Job ID = 6456793 SRX = SRX3981687 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:05:39 prefetch.2.10.7: 1) Downloading 'SRR7050445'... 2020-06-21T11:05:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:07:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:07:25 prefetch.2.10.7: 'SRR7050445' is valid 2020-06-21T11:07:25 prefetch.2.10.7: 1) 'SRR7050445' was downloaded successfully 2020-06-21T11:07:25 prefetch.2.10.7: 'SRR7050445' has 0 unresolved dependencies Read 17170440 spots for SRR7050445/SRR7050445.sra Written 17170440 spots for SRR7050445/SRR7050445.sra 2020-06-21T11:08:27 prefetch.2.10.7: 1) Downloading 'SRR7050446'... 2020-06-21T11:08:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:10:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:10:52 prefetch.2.10.7: 'SRR7050446' is valid 2020-06-21T11:10:52 prefetch.2.10.7: 1) 'SRR7050446' was downloaded successfully 2020-06-21T11:10:52 prefetch.2.10.7: 'SRR7050446' has 0 unresolved dependencies Read 17230833 spots for SRR7050446/SRR7050446.sra Written 17230833 spots for SRR7050446/SRR7050446.sra 2020-06-21T11:11:54 prefetch.2.10.7: 1) Downloading 'SRR7050447'... 2020-06-21T11:11:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:14:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:14:10 prefetch.2.10.7: 'SRR7050447' is valid 2020-06-21T11:14:10 prefetch.2.10.7: 1) 'SRR7050447' was downloaded successfully 2020-06-21T11:14:10 prefetch.2.10.7: 'SRR7050447' has 0 unresolved dependencies Read 17087076 spots for SRR7050447/SRR7050447.sra Written 17087076 spots for SRR7050447/SRR7050447.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: 00:12:07 51488349 reads; of these: 51488349 (100.00%) were unpaired; of these: 1610943 (3.13%) aligned 0 times 41610562 (80.82%) aligned exactly 1 time 8266844 (16.06%) aligned >1 times 96.87% overall alignment rate Time searching: 00:12:07 Overall time: 00:12:07 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 24 files... [bam_rmdupse_core] 11201871 / 49877406 = 0.2246 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 @ Sun, 21 Jun 2020 20:36:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.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 @ Sun, 21 Jun 2020 20:36:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:36:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:36:57: 1000000 INFO @ Sun, 21 Jun 2020 20:37:02: 2000000 INFO @ Sun, 21 Jun 2020 20:37:06: 3000000 INFO @ Sun, 21 Jun 2020 20:37:11: 4000000 INFO @ Sun, 21 Jun 2020 20:37:15: 5000000 INFO @ Sun, 21 Jun 2020 20:37:20: 6000000 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 @ Sun, 21 Jun 2020 20:37:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.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 @ Sun, 21 Jun 2020 20:37:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:37:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:37:24: 7000000 INFO @ Sun, 21 Jun 2020 20:37:27: 1000000 INFO @ Sun, 21 Jun 2020 20:37:29: 8000000 INFO @ Sun, 21 Jun 2020 20:37:32: 2000000 INFO @ Sun, 21 Jun 2020 20:37:33: 9000000 INFO @ Sun, 21 Jun 2020 20:37:36: 3000000 INFO @ Sun, 21 Jun 2020 20:37:38: 10000000 INFO @ Sun, 21 Jun 2020 20:37:41: 4000000 INFO @ Sun, 21 Jun 2020 20:37:43: 11000000 INFO @ Sun, 21 Jun 2020 20:37:45: 5000000 INFO @ Sun, 21 Jun 2020 20:37:47: 12000000 INFO @ Sun, 21 Jun 2020 20:37:50: 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 @ Sun, 21 Jun 2020 20:37:52: 13000000 INFO @ Sun, 21 Jun 2020 20:37:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.