Job ID = 6456723 SRX = SRX3981627 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:02:16 prefetch.2.10.7: 1) Downloading 'SRR7050265'... 2020-06-21T11:02:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:03:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:03:54 prefetch.2.10.7: 'SRR7050265' is valid 2020-06-21T11:03:54 prefetch.2.10.7: 1) 'SRR7050265' was downloaded successfully 2020-06-21T11:03:54 prefetch.2.10.7: 'SRR7050265' has 0 unresolved dependencies Read 14060408 spots for SRR7050265/SRR7050265.sra Written 14060408 spots for SRR7050265/SRR7050265.sra 2020-06-21T11:04:48 prefetch.2.10.7: 1) Downloading 'SRR7050266'... 2020-06-21T11:04:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:06:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:06:46 prefetch.2.10.7: 'SRR7050266' is valid 2020-06-21T11:06:46 prefetch.2.10.7: 1) 'SRR7050266' was downloaded successfully 2020-06-21T11:06:46 prefetch.2.10.7: 'SRR7050266' has 0 unresolved dependencies Read 13860439 spots for SRR7050266/SRR7050266.sra Written 13860439 spots for SRR7050266/SRR7050266.sra 2020-06-21T11:07:41 prefetch.2.10.7: 1) Downloading 'SRR7050267'... 2020-06-21T11:07:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:09:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:09:21 prefetch.2.10.7: 'SRR7050267' is valid 2020-06-21T11:09:21 prefetch.2.10.7: 1) 'SRR7050267' was downloaded successfully 2020-06-21T11:09:21 prefetch.2.10.7: 'SRR7050267' has 0 unresolved dependencies Read 14040987 spots for SRR7050267/SRR7050267.sra Written 14040987 spots for SRR7050267/SRR7050267.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: 00:09:37 41961834 reads; of these: 41961834 (100.00%) were unpaired; of these: 1888451 (4.50%) aligned 0 times 32155323 (76.63%) aligned exactly 1 time 7918060 (18.87%) aligned >1 times 95.50% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 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] 7114853 / 40073383 = 0.1775 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 20:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.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 20:27:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:27:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:27:44: 1000000 INFO @ Sun, 21 Jun 2020 20:27:49: 2000000 INFO @ Sun, 21 Jun 2020 20:27:54: 3000000 INFO @ Sun, 21 Jun 2020 20:27:59: 4000000 INFO @ Sun, 21 Jun 2020 20:28:04: 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 @ Sun, 21 Jun 2020 20:28:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.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 20:28:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:10: 6000000 INFO @ Sun, 21 Jun 2020 20:28:14: 1000000 INFO @ Sun, 21 Jun 2020 20:28:15: 7000000 INFO @ Sun, 21 Jun 2020 20:28:20: 2000000 INFO @ Sun, 21 Jun 2020 20:28:20: 8000000 INFO @ Sun, 21 Jun 2020 20:28:26: 3000000 INFO @ Sun, 21 Jun 2020 20:28:26: 9000000 INFO @ Sun, 21 Jun 2020 20:28:31: 4000000 INFO @ Sun, 21 Jun 2020 20:28:31: 10000000 INFO @ Sun, 21 Jun 2020 20:28:37: 11000000 INFO @ Sun, 21 Jun 2020 20:28:37: 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 @ Sun, 21 Jun 2020 20:28:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.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 20:28:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:42: 12000000 INFO @ Sun, 21 Jun 2020 20:28:43: 6000000 INFO @ Sun, 21 Jun 2020 20:28:44: 1000000 INFO @ Sun, 21 Jun 2020 20:28:48: 13000000 INFO @ Sun, 21 Jun 2020 20:28:48: 7000000 INFO @ Sun, 21 Jun 2020 20:28:50: 2000000 INFO @ Sun, 21 Jun 2020 20:28:53: 14000000 INFO @ Sun, 21 Jun 2020 20:28:54: 8000000 INFO @ Sun, 21 Jun 2020 20:28:56: 3000000 INFO @ Sun, 21 Jun 2020 20:28:59: 15000000 INFO @ Sun, 21 Jun 2020 20:29:00: 9000000 INFO @ Sun, 21 Jun 2020 20:29:01: 4000000 INFO @ Sun, 21 Jun 2020 20:29:05: 16000000 INFO @ Sun, 21 Jun 2020 20:29:05: 10000000 INFO @ Sun, 21 Jun 2020 20:29:07: 5000000 INFO @ Sun, 21 Jun 2020 20:29:10: 17000000 INFO @ Sun, 21 Jun 2020 20:29:11: 11000000 INFO @ Sun, 21 Jun 2020 20:29:13: 6000000 INFO @ Sun, 21 Jun 2020 20:29:16: 18000000 INFO @ Sun, 21 Jun 2020 20:29:17: 12000000 INFO @ Sun, 21 Jun 2020 20:29:18: 7000000 INFO @ Sun, 21 Jun 2020 20:29:22: 19000000 INFO @ Sun, 21 Jun 2020 20:29:22: 13000000 INFO @ Sun, 21 Jun 2020 20:29:24: 8000000 INFO @ Sun, 21 Jun 2020 20:29:28: 20000000 INFO @ Sun, 21 Jun 2020 20:29:28: 14000000 INFO @ Sun, 21 Jun 2020 20:29:30: 9000000 INFO @ Sun, 21 Jun 2020 20:29:33: 21000000 INFO @ Sun, 21 Jun 2020 20:29:34: 15000000 INFO @ Sun, 21 Jun 2020 20:29:35: 10000000 INFO @ Sun, 21 Jun 2020 20:29:39: 22000000 INFO @ Sun, 21 Jun 2020 20:29:40: 16000000 INFO @ Sun, 21 Jun 2020 20:29:41: 11000000 INFO @ Sun, 21 Jun 2020 20:29:45: 23000000 INFO @ Sun, 21 Jun 2020 20:29:45: 17000000 INFO @ Sun, 21 Jun 2020 20:29:46: 12000000 INFO @ Sun, 21 Jun 2020 20:29:50: 24000000 INFO @ Sun, 21 Jun 2020 20:29:51: 18000000 INFO @ Sun, 21 Jun 2020 20:29:52: 13000000 INFO @ Sun, 21 Jun 2020 20:29:56: 25000000 INFO @ Sun, 21 Jun 2020 20:29:57: 19000000 INFO @ Sun, 21 Jun 2020 20:29:58: 14000000 INFO @ Sun, 21 Jun 2020 20:30:02: 26000000 INFO @ Sun, 21 Jun 2020 20:30:03: 20000000 INFO @ Sun, 21 Jun 2020 20:30:03: 15000000 INFO @ Sun, 21 Jun 2020 20:30:07: 27000000 INFO @ Sun, 21 Jun 2020 20:30:09: 21000000 INFO @ Sun, 21 Jun 2020 20:30:09: 16000000 INFO @ Sun, 21 Jun 2020 20:30:13: 28000000 INFO @ Sun, 21 Jun 2020 20:30:14: 22000000 INFO @ Sun, 21 Jun 2020 20:30:15: 17000000 INFO @ Sun, 21 Jun 2020 20:30:19: 29000000 INFO @ Sun, 21 Jun 2020 20:30:20: 23000000 INFO @ Sun, 21 Jun 2020 20:30:20: 18000000 INFO @ Sun, 21 Jun 2020 20:30:25: 30000000 INFO @ Sun, 21 Jun 2020 20:30:26: 24000000 INFO @ Sun, 21 Jun 2020 20:30:26: 19000000 INFO @ Sun, 21 Jun 2020 20:30:30: 31000000 INFO @ Sun, 21 Jun 2020 20:30:32: 20000000 INFO @ Sun, 21 Jun 2020 20:30:32: 25000000 INFO @ Sun, 21 Jun 2020 20:30:36: 32000000 INFO @ Sun, 21 Jun 2020 20:30:37: 21000000 INFO @ Sun, 21 Jun 2020 20:30:37: 26000000 INFO @ Sun, 21 Jun 2020 20:30:42: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:30:42: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:30:42: #1 total tags in treatment: 32958530 INFO @ Sun, 21 Jun 2020 20:30:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:30:42: #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 20:30:42: #1 tags after filtering in treatment: 32958479 INFO @ Sun, 21 Jun 2020 20:30:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:30:42: #1 finished! INFO @ Sun, 21 Jun 2020 20:30:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:30:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:30:43: 22000000 INFO @ Sun, 21 Jun 2020 20:30:43: 27000000 INFO @ Sun, 21 Jun 2020 20:30:44: #2 number of paired peaks: 362 WARNING @ Sun, 21 Jun 2020 20:30:44: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Sun, 21 Jun 2020 20:30:44: start model_add_line... INFO @ Sun, 21 Jun 2020 20:30:45: start X-correlation... INFO @ Sun, 21 Jun 2020 20:30:45: end of X-cor INFO @ Sun, 21 Jun 2020 20:30:45: #2 finished! INFO @ Sun, 21 Jun 2020 20:30:45: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 20:30:45: #2 alternative fragment length(s) may be 3,137 bps INFO @ Sun, 21 Jun 2020 20:30:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.05_model.r INFO @ Sun, 21 Jun 2020 20:30:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:30:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:30:48: 23000000 INFO @ Sun, 21 Jun 2020 20:30:49: 28000000 INFO @ Sun, 21 Jun 2020 20:30:54: 24000000 INFO @ Sun, 21 Jun 2020 20:30:55: 29000000 INFO @ Sun, 21 Jun 2020 20:31:00: 25000000 INFO @ Sun, 21 Jun 2020 20:31:01: 30000000 INFO @ Sun, 21 Jun 2020 20:31:05: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:31:06: 31000000 INFO @ Sun, 21 Jun 2020 20:31:11: 27000000 