 INFO @ Fri, 26 Jun 2020 09:43:35: 26000000 INFO @ Fri, 26 Jun 2020 09:43:35: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:43:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:43:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:43:38: #1 total tags in treatment: 31960220 INFO @ Fri, 26 Jun 2020 09:43:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:43:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:43:39: #1 tags after filtering in treatment: 31960220 INFO @ Fri, 26 Jun 2020 09:43:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:43:39: #1 finished! INFO @ Fri, 26 Jun 2020 09:43:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:43:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:43:41: #2 number of paired peaks: 664 WARNING @ Fri, 26 Jun 2020 09:43:41: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Fri, 26 Jun 2020 09:43:41: start model_add_line... INFO @ Fri, 26 Jun 2020 09:43:41: start X-correlation... INFO @ Fri, 26 Jun 2020 09:43:41: end of X-cor INFO @ Fri, 26 Jun 2020 09:43:41: #2 finished! INFO @ Fri, 26 Jun 2020 09:43:41: #2 predicted fragment length is 151 bps INFO @ Fri, 26 Jun 2020 09:43:41: #2 alternative fragment length(s) may be 4,151 bps INFO @ Fri, 26 Jun 2020 09:43:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.05_model.r INFO @ Fri, 26 Jun 2020 09:43:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:43:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:43:42: 27000000 INFO @ Fri, 26 Jun 2020 09:43:43: 21000000 INFO @ Fri, 26 Jun 2020 09:43:49: 28000000 INFO @ Fri, 26 Jun 2020 09:43:51: 22000000 INFO @ Fri, 26 Jun 2020 09:43:56: 29000000 INFO @ Fri, 26 Jun 2020 09:44:00: 23000000 INFO @ Fri, 26 Jun 2020 09:44:03: 30000000 INFO @ Fri, 26 Jun 2020 09:44:08: 24000000 INFO @ Fri, 26 Jun 2020 09:44:10: 31000000 INFO @ Fri, 26 Jun 2020 09:44:16: 25000000 INFO @ Fri, 26 Jun 2020 09:44:18: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:44:18: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:44:18: #1 total tags in treatment: 31960220 INFO @ Fri, 26 Jun 2020 09:44:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:44:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:44:18: #1 tags after filtering in treatment: 31960220 INFO @ Fri, 26 Jun 2020 09:44:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:44:18: #1 finished! INFO @ Fri, 26 Jun 2020 09:44:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:44:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:44:21: #2 number of paired peaks: 664 WARNING @ Fri, 26 Jun 2020 09:44:21: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Fri, 26 Jun 2020 09:44:21: start model_add_line... INFO @ Fri, 26 Jun 2020 09:44:21: start X-correlation... INFO @ Fri, 26 Jun 2020 09:44:21: end of X-cor INFO @ Fri, 26 Jun 2020 09:44:21: #2 finished! INFO @ Fri, 26 Jun 2020 09:44:21: #2 predicted fragment length is 151 bps INFO @ Fri, 26 Jun 2020 09:44:21: #2 alternative fragment length(s) may be 4,151 bps INFO @ Fri, 26 Jun 2020 09:44:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.10_model.r INFO @ Fri, 26 Jun 2020 09:44:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:44:23: 26000000 INFO @ Fri, 26 Jun 2020 09:44:30: 27000000 INFO @ Fri, 26 Jun 2020 09:44:38: 28000000 INFO @ Fri, 26 Jun 2020 09:44:45: 29000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:44:53: 30000000 INFO @ Fri, 26 Jun 2020 09:44:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:45:00: 31000000 INFO @ Fri, 26 Jun 2020 09:45:07: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:45:07: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:45:07: #1 total tags in treatment: 31960220 INFO @ Fri, 26 Jun 2020 09:45:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:45:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:45:08: #1 tags after filtering in treatment: 31960220 INFO @ Fri, 26 Jun 2020 09:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:45:08: #1 finished! INFO @ Fri, 26 Jun 2020 09:45:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:45:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:45:10: #2 number of paired peaks: 664 WARNING @ Fri, 26 Jun 2020 09:45:10: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Fri, 26 Jun 2020 09:45:10: start model_add_line... INFO @ Fri, 26 Jun 2020 09:45:10: start X-correlation... INFO @ Fri, 26 Jun 2020 09:45:10: end of X-cor INFO @ Fri, 26 Jun 2020 09:45:10: #2 finished! INFO @ Fri, 26 Jun 2020 09:45:10: #2 predicted fragment length is 151 bps INFO @ Fri, 26 Jun 2020 09:45:10: #2 alternative fragment length(s) may be 4,151 bps INFO @ Fri, 26 Jun 2020 09:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.20_model.r INFO @ Fri, 26 Jun 2020 09:45:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:45:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:45:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:45:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:45:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.05_summits.bed INFO @ Fri, 26 Jun 2020 09:45:30: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12465 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:45:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:46:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:46:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:46:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.10_summits.bed INFO @ Fri, 26 Jun 2020 09:46:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10114 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:46:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:46:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:46:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:46:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX685463/SRX685463.20_summits.bed INFO @ Fri, 26 Jun 2020 09:46:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6737 records, 4 fields): 8 millis CompletedMACS2peakCalling