Job ID = 10223651 SRX = ERX2745126 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T19:54:37 prefetch.2.10.7: 1) Downloading 'ERR2731901'... 2020-10-15T19:54:37 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T19:56:06 prefetch.2.10.7: HTTPS download succeed 2020-10-15T19:56:06 prefetch.2.10.7: 1) 'ERR2731901' was downloaded successfully Read 71731353 spots for ERR2731901/ERR2731901.sra Written 71731353 spots for ERR2731901/ERR2731901.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: 00:35:32 71731353 reads; of these: 71731353 (100.00%) were unpaired; of these: 3333153 (4.65%) aligned 0 times 56540630 (78.82%) aligned exactly 1 time 11857570 (16.53%) aligned >1 times 95.35% overall alignment rate Time searching: 00:35:35 Overall time: 00:35:35 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 28 files... [bam_rmdupse_core] 38429580 / 68398200 = 0.5619 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 05:44:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.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 05:44:04: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:44:04: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:44:10: 1000000 INFO @ Fri, 16 Oct 2020 05:44:17: 2000000 INFO @ Fri, 16 Oct 2020 05:44:23: 3000000 INFO @ Fri, 16 Oct 2020 05:44:29: 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 @ Fri, 16 Oct 2020 05:44:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.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 05:44:34: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:44:34: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:44:36: 5000000 INFO @ Fri, 16 Oct 2020 05:44:41: 1000000 INFO @ Fri, 16 Oct 2020 05:44:43: 6000000 INFO @ Fri, 16 Oct 2020 05:44:48: 2000000 INFO @ Fri, 16 Oct 2020 05:44:50: 7000000 INFO @ Fri, 16 Oct 2020 05:44:54: 3000000 INFO @ Fri, 16 Oct 2020 05:44:57: 8000000 INFO @ Fri, 16 Oct 2020 05:45:01: 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 05:45:04: 9000000 INFO @ Fri, 16 Oct 2020 05:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.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 05:45:04: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:45:04: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:45:08: 5000000 INFO @ Fri, 16 Oct 2020 05:45:11: 10000000 INFO @ Fri, 16 Oct 2020 05:45:11: 1000000 INFO @ Fri, 16 Oct 2020 05:45:15: 6000000 INFO @ Fri, 16 Oct 2020 05:45:18: 11000000 INFO @ Fri, 16 Oct 2020 05:45:18: 2000000 INFO @ Fri, 16 Oct 2020 05:45:22: 7000000 INFO @ Fri, 16 Oct 2020 05:45:26: 12000000 INFO @ Fri, 16 Oct 2020 05:45:26: 3000000 INFO @ Fri, 16 Oct 2020 05:45:29: 8000000 INFO @ Fri, 16 Oct 2020 05:45:33: 13000000 INFO @ Fri, 16 Oct 2020 05:45:33: 4000000 INFO @ Fri, 16 Oct 2020 05:45:36: 9000000 INFO @ Fri, 16 Oct 2020 05:45:40: 5000000 INFO @ Fri, 16 Oct 2020 05:45:40: 14000000 INFO @ Fri, 16 Oct 2020 05:45:43: 10000000 INFO @ Fri, 16 Oct 2020 05:45:47: 6000000 INFO @ Fri, 16 Oct 2020 05:45:48: 15000000 INFO @ Fri, 16 Oct 2020 05:45:50: 11000000 INFO @ Fri, 16 Oct 2020 05:45:55: 7000000 INFO @ Fri, 16 Oct 2020 05:45:55: 16000000 INFO @ Fri, 16 Oct 2020 05:45:57: 12000000 INFO @ Fri, 16 Oct 2020 05:46:02: 8000000 INFO @ Fri, 16 Oct 2020 05:46:02: 17000000 INFO @ Fri, 16 Oct 2020 05:46:04: 13000000 INFO @ Fri, 16 Oct 2020 05:46:09: 9000000 INFO @ Fri, 16 Oct 2020 05:46:09: 18000000 INFO @ Fri, 16 Oct 2020 05:46:11: 14000000 INFO @ Fri, 16 Oct 2020 05:46:17: 19000000 INFO @ Fri, 16 Oct 2020 05:46:17: 10000000 INFO @ Fri, 16 Oct 2020 05:46:18: 