INFO @ Sun, 21 Jun 2020 20:31:12: 32000000 INFO @ Sun, 21 Jun 2020 20:31:17: 28000000 INFO @ Sun, 21 Jun 2020 20:31:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:31:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:31:18: #1 total tags in treatment: 32958530 INFO @ Sun, 21 Jun 2020 20:31:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:31:18: #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 20:31:19: #1 tags after filtering in treatment: 32958479 INFO @ Sun, 21 Jun 2020 20:31:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:31:19: #1 finished! INFO @ Sun, 21 Jun 2020 20:31:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:31:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:31:21: #2 number of paired peaks: 362 WARNING @ Sun, 21 Jun 2020 20:31:21: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Sun, 21 Jun 2020 20:31:21: start model_add_line... INFO @ Sun, 21 Jun 2020 20:31:21: start X-correlation... INFO @ Sun, 21 Jun 2020 20:31:21: end of X-cor INFO @ Sun, 21 Jun 2020 20:31:21: #2 finished! INFO @ Sun, 21 Jun 2020 20:31:21: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 20:31:21: #2 alternative fragment length(s) may be 3,137 bps INFO @ Sun, 21 Jun 2020 20:31:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.10_model.r INFO @ Sun, 21 Jun 2020 20:31:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:31:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:31:23: 29000000 INFO @ Sun, 21 Jun 2020 20:31:28: 30000000 INFO @ Sun, 21 Jun 2020 20:31:34: 31000000 INFO @ Sun, 21 Jun 2020 20:31:39: 32000000 INFO @ Sun, 21 Jun 2020 20:31:44: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:31:44: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:31:44: #1 total tags in treatment: 32958530 INFO @ Sun, 21 Jun 2020 20:31:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:31:44: #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 20:31:45: #1 tags after filtering in treatment: 32958479 INFO @ Sun, 21 Jun 2020 20:31:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:31:45: #1 finished! INFO @ Sun, 21 Jun 2020 20:31:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:31:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:31:47: #2 number of paired peaks: 362 WARNING @ Sun, 21 Jun 2020 20:31:47: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Sun, 21 Jun 2020 20:31:47: start model_add_line... INFO @ Sun, 21 Jun 2020 20:31:47: start X-correlation... INFO @ Sun, 21 Jun 2020 20:31:47: end of X-cor INFO @ Sun, 21 Jun 2020 20:31:47: #2 finished! INFO @ Sun, 21 Jun 2020 20:31:47: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 20:31:47: #2 alternative fragment length(s) may be 3,137 bps INFO @ Sun, 21 Jun 2020 20:31:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.20_model.r INFO @ Sun, 21 Jun 2020 20:31:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:31:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:31:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:32:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:32:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:32:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.05_summits.bed INFO @ Sun, 21 Jun 2020 20:32:20: Done! pass1 - making usageList (281 chroms): 2 millis pass2 - checking and writing primary data (10220 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:32:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:32:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.10_summits.bed INFO @ Sun, 21 Jun 2020 20:32:54: Done! pass1 - making usageList (183 chroms): 2 millis pass2 - checking and writing primary data (5949 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:33:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981627/SRX3981627.20_summits.bed INFO @ Sun, 21 Jun 2020 20:33:20: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (2171 records, 4 fields): 6 millis CompletedMACS2peakCalling