Job ID = 10223655 SRX = ERX2745130 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T20:05:58 prefetch.2.10.7: 1) Downloading 'ERR2731905'... 2020-10-15T20:05:58 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T20:09:17 prefetch.2.10.7: HTTPS download succeed 2020-10-15T20:09:17 prefetch.2.10.7: 1) 'ERR2731905' was downloaded successfully Read 94664531 spots for ERR2731905/ERR2731905.sra Written 94664531 spots for ERR2731905/ERR2731905.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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:46:55 94664531 reads; of these: 94664531 (100.00%) were unpaired; of these: 3164376 (3.34%) aligned 0 times 77470035 (81.84%) aligned exactly 1 time 14030120 (14.82%) aligned >1 times 96.66% overall alignment rate Time searching: 00:46:58 Overall time: 00:46:58 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 40 files... [bam_rmdupse_core] 40988533 / 91500155 = 0.4480 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 06:13:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.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 06:13:42: #1 read tag files... INFO @ Fri, 16 Oct 2020 06:13:42: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 06:13:47: 1000000 INFO @ Fri, 16 Oct 2020 06:13:52: 2000000 INFO @ Fri, 16 Oct 2020 06:13:57: 3000000 INFO @ Fri, 16 Oct 2020 06:14:02: 4000000 INFO @ Fri, 16 Oct 2020 06:14:07: 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 06:14:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.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 06:14:12: #1 read tag files... INFO @ Fri, 16 Oct 2020 06:14:12: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 06:14:12: 6000000 INFO @ Fri, 16 Oct 2020 06:14:18: 7000000 INFO @ Fri, 16 Oct 2020 06:14:18: 1000000 INFO @ Fri, 16 Oct 2020 06:14:24: 8000000 INFO @ Fri, 16 Oct 2020 06:14:25: 2000000 INFO @ Fri, 16 Oct 2020 06:14:29: 9000000 INFO @ Fri, 16 Oct 2020 06:14:31: 3000000 INFO @ Fri, 16 Oct 2020 06:14:35: 10000000 INFO @ Fri, 16 Oct 2020 06:14:38: 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 06:14:41: 11000000 INFO @ Fri, 16 Oct 2020 06:14:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.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 06:14:42: #1 read tag files... INFO @ Fri, 16 Oct 2020 06:14:42: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 06:14:45: 5000000 INFO @ Fri, 16 Oct 2020 06:14:47: 12000000 INFO @ Fri, 16 Oct 2020 06:14:49: 1000000 INFO @ Fri, 16 Oct 2020 06:14:53: 6000000 INFO @ Fri, 16 Oct 2020 06:14:53: 13000000 INFO @ Fri, 16 Oct 2020 06:14:56: 2000000 INFO @ Fri, 16 Oct 2020 06:14:59: 14000000 INFO @ Fri, 16 Oct 2020 06:15:00: 7000000 INFO @ Fri, 16 Oct 2020 06:15:02: 3000000 INFO @ Fri, 16 Oct 2020 06:15:05: 15000000 INFO @ Fri, 16 Oct 2020 06:15:07: 8000000 INFO @ Fri, 16 Oct 2020 06:15:09: 4000000 INFO @ Fri, 16 Oct 2020 06:15:12: 16000000 INFO @ Fri, 16 Oct 2020 06:15:15: 9000000 INFO @ Fri, 16 Oct 2020 06:15:16: 5000000 INFO @ Fri, 16 Oct 2020 06:15:18: 17000000 INFO @ Fri, 16 Oct 2020 06:15:22: 10000000 INFO @ Fri, 16 Oct 2020 06:15:23: 6000000 INFO @ Fri, 16 Oct 2020 06:15:24: 18000000 INFO @ Fri, 16 Oct 2020 06:15:28: 11000000 INFO @ Fri, 16 Oct 2020 06:15:30: 7000000 INFO @ Fri, 16 Oct 2020 06:15:30: 19000000 INFO @ Fri, 16 Oct 2020 06:15:34: 12000000 INFO @ Fri, 16 Oct 2020 06:15:36: 20000000 INFO @ Fri, 16 