Job ID = 6456718 SRX = SRX3981623 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:03:31 prefetch.2.10.7: 1) Downloading 'SRR7050253'... 2020-06-21T11:03:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:04:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:04:28 prefetch.2.10.7: 'SRR7050253' is valid 2020-06-21T11:04:28 prefetch.2.10.7: 1) 'SRR7050253' was downloaded successfully 2020-06-21T11:04:28 prefetch.2.10.7: 'SRR7050253' has 0 unresolved dependencies Read 13243305 spots for SRR7050253/SRR7050253.sra Written 13243305 spots for SRR7050253/SRR7050253.sra 2020-06-21T11:05:19 prefetch.2.10.7: 1) Downloading 'SRR7050254'... 2020-06-21T11:05:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:06:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:06:54 prefetch.2.10.7: 'SRR7050254' is valid 2020-06-21T11:06:54 prefetch.2.10.7: 1) 'SRR7050254' was downloaded successfully 2020-06-21T11:06:54 prefetch.2.10.7: 'SRR7050254' has 0 unresolved dependencies Read 13031080 spots for SRR7050254/SRR7050254.sra Written 13031080 spots for SRR7050254/SRR7050254.sra 2020-06-21T11:07:43 prefetch.2.10.7: 1) Downloading 'SRR7050255'... 2020-06-21T11:07:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:08:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:08:24 prefetch.2.10.7: 'SRR7050255' is valid 2020-06-21T11:08:24 prefetch.2.10.7: 1) 'SRR7050255' was downloaded successfully 2020-06-21T11:08:24 prefetch.2.10.7: 'SRR7050255' has 0 unresolved dependencies Read 13220701 spots for SRR7050255/SRR7050255.sra Written 13220701 spots for SRR7050255/SRR7050255.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: 00:10:08 39495086 reads; of these: 39495086 (100.00%) were unpaired; of these: 1210857 (3.07%) aligned 0 times 30035323 (76.05%) aligned exactly 1 time 8248906 (20.89%) aligned >1 times 96.93% overall alignment rate Time searching: 00:10:08 Overall time: 00:10:08 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 16 files... [bam_rmdupse_core] 5934693 / 38284229 = 0.1550 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 20:27:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.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 20:27:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:27:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:27:51: 1000000 INFO @ Sun, 21 Jun 2020 20:27:57: 2000000 INFO @ Sun, 21 Jun 2020 20:28:04: 3000000 INFO @ Sun, 21 Jun 2020 20:28:10: 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 @ Sun, 21 Jun 2020 20:28:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.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 20:28:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:17: 5000000 INFO @ Sun, 21 Jun 2020 20:28:21: 1000000 INFO @ Sun, 21 Jun 2020 20:28:24: 6000000 INFO @ Sun, 21 Jun 2020 20:28:27: 2000000 INFO @ Sun, 21 Jun 2020 20:28:31: 7000000 INFO @ Sun, 21 Jun 2020 20:28:33: 3000000 INFO @ Sun, 21 Jun 2020 20:28:38: 8000000 INFO @ Sun, 21 Jun 2020 20:28:40: 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 @ Sun, 21 Jun 2020 20:28:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.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 20:28:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:44: 9000000 INFO @ Sun, 21 Jun 2020 20:28:46: 5000000 INFO @ Sun, 21 Jun 2020 20:28:51: 10000000 INFO @ Sun, 21 Jun 2020 20:28:52: 1000000 INFO @ Sun, 21 Jun 2020 20:28:52: 6000000 INFO @ Sun, 21 Jun 2020 20:28:58: 11000000 INFO @ Sun, 21 Jun 2020 20:28:59: 7000000 INFO @ Sun, 21 Jun 2020 20:28:59: 2000000 INFO @ Sun, 21 Jun 2020 20:29:05: 8000000 INFO @ Sun, 21 Jun 2020 20:29:06: 12000000 INFO @ Sun, 21 Jun 2020 20:29:06: 3000000 INFO @ Sun, 21 Jun 2020 20:29:11: 9000000 INFO @ Sun, 21 Jun 2020 20:29:13: 13000000 INFO @ Sun, 21 Jun 2020 20:29:14: 4000000 INFO @ Sun, 21 Jun 2020 20:29:18: 10000000 INFO @ Sun, 21 Jun 2020 20:29:20: 14000000 INFO @ Sun, 21 Jun 2020 20:29:21: 5000000 INFO @ Sun, 21 Jun 2020 20:29:24: 11000000 INFO @ Sun, 21 Jun 2020 