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 @ Sun, 21 Jun 2020 20:37:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:37:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:37:55: 7000000 INFO @ Sun, 21 Jun 2020 20:37:57: 14000000 INFO @ Sun, 21 Jun 2020 20:37:57: 1000000 INFO @ Sun, 21 Jun 2020 20:37:59: 8000000 INFO @ Sun, 21 Jun 2020 20:38:01: 15000000 INFO @ Sun, 21 Jun 2020 20:38:02: 2000000 INFO @ Sun, 21 Jun 2020 20:38:04: 9000000 INFO @ Sun, 21 Jun 2020 20:38:06: 16000000 INFO @ Sun, 21 Jun 2020 20:38:06: 3000000 INFO @ Sun, 21 Jun 2020 20:38:08: 10000000 INFO @ Sun, 21 Jun 2020 20:38:11: 17000000 INFO @ Sun, 21 Jun 2020 20:38:11: 4000000 INFO @ Sun, 21 Jun 2020 20:38:13: 11000000 INFO @ Sun, 21 Jun 2020 20:38:16: 18000000 INFO @ Sun, 21 Jun 2020 20:38:16: 5000000 INFO @ Sun, 21 Jun 2020 20:38:18: 12000000 INFO @ Sun, 21 Jun 2020 20:38:20: 6000000 INFO @ Sun, 21 Jun 2020 20:38:20: 19000000 INFO @ Sun, 21 Jun 2020 20:38:22: 13000000 INFO @ Sun, 21 Jun 2020 20:38:25: 7000000 INFO @ Sun, 21 Jun 2020 20:38:25: 20000000 INFO @ Sun, 21 Jun 2020 20:38:27: 14000000 INFO @ Sun, 21 Jun 2020 20:38:29: 8000000 INFO @ Sun, 21 Jun 2020 20:38:30: 21000000 INFO @ Sun, 21 Jun 2020 20:38:31: 15000000 INFO @ Sun, 21 Jun 2020 20:38:34: 9000000 INFO @ Sun, 21 Jun 2020 20:38:35: 22000000 INFO @ Sun, 21 Jun 2020 20:38:36: 16000000 INFO @ Sun, 21 Jun 2020 20:38:38: 10000000 INFO @ Sun, 21 Jun 2020 20:38:39: 23000000 INFO @ Sun, 21 Jun 2020 20:38:41: 17000000 INFO @ Sun, 21 Jun 2020 20:38:43: 11000000 INFO @ Sun, 21 Jun 2020 20:38:44: 24000000 INFO @ Sun, 21 Jun 2020 20:38:46: 18000000 INFO @ Sun, 21 Jun 2020 20:38:48: 12000000 INFO @ Sun, 21 Jun 2020 20:38:49: 25000000 INFO @ Sun, 21 Jun 2020 20:38:50: 19000000 INFO @ Sun, 21 Jun 2020 20:38:52: 13000000 INFO @ Sun, 21 Jun 2020 20:38:53: 26000000 INFO @ Sun, 21 Jun 2020 20:38:55: 20000000 INFO @ Sun, 21 Jun 2020 20:38:57: 14000000 INFO @ Sun, 21 Jun 2020 20:38:58: 27000000 INFO @ Sun, 21 Jun 2020 20:39:00: 21000000 INFO @ Sun, 21 Jun 2020 20:39:02: 15000000 INFO @ Sun, 21 Jun 2020 20:39:03: 28000000 INFO @ Sun, 21 Jun 2020 20:39:05: 22000000 INFO @ Sun, 21 Jun 2020 20:39:07: 16000000 INFO @ Sun, 21 Jun 2020 20:39:08: 29000000 INFO @ Sun, 21 Jun 2020 20:39:09: 23000000 INFO @ Sun, 21 Jun 2020 20:39:11: 17000000 INFO @ Sun, 21 Jun 2020 20:39:13: 30000000 INFO @ Sun, 21 Jun 2020 20:39:14: 24000000 INFO @ Sun, 21 Jun 2020 20:39:16: 18000000 INFO @ Sun, 21 Jun 2020 20:39:17: 31000000 INFO @ Sun, 21 Jun 2020 20:39:19: 25000000 INFO @ Sun, 21 Jun 2020 20:39:21: 19000000 INFO @ Sun, 21 Jun 2020 20:39:22: 32000000 INFO @ Sun, 21 Jun 2020 20:39:23: 26000000 INFO @ Sun, 21 Jun 2020 20:39:25: 20000000 INFO @ Sun, 21 Jun 2020 20:39:27: 33000000 INFO @ Sun, 21 Jun 2020 20:39:28: 27000000 INFO @ Sun, 21 Jun 2020 20:39:30: 21000000 INFO @ Sun, 21 Jun 2020 20:39:32: 34000000 INFO @ Sun, 21 Jun 2020 20:39:33: 28000000 INFO @ Sun, 21 Jun 2020 20:39:35: 22000000 INFO @ Sun, 21 Jun 2020 20:39:36: 35000000 INFO @ Sun, 21 Jun 2020 20:39:37: 29000000 INFO @ Sun, 21 Jun 2020 20:39:40: 23000000 INFO @ Sun, 21 Jun 2020 20:39:41: 36000000 INFO @ Sun, 21 Jun 2020 20:39:42: 30000000 INFO @ Sun, 21 Jun 2020 20:39:44: 24000000 INFO @ Sun, 21 Jun 2020 20:39:46: 37000000 INFO @ Sun, 21 Jun 2020 20:39:47: 31000000 INFO @ Sun, 21 Jun 2020 20:39:49: 25000000 INFO @ Sun, 21 Jun 2020 20:39:50: 38000000 INFO @ Sun, 21 Jun 2020 20:39:51: 32000000 INFO @ Sun, 21 Jun 2020 20:39:54: 26000000 INFO @ Sun, 21 Jun 2020 20:39:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:39:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:39:54: #1 total tags in treatment: 38675535 INFO @ Sun, 21 Jun 2020 20:39:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:39:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:39:55: #1 tags after filtering in treatment: 38675475 INFO @ Sun, 21 Jun 2020 20:39:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:39:55: #1 finished! INFO @ Sun, 21 Jun 2020 20:39:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:39:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:39:56: 33000000 INFO @ Sun, 21 Jun 2020 20:39:57: #2 number of paired peaks: 270 WARNING @ Sun, 21 Jun 2020 20:39:57: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Sun, 21 Jun 2020 20:39:57: start model_add_line... INFO @ Sun, 21 Jun 2020 20:39:57: start X-correlation... INFO @ Sun, 21 Jun 2020 20:39:57: end of X-cor INFO @ Sun, 21 Jun 2020 20:39:57: #2 finished! INFO @ Sun, 21 Jun 2020 20:39:57: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 20:39:57: #2 alternative fragment length(s) may be 3,126 bps INFO @ Sun, 21 Jun 2020 20:39:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.05_model.r INFO @ Sun, 21 Jun 2020 