Job ID = 10223647 SRX = ERX2745123 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T19:50:47 prefetch.2.10.7: 1) Downloading 'ERR2731898'... 2020-10-15T19:50:47 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T19:52:34 prefetch.2.10.7: HTTPS download succeed 2020-10-15T19:52:34 prefetch.2.10.7: 1) 'ERR2731898' was downloaded successfully Read 88450733 spots for ERR2731898/ERR2731898.sra Written 88450733 spots for ERR2731898/ERR2731898.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:39:34 88450733 reads; of these: 88450733 (100.00%) were unpaired; of these: 3391127 (3.83%) aligned 0 times 71529139 (80.87%) aligned exactly 1 time 13530467 (15.30%) aligned >1 times 96.17% overall alignment rate Time searching: 00:39:35 Overall time: 00:39:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 36 files... [bam_rmdupse_core] 39362923 / 85059606 = 0.4628 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, 16 Oct 2020 05:47:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 16 Oct 2020 05:47:32: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:47:32: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:47:37: 1000000 INFO @ Fri, 16 Oct 2020 05:47:42: 2000000 INFO @ Fri, 16 Oct 2020 05:47:48: 3000000 INFO @ Fri, 16 Oct 2020 05:47:53: 4000000 INFO @ Fri, 16 Oct 2020 05:47:59: 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 @ Fri, 16 Oct 2020 05:48:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 16 Oct 2020 05:48:02: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:48:02: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:48:04: 6000000 INFO @ Fri, 16 Oct 2020 05:48:09: 1000000 INFO @ Fri, 16 Oct 2020 05:48:11: 7000000 INFO @ Fri, 16 Oct 2020 05:48:15: 2000000 INFO @ Fri, 16 Oct 2020 05:48:18: 8000000 INFO @ Fri, 16 Oct 2020 05:48:22: 3000000 INFO @ Fri, 16 Oct 2020 05:48:24: 9000000 INFO @ Fri, 16 Oct 2020 05:48:28: 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, 16 Oct 2020 05:48:31: 10000000 INFO @ Fri, 16 Oct 2020 05:48:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 16 Oct 2020 05:48:32: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:48:32: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:48:35: 5000000 INFO @ Fri, 16 Oct 2020 05:48:38: 11000000 INFO @ Fri, 16 Oct 2020 05:48:40: 1000000 INFO @ Fri, 16 Oct 2020 05:48:42: 6000000 INFO @ Fri, 16 Oct 2020 05:48:45: 12000000 INFO @ Fri, 16 Oct 2020 05:48:47: 2000000 INFO @ Fri, 16 Oct 2020 05:48:49: 7000000 INFO @ Fri, 16 Oct 2020 05:48:52: 13000000 INFO @ Fri, 16 Oct 2020 05:48:55: 3000000 INFO @ Fri, 16 Oct 2020 05:48:56: 8000000 INFO @ Fri, 16 Oct 2020 05:48:59: 14000000 INFO @ Fri, 16 Oct 2020 05:49:03: 4000000 INFO @ Fri, 16 Oct 2020 05:49:03: 9000000 INFO @ Fri, 16 Oct 2020 05:49:06: 15000000 INFO @ Fri, 16 Oct 2020 05:49:10: 10000000 INFO @ Fri, 16 Oct 2020 05:49:10: 5000000 INFO @ Fri, 16 Oct 2020 05:49:12: 16000000 INFO @ Fri, 16 Oct 2020 05:49:17: 11000000 INFO @ Fri, 16 Oct 2020 05:49:18: 6000000 INFO @ Fri, 16 Oct 2020 05:49:19: 17000000 INFO @ Fri, 16 Oct 2020 05:49:24: 12000000 INFO @ Fri, 16 Oct 2020 05:49:26: 7000000 INFO @ Fri, 16 Oct 2020 05:49:26: 18000000 INFO @ Fri, 16 Oct 2020 05:49:31: 13000000 INFO @ Fri, 16 Oct 2020 05:49:33: 19000000 INFO @ Fri, 16 Oct 2020 05:49:34: 8000000 INFO @ Fri, 16 Oct 2020 05:49:38: 14000000 INFO @ Fri, 16 Oct 2020 05:49:40: 20000000 INFO @ Fri, 16 Oct 2020 05:49:41: 9000000 INFO @ Fri, 16 Oct 2020 05:49:45: 15000000 INFO @ Fri, 16 Oct 2020 05:49:47: 21000000 INFO @ Fri, 16 Oct 2020 05:49:49: 10000000 INFO @ Fri, 16 Oct 2020 05:49:52: 16000000 INFO @ Fri, 16 Oct 2020 05:49:54: 22000000 INFO @ Fri, 16 Oct 2020 05:49:57: 11000000 INFO @ Fri, 16 Oct 2020 05:49:59: 17000000 INFO @ Fri, 16 Oct 2020 05:50:01: 23000000 INFO @ Fri, 16 Oct 2020 05:50:04: 12000000 INFO @ Fri, 16 Oct 2020 05:50:06: 18000000 INFO @ Fri, 16 Oct 2020 05:50:08: 24000000 INFO @ Fri, 16 Oct 2020 05:50:12: 13000000 INFO @ Fri, 16 Oct 2020 05:50:13: 19000000 INFO @ Fri, 16 Oct 2020 05:50:15: 25000000 INFO @ Fri, 16 Oct 2020 05:50:20: 14000000 INFO @ Fri, 16 Oct 2020 05:50:20: 20000000 INFO @ Fri, 16 Oct 2020 05:50:22: 26000000 INFO @ Fri, 16 Oct 2020 