15000000 INFO @ Fri, 16 Oct 2020 05:46:24: 20000000 INFO @ Fri, 16 Oct 2020 05:46:24: 11000000 INFO @ Fri, 16 Oct 2020 05:46:25: 16000000 INFO @ Fri, 16 Oct 2020 05:46:31: 21000000 INFO @ Fri, 16 Oct 2020 05:46:31: 12000000 INFO @ Fri, 16 Oct 2020 05:46:31: 17000000 INFO @ Fri, 16 Oct 2020 05:46:38: 18000000 INFO @ Fri, 16 Oct 2020 05:46:39: 22000000 INFO @ Fri, 16 Oct 2020 05:46:39: 13000000 INFO @ Fri, 16 Oct 2020 05:46:45: 19000000 INFO @ Fri, 16 Oct 2020 05:46:46: 23000000 INFO @ Fri, 16 Oct 2020 05:46:46: 14000000 INFO @ Fri, 16 Oct 2020 05:46:52: 20000000 INFO @ Fri, 16 Oct 2020 05:46:53: 24000000 INFO @ Fri, 16 Oct 2020 05:46:53: 15000000 INFO @ Fri, 16 Oct 2020 05:46:59: 21000000 INFO @ Fri, 16 Oct 2020 05:47:01: 25000000 INFO @ Fri, 16 Oct 2020 05:47:01: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 05:47:06: 22000000 INFO @ Fri, 16 Oct 2020 05:47:08: 26000000 INFO @ Fri, 16 Oct 2020 05:47:08: 17000000 INFO @ Fri, 16 Oct 2020 05:47:13: 23000000 INFO @ Fri, 16 Oct 2020 05:47:15: 27000000 INFO @ Fri, 16 Oct 2020 05:47:15: 18000000 INFO @ Fri, 16 Oct 2020 05:47:20: 24000000 INFO @ Fri, 16 Oct 2020 05:47:23: 28000000 INFO @ Fri, 16 Oct 2020 05:47:23: 19000000 INFO @ Fri, 16 Oct 2020 05:47:27: 25000000 INFO @ Fri, 16 Oct 2020 05:47:30: 20000000 INFO @ Fri, 16 Oct 2020 05:47:30: 29000000 INFO @ Fri, 16 Oct 2020 05:47:34: 26000000 INFO @ Fri, 16 Oct 2020 05:47:37: 21000000 INFO @ Fri, 16 Oct 2020 05:47:37: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:47:37: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:47:37: #1 total tags in treatment: 29968620 INFO @ Fri, 16 Oct 2020 05:47:37: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:47:37: #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 05:47:38: #1 tags after filtering in treatment: 29968503 INFO @ Fri, 16 Oct 2020 05:47:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:47:38: #1 finished! INFO @ Fri, 16 Oct 2020 05:47:38: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:47:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:47:41: 27000000 INFO @ Fri, 16 Oct 2020 05:47:42: #2 number of paired peaks: 32821 INFO @ Fri, 16 Oct 2020 05:47:42: start model_add_line... INFO @ Fri, 16 Oct 2020 05:47:42: start X-correlation... INFO @ Fri, 16 Oct 2020 05:47:42: end of X-cor INFO @ Fri, 16 Oct 2020 05:47:42: #2 finished! INFO @ Fri, 16 Oct 2020 05:47:42: #2 predicted fragment length is 233 bps INFO @ Fri, 16 Oct 2020 05:47:42: #2 alternative fragment length(s) may be 233 bps INFO @ Fri, 16 Oct 2020 05:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.05_model.r INFO @ Fri, 16 Oct 2020 05:47:42: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:47:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:47:44: 22000000 INFO @ Fri, 16 Oct 2020 05:47:48: 28000000 INFO @ Fri, 16 Oct 2020 05:47:51: 23000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 05:47:55: 29000000 INFO @ Fri, 16 Oct 2020 05:47:58: 24000000 INFO @ Fri, 16 Oct 2020 05:48:02: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:48:02: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:48:02: #1 total tags in treatment: 29968620 INFO @ Fri, 16 Oct 2020 05:48:02: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:48:02: #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 05:48:02: #1 tags after filtering in treatment: 29968503 INFO @ Fri, 16 Oct 2020 05:48:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:48:02: #1 finished! INFO @ Fri, 16 Oct 2020 05:48:02: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:48:05: 