Job ID = 10223558 SRX = ERX2745102 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T17:52:33 prefetch.2.10.7: 1) Downloading 'ERR2731877'... 2020-10-15T17:52:33 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T17:54:11 prefetch.2.10.7: HTTPS download succeed 2020-10-15T17:54:11 prefetch.2.10.7: 1) 'ERR2731877' was downloaded successfully Read 62485760 spots for ERR2731877/ERR2731877.sra Written 62485760 spots for ERR2731877/ERR2731877.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:41:58 62485760 reads; of these: 62485760 (100.00%) were unpaired; of these: 1827768 (2.93%) aligned 0 times 52888281 (84.64%) aligned exactly 1 time 7769711 (12.43%) aligned >1 times 97.07% overall alignment rate Time searching: 00:42:02 Overall time: 00:42:02 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 28 files... [bam_rmdupse_core] 17387167 / 60657992 = 0.2866 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 03:49:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.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 03:49:06: #1 read tag files... INFO @ Fri, 16 Oct 2020 03:49:06: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 03:49:12: 1000000 INFO @ Fri, 16 Oct 2020 03:49:18: 2000000 INFO @ Fri, 16 Oct 2020 03:49:23: 3000000 INFO @ Fri, 16 Oct 2020 03:49:28: 4000000 INFO @ Fri, 16 Oct 2020 03:49:34: 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 03:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.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 03:49:36: #1 read tag files... INFO @ Fri, 16 Oct 2020 03:49:36: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 03:49:39: 6000000 INFO @ Fri, 16 Oct 2020 03:49:42: 1000000 INFO @ Fri, 16 Oct 2020 03:49:44: 7000000 INFO @ Fri, 16 Oct 2020 03:49:48: 2000000 INFO @ Fri, 16 Oct 2020 03:49:49: 8000000 INFO @ Fri, 16 Oct 2020 03:49:53: 3000000 INFO @ Fri, 16 Oct 2020 03:49:54: 9000000 INFO @ Fri, 16 Oct 2020 03:49:58: 4000000 INFO @ Fri, 16 Oct 2020 03:50:00: 10000000 INFO @ Fri, 16 Oct 2020 03:50:04: 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 @ Fri, 16 Oct 2020 03:50:05: 11000000 INFO @ Fri, 16 Oct 2020 03:50:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.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 03:50:06: #1 read tag files... INFO @ Fri, 16 Oct 2020 03:50:06: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 03:50:09: 6000000 INFO @ Fri, 16 Oct 2020 03:50:10: 12000000 INFO @ Fri, 16 Oct 2020 03:50:13: 1000000 INFO @ Fri, 16 Oct 2020 03:50:15: 7000000 INFO @ Fri, 16 Oct 2020 03:50:16: 13000000 INFO @ Fri, 16 Oct 2020 03:50:19: 2000000 INFO @ Fri, 16 Oct 2020 03:50:20: 8000000 INFO @ Fri, 16 Oct 2020 03:50:21: 14000000 INFO @ Fri, 16 Oct 2020 03:50:25: 3000000 INFO @ Fri, 16 Oct 2020 03:50:26: 9000000 INFO @ Fri, 16 Oct 2020 03:50:27: 15000000 INFO @ Fri, 16 Oct 2020 03:50:30: 4000000 INFO @ Fri, 16 Oct 2020 03:50:31: 10000000 INFO @ Fri, 16 Oct 2020 03:50:33: 16000000 INFO @ Fri, 16 Oct 2020 03:50:36: 5000000 INFO @ Fri, 16 Oct 2020 03:50:37: 11000000 INFO @ Fri, 16 Oct 2020 03:50:38: 17000000 INFO @ Fri, 16 Oct 2020 03:50:41: 6000000 INFO @ Fri, 16 Oct 