05:50:27: 21000000 INFO @ Fri, 16 Oct 2020 05:50:27: 15000000 INFO @ Fri, 16 Oct 2020 05:50:29: 27000000 INFO @ Fri, 16 Oct 2020 05:50:34: 22000000 INFO @ Fri, 16 Oct 2020 05:50:35: 16000000 INFO @ Fri, 16 Oct 2020 05:50:36: 28000000 INFO @ Fri, 16 Oct 2020 05:50:41: 23000000 INFO @ Fri, 16 Oct 2020 05:50:42: 17000000 INFO @ Fri, 16 Oct 2020 05:50:43: 29000000 INFO @ Fri, 16 Oct 2020 05:50:48: 24000000 INFO @ Fri, 16 Oct 2020 05:50:50: 30000000 INFO @ Fri, 16 Oct 2020 05:50:50: 18000000 INFO @ Fri, 16 Oct 2020 05:50:54: 25000000 INFO @ Fri, 16 Oct 2020 05:50:57: 31000000 INFO @ Fri, 16 Oct 2020 05:50:58: 19000000 INFO @ Fri, 16 Oct 2020 05:51:01: 26000000 INFO @ Fri, 16 Oct 2020 05:51:04: 32000000 INFO @ Fri, 16 Oct 2020 05:51:05: 20000000 INFO @ Fri, 16 Oct 2020 05:51:08: 27000000 INFO @ Fri, 16 Oct 2020 05:51:11: 33000000 INFO @ Fri, 16 Oct 2020 05:51:13: 21000000 INFO @ Fri, 16 Oct 2020 05:51:15: 28000000 INFO @ Fri, 16 Oct 2020 05:51:18: 34000000 INFO @ Fri, 16 Oct 2020 05:51:21: 22000000 INFO @ Fri, 16 Oct 2020 05:51:22: 29000000 INFO @ Fri, 16 Oct 2020 05:51:25: 35000000 INFO @ Fri, 16 Oct 2020 05:51:28: 23000000 INFO @ Fri, 16 Oct 2020 05:51:29: 30000000 INFO @ Fri, 16 Oct 2020 05:51:32: 36000000 INFO @ Fri, 16 Oct 2020 05:51:36: 24000000 INFO @ Fri, 16 Oct 2020 05:51:36: 31000000 INFO @ Fri, 16 Oct 2020 05:51:39: 37000000 INFO @ Fri, 16 Oct 2020 05:51:43: 32000000 INFO @ Fri, 16 Oct 2020 05:51:44: 25000000 INFO @ Fri, 16 Oct 2020 05:51:46: 38000000 INFO @ Fri, 16 Oct 2020 05:51:50: 33000000 INFO @ Fri, 16 Oct 2020 05:51:52: 26000000 INFO @ Fri, 16 Oct 2020 05:51:53: 39000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 05:51:57: 34000000 INFO @ Fri, 16 Oct 2020 05:52:00: 27000000 INFO @ Fri, 16 Oct 2020 05:52:00: 40000000 INFO @ Fri, 16 Oct 2020 05:52:04: 35000000 INFO @ Fri, 16 Oct 2020 05:52:07: 41000000 INFO @ Fri, 16 Oct 2020 05:52:07: 28000000 INFO @ Fri, 16 Oct 2020 05:52:11: 36000000 INFO @ Fri, 16 Oct 2020 05:52:14: 42000000 INFO @ Fri, 16 Oct 2020 05:52:15: 29000000 INFO @ Fri, 16 Oct 2020 05:52:18: 37000000 INFO @ Fri, 16 Oct 2020 05:52:21: 43000000 INFO @ Fri, 16 Oct 2020 05:52:23: 30000000 INFO @ Fri, 16 Oct 2020 05:52:25: 38000000 INFO @ Fri, 16 Oct 2020 05:52:28: 44000000 INFO @ Fri, 16 Oct 2020 05:52:31: 31000000 INFO @ Fri, 16 Oct 2020 05:52:32: 39000000 INFO @ Fri, 16 Oct 2020 05:52:35: 45000000 INFO @ Fri, 16 Oct 2020 05:52:39: 32000000 INFO @ Fri, 16 Oct 2020 05:52:39: 40000000 INFO @ Fri, 16 Oct 2020 05:52:40: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:52:40: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:52:40: #1 total tags in treatment: 45696683 INFO @ Fri, 16 Oct 2020 05:52:40: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:52:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 05:52:41: #1 tags after filtering in treatment: 45696517 INFO @ Fri, 16 Oct 2020 05:52:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:52:41: #1 finished! INFO @ Fri, 16 Oct 2020 05:52:41: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:52:46: 41000000 INFO @ Fri, 16 Oct 2020 05:52:47: 33000000 INFO @ Fri, 16 Oct 2020 05:52:49: #2 number of paired peaks: 102812 INFO @ Fri, 16 Oct 2020 05:52:49: start model_add_line... INFO @ Fri, 16 Oct 2020 05:52:50: start X-correlation... INFO @ Fri, 16 Oct 2020 05:52:50: end of X-cor INFO @ Fri, 16 Oct 2020 05:52:50: #2 finished! INFO @ Fri, 16 Oct 2020 05:52:50: #2 predicted fragment length is 208 bps INFO @ Fri, 16 Oct 2020 05:52:50: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 16 Oct 2020 05:52:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.05_model.r INFO @ Fri, 16 Oct 2020 05:52:50: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:52:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:52:53: 42000000 INFO @ Fri, 16 Oct 2020 05:52:54: 34000000 INFO @ Fri, 16 Oct 2020 05:53:00: 43000000 INFO @ Fri, 16 Oct 2020 05:53:02: 35000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 05:53:07: 44000000 INFO @ Fri, 16 Oct 2020 05:53:10: 36000000 INFO @ Fri, 16 Oct 2020 05:53:14: 45000000 INFO @ Fri, 16 Oct 2020 05:53:18: 37000000 INFO @ Fri, 16 Oct 2020 