25000000 INFO @ Fri, 16 Oct 2020 05:48:06: #2 number of paired peaks: 32821 INFO @ Fri, 16 Oct 2020 05:48:06: start model_add_line... INFO @ Fri, 16 Oct 2020 05:48:06: start X-correlation... INFO @ Fri, 16 Oct 2020 05:48:06: end of X-cor INFO @ Fri, 16 Oct 2020 05:48:06: #2 finished! INFO @ Fri, 16 Oct 2020 05:48:06: #2 predicted fragment length is 233 bps INFO @ Fri, 16 Oct 2020 05:48:06: #2 alternative fragment length(s) may be 233 bps INFO @ Fri, 16 Oct 2020 05:48:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.10_model.r INFO @ Fri, 16 Oct 2020 05:48:06: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:48:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:48:11: 26000000 INFO @ Fri, 16 Oct 2020 05:48:18: 27000000 INFO @ Fri, 16 Oct 2020 05:48:24: 28000000 INFO @ Fri, 16 Oct 2020 05:48:31: 29000000 INFO @ Fri, 16 Oct 2020 05:48:37: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:48:37: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:48:37: #1 total tags in treatment: 29968620 INFO @ Fri, 16 Oct 2020 05:48:37: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:48:37: #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 05:48:38: #1 tags after filtering in treatment: 29968503 INFO @ Fri, 16 Oct 2020 05:48:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:48:38: #1 finished! INFO @ Fri, 16 Oct 2020 05:48:38: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:48:41: #2 number of paired peaks: 32821 INFO @ Fri, 16 Oct 2020 05:48:41: start model_add_line... INFO @ Fri, 16 Oct 2020 05:48:42: start X-correlation... INFO @ Fri, 16 Oct 2020 05:48:42: end of X-cor INFO @ Fri, 16 Oct 2020 05:48:42: #2 finished! INFO @ Fri, 16 Oct 2020 05:48:42: #2 predicted fragment length is 233 bps INFO @ Fri, 16 Oct 2020 05:48:42: #2 alternative fragment length(s) may be 233 bps INFO @ Fri, 16 Oct 2020 05:48:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.20_model.r INFO @ Fri, 16 Oct 2020 05:48:42: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:48:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:48:56: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:49:19: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:49:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.05_peaks.xls INFO @ Fri, 16 Oct 2020 05:49:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:49:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.05_summits.bed INFO @ Fri, 16 Oct 2020 05:49:34: Done! pass1 - making usageList (132 chroms): 3 millis pass2 - checking and writing primary data (20069 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:49:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.10_peaks.xls INFO @ Fri, 16 Oct 2020 05:49:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:49:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.10_summits.bed INFO @ Fri, 16 Oct 2020 05:49:56: Done! pass1 - making usageList (123 chroms): 3 millis pass2 - checking and writing primary data (18247 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:49:58: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:50:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.20_peaks.xls INFO @ Fri, 16 Oct 2020 05:50:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:50:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745126/ERX2745126.20_summits.bed INFO @ Fri, 16 Oct 2020 05:50:37: Done! pass1 - making usageList (103 chroms): 3 millis pass2 - checking and writing primary data (16150 records, 4 fields): 18 millis CompletedMACS2peakCalling