2020 03:50:42: 12000000 INFO @ Fri, 16 Oct 2020 03:50:43: 18000000 INFO @ Fri, 16 Oct 2020 03:50:47: 7000000 INFO @ Fri, 16 Oct 2020 03:50:48: 13000000 INFO @ Fri, 16 Oct 2020 03:50:49: 19000000 INFO @ Fri, 16 Oct 2020 03:50:52: 8000000 INFO @ Fri, 16 Oct 2020 03:50:53: 14000000 INFO @ Fri, 16 Oct 2020 03:50:54: 20000000 INFO @ Fri, 16 Oct 2020 03:50:57: 9000000 INFO @ Fri, 16 Oct 2020 03:50:59: 15000000 INFO @ Fri, 16 Oct 2020 03:51:00: 21000000 INFO @ Fri, 16 Oct 2020 03:51:03: 10000000 INFO @ Fri, 16 Oct 2020 03:51:04: 16000000 INFO @ Fri, 16 Oct 2020 03:51:06: 22000000 INFO @ Fri, 16 Oct 2020 03:51:08: 11000000 INFO @ Fri, 16 Oct 2020 03:51:10: 17000000 INFO @ Fri, 16 Oct 2020 03:51:11: 23000000 INFO @ Fri, 16 Oct 2020 03:51:14: 12000000 INFO @ Fri, 16 Oct 2020 03:51:15: 18000000 INFO @ Fri, 16 Oct 2020 03:51:16: 24000000 INFO @ Fri, 16 Oct 2020 03:51:19: 13000000 INFO @ Fri, 16 Oct 2020 03:51:21: 19000000 INFO @ Fri, 16 Oct 2020 03:51:22: 25000000 INFO @ Fri, 16 Oct 2020 03:51:24: 14000000 INFO @ Fri, 16 Oct 2020 03:51:26: 20000000 INFO @ Fri, 16 Oct 2020 03:51:27: 26000000 INFO @ Fri, 16 Oct 2020 03:51:30: 15000000 INFO @ Fri, 16 Oct 2020 03:51:31: 21000000 INFO @ Fri, 16 Oct 2020 03:51:33: 27000000 INFO @ Fri, 16 Oct 2020 03:51:35: 16000000 INFO @ Fri, 16 Oct 2020 03:51:37: 22000000 INFO @ Fri, 16 Oct 2020 03:51:38: 28000000 INFO @ Fri, 16 Oct 2020 03:51:40: 17000000 INFO @ Fri, 16 Oct 2020 03:51:42: 23000000 INFO @ Fri, 16 Oct 2020 03:51:43: 29000000 INFO @ Fri, 16 Oct 2020 03:51:45: 18000000 INFO @ Fri, 16 Oct 2020 03:51:48: 24000000 INFO @ Fri, 16 Oct 2020 03:51:49: 30000000 INFO @ Fri, 16 Oct 2020 03:51:51: 19000000 INFO @ Fri, 16 Oct 2020 03:51:53: 25000000 INFO @ Fri, 16 Oct 2020 03:51:54: 31000000 INFO @ Fri, 16 Oct 2020 03:51:56: 20000000 INFO @ Fri, 16 Oct 2020 03:51:58: 26000000 INFO @ Fri, 16 Oct 2020 03:51:59: 32000000 INFO @ Fri, 16 Oct 2020 03:52:01: 21000000 INFO @ Fri, 16 Oct 2020 03:52:04: 27000000 INFO @ Fri, 16 Oct 2020 03:52:04: 33000000 INFO @ Fri, 16 Oct 2020 03:52:07: 22000000 INFO @ Fri, 16 Oct 2020 03:52:09: 28000000 INFO @ Fri, 16 Oct 2020 03:52:10: 34000000 INFO @ Fri, 16 Oct 2020 03:52:12: 23000000 INFO @ Fri, 16 Oct 2020 03:52:14: 29000000 INFO @ Fri, 16 Oct 2020 03:52:15: 35000000 INFO @ Fri, 16 Oct 2020 03:52:17: 24000000 INFO @ Fri, 16 Oct 2020 03:52:20: 30000000 INFO @ Fri, 16 Oct 2020 03:52:20: 36000000 INFO @ Fri, 16 Oct 2020 03:52:22: 25000000 INFO @ Fri, 16 Oct 2020 03:52:25: 31000000 INFO @ Fri, 16 Oct 2020 03:52:25: 37000000 INFO @ Fri, 16 Oct 2020 03:52:28: 26000000 INFO @ Fri, 16 Oct 2020 03:52:31: 32000000 INFO @ Fri, 16 Oct 2020 03:52:31: 38000000 INFO @ Fri, 16 Oct 2020 03:52:33: 27000000 INFO @ Fri, 16 Oct 2020 03:52:36: 33000000 INFO @ Fri, 16 Oct 2020 03:52:36: 39000000 INFO @ Fri, 16 Oct 2020 03:52:38: 28000000 INFO @ Fri, 16 Oct 2020 03:52:41: 34000000 INFO @ Fri, 16 Oct 2020 03:52:41: 40000000 INFO @ Fri, 16 Oct 2020 03:52:44: 29000000 INFO @ Fri, 16 Oct 2020 03:52:46: 35000000 INFO @ Fri, 16 Oct 2020 03:52:47: 41000000 INFO @ Fri, 16 Oct 2020 03:52:49: 30000000 INFO @ Fri, 16 Oct 2020 03:52:52: 36000000 INFO @ Fri, 16 Oct 2020 03:52:52: 42000000 INFO @ Fri, 16 Oct 2020 03:52:54: 31000000 INFO @ Fri, 16 Oct 2020 03:52:57: 37000000 INFO @ Fri, 16 Oct 2020 03:52:57: 43000000 INFO @ Fri, 16 Oct 2020 03:52:59: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 03:52:59: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 03:52:59: #1 total tags in treatment: 43270825 INFO @ Fri, 16 Oct 2020 03:52:59: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 03:52:59: #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 03:52:59: 32000000 INFO @ Fri, 16 Oct 2020 03:53:00: #1 tags after filtering in treatment: 43270652 INFO @ Fri, 16 Oct 2020 03:53:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 03:53:00: #1 finished! INFO @ Fri, 16 Oct 2020 03:53:00: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 03:53:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 03:53:02: 38000000 INFO @ Fri, 16 Oct 2020 03:53:04: 33000000 INFO @ Fri, 16 Oct 2020 03:53:06: #2 number of paired peaks: 108164 INFO @ Fri, 16 Oct 2020 03:53:06: start model_add_line... INFO @ Fri, 16 Oct 2020 03:53:07: start X-correlation... INFO @ Fri, 16 Oct 2020 03:53:07: end of X-cor INFO @ Fri, 16 Oct 2020 03:53:07: #2 finished! INFO @ Fri, 16 Oct 2020 03:53:07: #2 predicted fragment length is 233 bps INFO @ Fri, 16 Oct 2020 03:53:07: #2 alternative fragment length(s) may be 233 bps INFO @ Fri, 16 Oct 2020 03:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.05_model.r INFO @ Fri, 16 Oct 2020 03:53:07: #3 Call peaks... INFO @ Fri, 16 Oct 2020 03:53:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 03:53:07: 39000000 INFO @ Fri, 16 Oct 2020 03:53:10: 34000000 INFO @ Fri, 16 Oct 2020 03:53:13: 40000000 INFO @ Fri, 16 Oct 2020 03:53:15: 35000000 INFO @ Fri, 16 Oct 2020 03:53:18: 41000000 INFO @ Fri, 16 Oct 2020 03:53:20: 36000000 INFO @ Fri, 16 Oct 2020 03:53:23: 42000000 INFO @ Fri, 16 Oct 2020 03:53:25: 37000000 INFO @ Fri, 16 Oct 2020 03:53:29: 43000000 INFO @ Fri, 16 Oct 2020 03:53:30: 38000000 INFO @ Fri, 16 Oct 2020 03:53:30: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 03:53:30: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 03:53:30: #1 total tags in treatment: 43270825 INFO @ Fri, 16 Oct 2020 03:53:30: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 03:53:30: #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 03:53:31: #1 tags after filtering in treatment: 43270652 INFO @ Fri, 16 Oct 2020 03:53:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 03:53:31: #1 finished! INFO @ Fri, 16 Oct 2020 03:53:31: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 03:53:31: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 03:53:35: 39000000 INFO @ Fri, 16 Oct 2020 03:53:38: #2 number of paired peaks: 108164 INFO @ Fri, 16 Oct 2020 03:53:38: start model_add_line... INFO @ Fri, 16 Oct 2020 03:53:38: start X-correlation... INFO @ Fri, 16 Oct 2020 03:53:38: end of X-cor INFO @ Fri, 16 Oct 2020 03:53:38: #2 finished! INFO @ Fri, 16 Oct 2020 03:53:38: #2 predicted fragment length is 233 bps INFO @ Fri, 16 Oct 2020 03:53:38: #2 alternative fragment length(s) may be 233 bps INFO @ Fri, 16 Oct 2020 03:53:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.10_model.r INFO @ Fri, 16 Oct 2020 03:53:38: #3 Call peaks... INFO @ Fri, 16 Oct 2020 03:53:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 03:53:41: 40000000 INFO @ Fri, 16 Oct 2020 03:53:46: 41000000 INFO @ Fri, 16 Oct 2020 03:53:51: 42000000 INFO @ Fri, 16 Oct 2020 03:53:56: 43000000 INFO @ Fri, 16 Oct 2020 03:53:57: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 03:53:57: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 03:53:57: #1 total tags in treatment: 43270825 INFO @ Fri, 16 Oct 2020 03:53:57: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 03:53:57: #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 03:53:58: #1 tags after filtering in treatment: 43270652 INFO @ Fri, 16 Oct 2020 03:53:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 03:53:58: #1 finished! INFO @ Fri, 16 Oct 2020 03:53:58: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 03:53:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 03:54:05: #2 number of paired peaks: 108164 INFO @ Fri, 16 Oct 2020 03:54:05: start model_add_line... INFO @ Fri, 16 Oct 2020 03:54:05: start X-correlation... INFO @ Fri, 16 Oct 2020 03:54:05: end of X-cor INFO @ Fri, 16 Oct 2020 03:54:05: #2 finished! INFO @ Fri, 16 Oct 2020 03:54:05: #2 predicted fragment length is 233 bps INFO @ Fri, 16 Oct 2020 03:54:05: #2 alternative fragment length(s) may be 233 bps INFO @ Fri, 16 Oct 2020 03:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.20_model.r INFO @ Fri, 16 Oct 2020 03:54:05: #3 Call peaks... INFO @ Fri, 16 Oct 2020 03:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 03:54:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 03:55:19: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 03:55:50: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 03:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.05_peaks.xls INFO @ Fri, 16 Oct 2020 03:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 03:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.05_summits.bed INFO @ Fri, 16 Oct 2020 03:55:51: Done! pass1 - making usageList (125 chroms): 5 millis pass2 - checking and writing primary data (33548 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 03:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.10_peaks.xls INFO @ Fri, 16 Oct 2020 03:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 03:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.10_summits.bed INFO @ Fri, 16 Oct 2020 03:56:18: Done! pass1 - making usageList (95 chroms): 3 millis pass2 - checking and writing primary data (20096 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 03:56:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.20_peaks.xls INFO @ Fri, 16 Oct 2020 03:56:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 03:56:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745102/ERX2745102.20_summits.bed INFO @ Fri, 16 Oct 2020 03:56:49: Done! pass1 - making usageList (69 chroms): 2 millis pass2 - checking and writing primary data (11399 records, 4 fields): 12 millis CompletedMACS2peakCalling