05:53:19: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:53:19: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:53:19: #1 total tags in treatment: 45696683 INFO @ Fri, 16 Oct 2020 05:53:19: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:53:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 05:53:20: #1 tags after filtering in treatment: 45696517 INFO @ Fri, 16 Oct 2020 05:53:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:53:20: #1 finished! INFO @ Fri, 16 Oct 2020 05:53:20: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:53:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:53:25: 38000000 INFO @ Fri, 16 Oct 2020 05:53:27: #2 number of paired peaks: 102812 INFO @ Fri, 16 Oct 2020 05:53:27: start model_add_line... INFO @ Fri, 16 Oct 2020 05:53:28: start X-correlation... INFO @ Fri, 16 Oct 2020 05:53:28: end of X-cor INFO @ Fri, 16 Oct 2020 05:53:28: #2 finished! INFO @ Fri, 16 Oct 2020 05:53:28: #2 predicted fragment length is 208 bps INFO @ Fri, 16 Oct 2020 05:53:28: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 16 Oct 2020 05:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.10_model.r INFO @ Fri, 16 Oct 2020 05:53:28: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:53:32: 39000000 INFO @ Fri, 16 Oct 2020 05:53:39: 40000000 INFO @ Fri, 16 Oct 2020 05:53:46: 41000000 INFO @ Fri, 16 Oct 2020 05:53:53: 42000000 INFO @ Fri, 16 Oct 2020 05:54:00: 43000000 INFO @ Fri, 16 Oct 2020 05:54:07: 44000000 INFO @ Fri, 16 Oct 2020 05:54:14: 45000000 INFO @ Fri, 16 Oct 2020 05:54:19: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:54:19: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:54:19: #1 total tags in treatment: 45696683 INFO @ Fri, 16 Oct 2020 05:54:19: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:54:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 05:54:20: #1 tags after filtering in treatment: 45696517 INFO @ Fri, 16 Oct 2020 05:54:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:54:20: #1 finished! INFO @ Fri, 16 Oct 2020 05:54:20: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:54:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:54:28: #2 number of paired peaks: 102812 INFO @ Fri, 16 Oct 2020 05:54:28: start model_add_line... INFO @ Fri, 16 Oct 2020 05:54:29: start X-correlation... INFO @ Fri, 16 Oct 2020 05:54:29: end of X-cor INFO @ Fri, 16 Oct 2020 05:54:29: #2 finished! INFO @ Fri, 16 Oct 2020 05:54:29: #2 predicted fragment length is 208 bps INFO @ Fri, 16 Oct 2020 05:54:29: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 16 Oct 2020 05:54:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.20_model.r INFO @ Fri, 16 Oct 2020 05:54:29: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:54:38: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:55:21: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:55:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.05_peaks.xls INFO @ Fri, 16 Oct 2020 05:55:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:55:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.05_summits.bed INFO @ Fri, 16 Oct 2020 05:55:36: Done! pass1 - making usageList (228 chroms): 8 millis pass2 - checking and writing primary data (58458 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:56:16: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:56:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.10_peaks.xls INFO @ Fri, 16 Oct 2020 05:56:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:56:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.10_summits.bed INFO @ Fri, 16 Oct 2020 05:56:22: Done! pass1 - making usageList (196 chroms): 6 millis pass2 - checking and writing primary data (45790 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:57:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.20_peaks.xls INFO @ Fri, 16 Oct 2020 05:57:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:57:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.20_summits.bed INFO @ Fri, 16 Oct 2020 05:57:14: Done! pass1 - making usageList (163 chroms): 5 millis pass2 - checking and writing primary data (32548 records, 4 fields): 33 millis CompletedMACS2peakCalling