20:39:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:39:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:39:58: 27000000 INFO @ Sun, 21 Jun 2020 20:40:01: 34000000 INFO @ Sun, 21 Jun 2020 20:40:03: 28000000 INFO @ Sun, 21 Jun 2020 20:40:05: 35000000 INFO @ Sun, 21 Jun 2020 20:40:08: 29000000 INFO @ Sun, 21 Jun 2020 20:40:10: 36000000 INFO @ Sun, 21 Jun 2020 20:40:12: 30000000 INFO @ Sun, 21 Jun 2020 20:40:15: 37000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:40:17: 31000000 INFO @ Sun, 21 Jun 2020 20:40:19: 38000000 INFO @ Sun, 21 Jun 2020 20:40:22: 32000000 INFO @ Sun, 21 Jun 2020 20:40:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:40:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:40:23: #1 total tags in treatment: 38675535 INFO @ Sun, 21 Jun 2020 20:40:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:40:24: #1 tags after filtering in treatment: 38675475 INFO @ Sun, 21 Jun 2020 20:40:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:24: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:26: #2 number of paired peaks: 270 WARNING @ Sun, 21 Jun 2020 20:40:26: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Sun, 21 Jun 2020 20:40:26: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:26: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:27: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:27: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:27: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 20:40:27: #2 alternative fragment length(s) may be 3,126 bps INFO @ Sun, 21 Jun 2020 20:40:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.10_model.r INFO @ Sun, 21 Jun 2020 20:40:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:27: 33000000 INFO @ Sun, 21 Jun 2020 20:40:31: 34000000 INFO @ Sun, 21 Jun 2020 20:40:36: 35000000 INFO @ Sun, 21 Jun 2020 20:40:40: 36000000 INFO @ Sun, 21 Jun 2020 20:40:45: 37000000 INFO @ Sun, 21 Jun 2020 20:40:50: 38000000 INFO @ Sun, 21 Jun 2020 20:40:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:40:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:40:53: #1 total tags in treatment: 38675535 INFO @ Sun, 21 Jun 2020 20:40:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:40:54: #1 tags after filtering in treatment: 38675475 INFO @ Sun, 21 Jun 2020 20:40:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:54: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:56: #2 number of paired peaks: 270 WARNING @ Sun, 21 Jun 2020 20:40:56: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Sun, 21 Jun 2020 20:40:56: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:57: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:57: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:57: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:57: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 20:40:57: #2 alternative fragment length(s) may be 3,126 bps INFO @ Sun, 21 Jun 2020 20:40:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.20_model.r INFO @ Sun, 21 Jun 2020 20:40:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:41:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.05_summits.bed INFO @ Sun, 21 Jun 2020 20:41:42: Done! pass1 - making usageList (272 chroms): 2 millis pass2 - checking and writing primary data (9366 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:42:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:42:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:42:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:42:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.10_summits.bed INFO @ Sun, 21 Jun 2020 20:42:10: Done! pass1 - making usageList (200 chroms): 1 millis pass2 - checking and writing primary data (6032 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:42:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:42:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:42:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981687/SRX3981687.20_summits.bed INFO @ Sun, 21 Jun 2020 20:42:39: Done! pass1 - making usageList (120 chroms): 1 millis pass2 - checking and writing primary data (2381 records, 4 fields): 6 millis CompletedMACS2peakCalling