Oct 2020 06:15:37: 8000000 INFO @ Fri, 16 Oct 2020 06:15:41: 13000000 INFO @ Fri, 16 Oct 2020 06:15:42: 21000000 INFO @ Fri, 16 Oct 2020 06:15:43: 9000000 INFO @ Fri, 16 Oct 2020 06:15:47: 14000000 INFO @ Fri, 16 Oct 2020 06:15:49: 22000000 INFO @ Fri, 16 Oct 2020 06:15:50: 10000000 INFO @ Fri, 16 Oct 2020 06:15:53: 15000000 INFO @ Fri, 16 Oct 2020 06:15:55: 23000000 INFO @ Fri, 16 Oct 2020 06:15:57: 11000000 INFO @ Fri, 16 Oct 2020 06:15:59: 16000000 INFO @ Fri, 16 Oct 2020 06:16:01: 24000000 INFO @ Fri, 16 Oct 2020 06:16:04: 12000000 INFO @ Fri, 16 Oct 2020 06:16:05: 17000000 INFO @ Fri, 16 Oct 2020 06:16:07: 25000000 INFO @ Fri, 16 Oct 2020 06:16:11: 13000000 INFO @ Fri, 16 Oct 2020 06:16:11: 18000000 INFO @ Fri, 16 Oct 2020 06:16:13: 26000000 INFO @ Fri, 16 Oct 2020 06:16:17: 19000000 INFO @ Fri, 16 Oct 2020 06:16:18: 14000000 INFO @ Fri, 16 Oct 2020 06:16:19: 27000000 INFO @ Fri, 16 Oct 2020 06:16:24: 20000000 INFO @ Fri, 16 Oct 2020 06:16:25: 15000000 INFO @ Fri, 16 Oct 2020 06:16:26: 28000000 INFO @ Fri, 16 Oct 2020 06:16:30: 21000000 INFO @ Fri, 16 Oct 2020 06:16:31: 16000000 INFO @ Fri, 16 Oct 2020 06:16:32: 29000000 INFO @ Fri, 16 Oct 2020 06:16:36: 22000000 INFO @ Fri, 16 Oct 2020 06:16:38: 30000000 INFO @ Fri, 16 Oct 2020 06:16:38: 17000000 INFO @ Fri, 16 Oct 2020 06:16:42: 23000000 INFO @ Fri, 16 Oct 2020 06:16:44: 31000000 INFO @ Fri, 16 Oct 2020 06:16:45: 18000000 INFO @ Fri, 16 Oct 2020 06:16:48: 24000000 INFO @ Fri, 16 Oct 2020 06:16:50: 32000000 INFO @ Fri, 16 Oct 2020 06:16:52: 19000000 INFO @ Fri, 16 Oct 2020 06:16:55: 25000000 INFO @ Fri, 16 Oct 2020 06:16:57: 33000000 INFO @ Fri, 16 Oct 2020 06:16:59: 20000000 INFO @ Fri, 16 Oct 2020 06:17:01: 26000000 INFO @ Fri, 16 Oct 2020 06:17:03: 34000000 INFO @ Fri, 16 Oct 2020 06:17:06: 21000000 INFO @ Fri, 16 Oct 2020 06:17:07: 27000000 INFO @ Fri, 16 Oct 2020 06:17:09: 35000000 INFO @ Fri, 16 Oct 2020 06:17:12: 22000000 INFO @ Fri, 16 Oct 2020 06:17:13: 28000000 INFO @ Fri, 16 Oct 2020 06:17:15: 36000000 INFO @ Fri, 16 Oct 2020 06:17:19: 23000000 INFO @ Fri, 16 Oct 2020 06:17:19: 29000000 INFO @ Fri, 16 Oct 2020 06:17:21: 37000000 INFO @ Fri, 16 Oct 2020 06:17:25: 30000000 INFO @ Fri, 16 Oct 2020 06:17:26: 24000000 INFO @ Fri, 16 Oct 2020 06:17:27: 38000000 INFO @ Fri, 16 Oct 2020 06:17:32: 31000000 INFO @ Fri, 16 Oct 2020 06:17:32: 25000000 INFO @ Fri, 16 Oct 2020 06:17:34: 39000000 INFO @ Fri, 16 Oct 2020 06:17:38: 32000000 INFO @ Fri, 16 Oct 2020 06:17:39: 26000000 INFO @ Fri, 16 Oct 2020 06:17:40: 40000000 INFO @ Fri, 16 Oct 2020 06:17:44: 33000000 INFO @ Fri, 16 Oct 2020 06:17:46: 27000000 INFO @ Fri, 16 Oct 2020 06:17:46: 41000000 INFO @ Fri, 16 Oct 2020 06:17:50: 34000000 INFO @ Fri, 16 Oct 2020 06:17:52: 42000000 INFO @ Fri, 16 Oct 2020 06:17:52: 28000000 INFO @ Fri, 16 Oct 2020 06:17:56: 35000000 INFO @ Fri, 16 Oct 2020 06:17:58: 43000000 INFO @ Fri, 16 Oct 2020 06:17:59: 29000000 INFO @ Fri, 16 Oct 2020 06:18:02: 36000000 INFO @ Fri, 16 Oct 2020 06:18:04: 44000000 INFO @ Fri, 16 Oct 2020 06:18:06: 30000000 INFO @ Fri, 16 Oct 2020 06:18:08: 37000000 INFO @ Fri, 16 Oct 2020 06:18:10: 45000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 06:18:12: 31000000 INFO @ Fri, 16 Oct 2020 06:18:14: 38000000 INFO @ Fri, 16 Oct 2020 06:18:16: 46000000 INFO @ Fri, 16 Oct 2020 06:18:19: 32000000 INFO @ Fri, 16 Oct 2020 06:18:20: 39000000 INFO @ Fri, 16 Oct 2020 06:18:22: 47000000 INFO @ Fri, 16 Oct 2020 06:18:25: 33000000 INFO @ Fri, 16 Oct 2020 06:18:26: 40000000 INFO @ Fri, 16 Oct 2020 06:18:28: 48000000 INFO @ Fri, 16 Oct 2020 06:18:32: 34000000 INFO @ Fri, 16 Oct 2020 06:18:32: 41000000 INFO @ Fri, 16 Oct 2020 06:18:34: 49000000 INFO @ Fri, 16 Oct 2020 06:18:38: 42000000 INFO @ Fri, 16 Oct 2020 06:18:38: 35000000 INFO @ Fri, 16 Oct 2020 06:18:40: 50000000 INFO @ Fri, 16 Oct 2020 06:18:44: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 06:18:44: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 06:18:44: #1 total tags in treatment: 50511622 INFO @ Fri, 16 Oct 2020 06:18:44: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 06:18:44: #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 06:18:44: 43000000 INFO @ Fri, 16 Oct 2020 06:18:45: #1 tags after filtering in treatment: 50511427 INFO @ Fri, 16 Oct 2020 06:18:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 06:18:45: #1 finished! INFO @ Fri, 16 Oct 2020 06:18:45: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 06:18:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 06:18:45: 36000000 INFO @ Fri, 16 Oct 2020 06:18:50: 44000000 INFO @ Fri, 16 Oct 2020 06:18:52: 37000000 INFO @ Fri, 16 Oct 2020 06:18:54: #2 number of paired peaks: 111772 INFO @ Fri, 16 Oct 2020 06:18:54: start model_add_line... INFO @ Fri, 16 Oct 2020 06:18:55: start X-correlation... INFO @ Fri, 16 Oct 2020 06:18:55: end of X-cor INFO @ Fri, 16 Oct 2020 06:18:55: #2 finished! INFO @ Fri, 16 Oct 2020 06:18:55: #2 predicted fragment length is 244 bps INFO @ Fri, 16 Oct 2020 06:18:55: #2 alternative fragment length(s) may be 244 bps INFO @ Fri, 16 Oct 2020 06:18:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.05_model.r INFO @ Fri, 16 Oct 2020 06:18:55: #3 Call peaks... INFO @ Fri, 16 Oct 2020 06:18:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 06:18:56: 45000000 INFO @ Fri, 16 Oct 2020 06:18:58: 38000000 INFO @ Fri, 16 Oct 2020 06:19:02: 46000000 INFO @ Fri, 16 Oct 2020 06:19:05: 39000000 INFO @ Fri, 16 Oct 2020 06:19:08: 47000000 INFO @ Fri, 16 Oct 2020 06:19:12: 40000000 INFO @ Fri, 16 Oct 2020 06:19:14: 48000000 INFO @ Fri, 16 Oct 2020 06:19:18: 41000000 INFO @ Fri, 16 Oct 2020 06:19:20: 49000000 INFO @ Fri, 16 Oct 2020 06:19:25: 42000000 INFO @ Fri, 16 Oct 2020 06:19:26: 50000000 INFO @ Fri, 16 Oct 2020 06:19:30: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 06:19:30: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 06:19:30: #1 total tags in treatment: 50511622 INFO @ Fri, 16 Oct 2020 06:19:30: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 06:19:30: #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 06:19:31: #1 tags after filtering in treatment: 50511427 INFO @ Fri, 16 Oct 2020 06:19:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 06:19:31: #1 finished! INFO @ Fri, 16 Oct 2020 06:19:31: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 06:19:31: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 06:19:31: 43000000 INFO @ Fri, 16 Oct 2020 06:19:38: 44000000 INFO @ Fri, 16 Oct 2020 06:19:39: #2 number of paired peaks: 111772 INFO @ Fri, 16 Oct 2020 06:19:39: start model_add_line... INFO @ Fri, 16 Oct 2020 06:19:41: start X-correlation... INFO @ Fri, 16 Oct 2020 06:19:41: end of X-cor INFO @ Fri, 16 Oct 2020 06:19:41: #2 finished! INFO @ Fri, 16 Oct 2020 