20:29:27: 15000000 INFO @ Sun, 21 Jun 2020 20:29:28: 6000000 INFO @ Sun, 21 Jun 2020 20:29:31: 12000000 INFO @ Sun, 21 Jun 2020 20:29:34: 16000000 INFO @ Sun, 21 Jun 2020 20:29:36: 7000000 INFO @ Sun, 21 Jun 2020 20:29:38: 13000000 INFO @ Sun, 21 Jun 2020 20:29:41: 17000000 INFO @ Sun, 21 Jun 2020 20:29:43: 8000000 INFO @ Sun, 21 Jun 2020 20:29:45: 14000000 INFO @ Sun, 21 Jun 2020 20:29:48: 18000000 INFO @ Sun, 21 Jun 2020 20:29:50: 9000000 INFO @ Sun, 21 Jun 2020 20:29:51: 15000000 INFO @ Sun, 21 Jun 2020 20:29:55: 19000000 INFO @ Sun, 21 Jun 2020 20:29:57: 10000000 INFO @ Sun, 21 Jun 2020 20:29:58: 16000000 INFO @ Sun, 21 Jun 2020 20:30:02: 20000000 INFO @ Sun, 21 Jun 2020 20:30:04: 17000000 INFO @ Sun, 21 Jun 2020 20:30:04: 11000000 INFO @ Sun, 21 Jun 2020 20:30:09: 21000000 INFO @ Sun, 21 Jun 2020 20:30:11: 18000000 INFO @ Sun, 21 Jun 2020 20:30:12: 12000000 INFO @ Sun, 21 Jun 2020 20:30:16: 22000000 INFO @ Sun, 21 Jun 2020 20:30:17: 19000000 INFO @ Sun, 21 Jun 2020 20:30:19: 13000000 INFO @ Sun, 21 Jun 2020 20:30:23: 23000000 INFO @ Sun, 21 Jun 2020 20:30:24: 20000000 INFO @ Sun, 21 Jun 2020 20:30:26: 14000000 INFO @ Sun, 21 Jun 2020 20:30:30: 21000000 INFO @ Sun, 21 Jun 2020 20:30:30: 24000000 INFO @ Sun, 21 Jun 2020 20:30:34: 15000000 INFO @ Sun, 21 Jun 2020 20:30:37: 22000000 INFO @ Sun, 21 Jun 2020 20:30:38: 25000000 INFO @ Sun, 21 Jun 2020 20:30:41: 16000000 INFO @ Sun, 21 Jun 2020 20:30:43: 23000000 INFO @ Sun, 21 Jun 2020 20:30:45: 26000000 INFO @ Sun, 21 Jun 2020 20:30:49: 17000000 INFO @ Sun, 21 Jun 2020 20:30:49: 24000000 INFO @ Sun, 21 Jun 2020 20:30:52: 27000000 INFO @ Sun, 21 Jun 2020 20:30:56: 18000000 INFO @ Sun, 21 Jun 2020 20:30:56: 25000000 INFO @ Sun, 21 Jun 2020 20:31:00: 28000000 INFO @ Sun, 21 Jun 2020 20:31:02: 26000000 INFO @ Sun, 21 Jun 2020 20:31:03: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:31:07: 29000000 INFO @ Sun, 21 Jun 2020 20:31:09: 27000000 INFO @ Sun, 21 Jun 2020 20:31:10: 20000000 INFO @ Sun, 21 Jun 2020 20:31:15: 30000000 INFO @ Sun, 21 Jun 2020 20:31:16: 28000000 INFO @ Sun, 21 Jun 2020 20:31:17: 21000000 INFO @ Sun, 21 Jun 2020 20:31:22: 31000000 INFO @ Sun, 21 Jun 2020 20:31:22: 29000000 INFO @ Sun, 21 Jun 2020 20:31:25: 22000000 INFO @ Sun, 21 Jun 2020 20:31:29: 30000000 INFO @ Sun, 21 Jun 2020 20:31:30: 32000000 INFO @ Sun, 21 Jun 2020 20:31:32: 23000000 INFO @ Sun, 21 Jun 2020 20:31:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:31:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:31:33: #1 total tags in treatment: 32349536 INFO @ Sun, 21 Jun 2020 20:31:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:31:33: #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 20:31:33: #1 tags after filtering in treatment: 32349479 INFO @ Sun, 21 Jun 2020 20:31:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:31:33: #1 finished! INFO @ Sun, 21 Jun 2020 20:31:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:31:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:31:36: #2 number of paired peaks: 219 WARNING @ Sun, 21 Jun 2020 20:31:36: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sun, 21 Jun 2020 20:31:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:31:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:31:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:31:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:31:36: #2 predicted fragment length is 105 bps INFO @ Sun, 21 Jun 2020 20:31:36: #2 alternative fragment length(s) may be 2,56,77,105,583 bps INFO @ Sun, 21 Jun 2020 20:31:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.05_model.r INFO @ Sun, 21 Jun 2020 20:31:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:31:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:31:36: 31000000 INFO @ Sun, 21 Jun 2020 20:31:39: 24000000 INFO @ Sun, 21 Jun 2020 20:31:43: 32000000 INFO @ Sun, 21 Jun 2020 20:31:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:31:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:31:45: #1 total tags in treatment: 32349536 INFO @ Sun, 21 Jun 2020 20:31:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:31:45: #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 20:31:46: 25000000 INFO @ Sun, 21 Jun 2020 20:31:46: #1 tags after filtering in treatment: 32349479 INFO @ Sun, 21 Jun 2020 20:31:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:31:46: #1 finished! INFO @ Sun, 21 Jun 2020 20:31:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:31:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:31:48: #2 number of paired peaks: 219 WARNING @ Sun, 21 Jun 2020 20:31:48: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sun, 21 Jun 2020 20:31:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:31:49: start X-correlation... INFO @ Sun, 21 Jun 2020 20:31:49: end of X-cor INFO @ Sun, 21 Jun 2020 20:31:49: #2 finished! INFO @ Sun, 21 Jun 2020 20:31:49: #2 predicted fragment length is 105 bps INFO @ Sun, 21 Jun 2020 20:31:49: #2 alternative fragment length(s) may be 2,56,77,105,583 bps INFO @ Sun, 21 Jun 2020 20:31:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.10_model.r INFO @ Sun, 21 Jun 2020 20:31:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:31:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:31:52: 26000000 INFO @ Sun, 21 Jun 2020 20:31:58: 27000000 INFO @ Sun, 21 Jun 2020 20:32:05: 28000000 INFO @ Sun, 21 Jun 2020 20:32:12: 29000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:32:18: 30000000 INFO @ Sun, 21 Jun 2020 20:32:25: 31000000 INFO @ Sun, 21 Jun 2020 20:32:31: 32000000 INFO @ Sun, 21 Jun 2020 20:32:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:32:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:32:34: #1 total tags in treatment: 32349536 INFO @ Sun, 21 Jun 2020 20:32:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:32:34: #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 20:32:35: #1 tags after filtering in treatment: 32349479 INFO @ Sun, 21 Jun 2020 20:32:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:32:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:32:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:32:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:32:37: #2 number of paired peaks: 219 WARNING @ Sun, 21 Jun 2020 20:32:37: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sun, 21 Jun 2020 20:32:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:32:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:32:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:32:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:32:37: #2 predicted fragment length is 105 bps INFO @ Sun, 21 Jun 2020 20:32:37: #2 alternative fragment length(s) may be 2,56,77,105,583 bps INFO @ Sun, 21 Jun 2020 20:32:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.20_model.r INFO @ Sun, 21 Jun 2020 20:32:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:32:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:32:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:32:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:33:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.05_summits.bed INFO @ Sun, 21 Jun 2020 20:33:12: Done! pass1 - making usageList (357 chroms): 2 millis pass2 - checking and writing primary data (8155 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:33:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.10_summits.bed INFO @ Sun, 21 Jun 2020 20:33:31: Done! pass1 - making usageList (222 chroms): 2 millis pass2 - checking and writing primary data (3494 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:33:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:34:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:34:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981623/SRX3981623.20_summits.bed INFO @ Sun, 21 Jun 2020 20:34:15: Done! pass1 - making usageList (131 chroms): 1 millis pass2 - checking and writing primary data (729 records, 4 fields): 8 millis CompletedMACS2peakCalling