06:19:41: #2 predicted fragment length is 244 bps INFO @ Fri, 16 Oct 2020 06:19:41: #2 alternative fragment length(s) may be 244 bps INFO @ Fri, 16 Oct 2020 06:19:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.10_model.r INFO @ Fri, 16 Oct 2020 06:19:41: #3 Call peaks... INFO @ Fri, 16 Oct 2020 06:19:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 06:19:44: 45000000 INFO @ Fri, 16 Oct 2020 06:19:50: 46000000 INFO @ Fri, 16 Oct 2020 06:19:56: 47000000 INFO @ Fri, 16 Oct 2020 06:20:02: 48000000 INFO @ Fri, 16 Oct 2020 06:20:08: 49000000 INFO @ Fri, 16 Oct 2020 06:20:15: 50000000 INFO @ Fri, 16 Oct 2020 06:20:18: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 06:20:18: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 06:20:18: #1 total tags in treatment: 50511622 INFO @ Fri, 16 Oct 2020 06:20:18: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 06:20:18: #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 06:20:19: #1 tags after filtering in treatment: 50511427 INFO @ Fri, 16 Oct 2020 06:20:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 06:20:19: #1 finished! INFO @ Fri, 16 Oct 2020 06:20:19: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 06:20:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 06:20:28: #2 number of paired peaks: 111772 INFO @ Fri, 16 Oct 2020 06:20:28: start model_add_line... INFO @ Fri, 16 Oct 2020 06:20:29: start X-correlation... INFO @ Fri, 16 Oct 2020 06:20:29: end of X-cor INFO @ Fri, 16 Oct 2020 06:20:29: #2 finished! INFO @ Fri, 16 Oct 2020 06:20:29: #2 predicted fragment length is 244 bps INFO @ Fri, 16 Oct 2020 06:20:29: #2 alternative fragment length(s) may be 244 bps INFO @ Fri, 16 Oct 2020 06:20:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.20_model.r INFO @ Fri, 16 Oct 2020 06:20:29: #3 Call peaks... INFO @ Fri, 16 Oct 2020 06:20:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 06:21:02: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 06:21:49: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 06:22:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.05_peaks.xls INFO @ Fri, 16 Oct 2020 06:22:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 06:22:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.05_summits.bed INFO @ Fri, 16 Oct 2020 06:22:10: Done! pass1 - making usageList (235 chroms): 8 millis pass2 - checking and writing primary data (62917 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 06:22:37: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 06:22:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.10_peaks.xls INFO @ Fri, 16 Oct 2020 06:22:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 06:22:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.10_summits.bed INFO @ Fri, 16 Oct 2020 06:22:56: Done! pass1 - making usageList (209 chroms): 7 millis pass2 - checking and writing primary data (50418 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 06:23:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.20_peaks.xls INFO @ Fri, 16 Oct 2020 06:23:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 06:23:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745130/ERX2745130.20_summits.bed INFO @ Fri, 16 Oct 2020 06:23:42: Done! pass1 - making usageList (179 chroms): 5 millis pass2 - checking and writing primary data (37236 records, 4 fields): 39 millis CompletedMACS2peakCalling