Job ID = 10223656 SRX = ERX2745131 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T20:10:58 prefetch.2.10.7: 1) Downloading 'ERR2731906'... 2020-10-15T20:10:58 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T20:13:43 prefetch.2.10.7: HTTPS download succeed 2020-10-15T20:13:43 prefetch.2.10.7: 1) 'ERR2731906' was downloaded successfully Read 93458226 spots for ERR2731906/ERR2731906.sra Written 93458226 spots for ERR2731906/ERR2731906.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: 00:00:00 Multiseed full-index search: 00:43:42 93458226 reads; of these: 93458226 (100.00%) were unpaired; of these: 3440790 (3.68%) aligned 0 times 80970109 (86.64%) aligned exactly 1 time 9047327 (9.68%) aligned >1 times 96.32% overall alignment rate Time searching: 00:43:44 Overall time: 00:43:44 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] 48258462 / 90017436 = 0.5361 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 06:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.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 06:13:50: #1 read tag files... INFO @ Fri, 16 Oct 2020 06:13:50: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 06:13:54: 1000000 INFO @ Fri, 16 Oct 2020 06:13:59: 2000000 INFO @ Fri, 16 Oct 2020 06:14:04: 3000000 INFO @ Fri, 16 Oct 2020 06:14:08: 4000000 INFO @ Fri, 16 Oct 2020 06:14:13: 5000000 INFO @ Fri, 16 Oct 2020 06:14:18: 6000000 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 06:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.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 06:14:20: #1 read tag files... INFO @ Fri, 16 Oct 2020 06:14:20: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 06:14:23: 7000000 INFO @ Fri, 16 Oct 2020 06:14:25: 1000000 INFO @ Fri, 16 Oct 2020 06:14:28: 8000000 INFO @ Fri, 16 Oct 2020 06:14:30: 2000000 INFO @ Fri, 16 Oct 2020 06:14:33: 9000000 INFO @ Fri, 16 Oct 2020 06:14:35: 3000000 INFO @ Fri, 16 Oct 2020 06:14:38: 10000000 INFO @ Fri, 16 Oct 2020 06:14:40: 4000000 INFO @ Fri, 16 Oct 2020 06:14:43: 11000000 INFO @ Fri, 16 Oct 2020 06:14:45: 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 06:14:49: 12000000 INFO @ Fri, 16 Oct 2020 06:14:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.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 06:14:50: #1 read tag files... INFO @ Fri, 16 Oct 2020 06:14:50: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 06:14:51: 6000000 INFO @ Fri, 16 Oct 2020 06:14:54: 13000000 INFO @ Fri, 16 Oct 2020 06:14:56: 1000000 INFO @ Fri, 16 Oct 2020 06:14:56: 7000000 INFO @ Fri, 16 Oct 2020 06:14:59: 14000000 INFO @ Fri, 16 Oct 2020 06:15:02: 8000000 INFO @ Fri, 16 Oct 2020 06:15:02: 2000000 INFO @ Fri, 16 Oct 2020 06:15:05: 15000000 INFO @ Fri, 16 Oct 2020 06:15:07: 9000000 INFO @ Fri, 16 Oct 2020 06:15:08: 3000000 INFO @ Fri, 16 Oct 2020 06:15:10: 16000000 INFO @ Fri, 16 Oct 2020 06:15:13: 10000000 INFO @ Fri, 16 Oct 2020 06:15:14: 4000000 INFO @ Fri, 16 Oct 2020 06:15:16: 17000000 INFO @ Fri, 16 Oct 2020 06:15:18: 11000000 INFO @ Fri, 16 Oct 2020 06:15:20: 5000000 INFO @ Fri, 16 Oct 2020 06:15:21: 18000000 INFO @ Fri, 16 Oct 2020 06:15:23: 12000000 INFO @ Fri, 16 Oct 2020 06:15:26: 6000000 INFO @ Fri, 16 Oct 2020 06:15:27: 19000000 INFO @ Fri, 16 Oct 2020 06:15:29: 13000000 INFO @ Fri, 16 Oct 2020 06:15:32: 20000000 INFO @ Fri, 16 Oct 2020 06:15:32: 7000000 INFO @ Fri, 16 Oct 2020 06:15:34: 14000000 INFO @ Fri, 16 Oct 2020 06:15:37: 21000000 INFO @ Fri, 16 Oct 2020 06:15:38: 8000000 INFO @ Fri, 16 Oct 2020 06:15:40: 15000000 INFO @ Fri, 16 Oct 2020 06:15:43: 22000000 INFO @ Fri, 16 Oct 2020 06:15:45: 9000000 INFO @ Fri, 16 Oct 2020 06:15:45: 16000000 INFO @ Fri, 16 Oct 2020 06:15:48: 23000000 INFO @ Fri, 16 Oct 2020 06:15:51: 17000000 INFO @ Fri, 16 Oct 2020 06:15:51: 10000000 INFO @ Fri, 16 Oct 2020 06:15:54: 24000000 INFO @ Fri, 16 Oct 2020 06:15:56: 18000000 INFO @ Fri, 16 Oct 2020 06:15:57: 11000000 INFO @ Fri, 16 Oct 2020 06:15:59: 25000000 INFO @ Fri, 16 Oct 2020 06:16:02: 19000000 INFO @ Fri, 16 Oct 2020 06:16:03: 12000000 INFO @ Fri, 16 Oct 2020 06:16:05: 26000000 INFO @ Fri, 16 Oct 2020 06:16:07: 20000000 INFO @ Fri, 16 Oct 2020 06:16:09: 13000000 INFO @ Fri, 16 Oct 2020 06:16:10: 27000000 INFO @ Fri, 16 Oct 2020 06:16:13: 21000000 INFO @ Fri, 16 Oct 2020 06:16:15: 14000000 INFO @ Fri, 16 Oct 2020 06:16:15: 28000000 INFO @ Fri, 16 Oct 2020 06:16:18: 22000000 INFO @ Fri, 16 Oct 2020 06:16:21: 15000000 INFO @ Fri, 16 Oct 2020 06:16:21: 29000000 INFO @ Fri, 16 Oct 2020 06:16:24: 23000000 INFO @ Fri, 16 Oct 2020 06:16:26: 30000000 INFO @ Fri, 16 Oct 2020 06:16:26: 16000000 INFO @ Fri, 16 Oct 2020 06:16:30: 24000000 INFO @ Fri, 16 Oct 2020 06:16:32: 31000000 INFO @ Fri, 16 Oct 2020 06:16:32: 17000000 INFO @ Fri, 16 Oct 2020 06:16:35: 25000000 INFO @ Fri, 16 Oct 2020 06:16:37: 32000000 INFO @ Fri, 16 Oct 2020 06:16:37: 18000000 INFO @ Fri, 16 Oct 2020 06:16:41: 26000000 INFO @ Fri, 16 Oct 2020 06:16:42: 33000000 INFO @ Fri, 16 Oct 2020 06:16:43: 19000000 INFO @ Fri, 16 Oct 2020 06:16:46: 27000000 INFO @ Fri, 16 Oct 2020 06:16:48: 34000000 INFO @ Fri, 16 Oct 2020 06:16:48: 20000000 INFO @ Fri, 16 Oct 2020 06:16:52: 28000000 INFO @ Fri, 16 Oct 2020 06:16:53: 35000000 INFO @ Fri, 16 Oct 2020 06:16:54: 21000000 INFO @ Fri, 16 Oct 2020 06:16:57: 29000000 INFO @ Fri, 16 Oct 2020 06:16:58: 36000000 INFO @ Fri, 16 Oct 2020 06:16:59: 22000000 INFO @ Fri, 16 Oct 2020 06:17:02: 30000000 INFO @ Fri, 16 Oct 2020 06:17:03: 37000000 INFO @ Fri, 16 Oct 2020 06:17:05: 23000000 INFO @ Fri, 16 Oct 2020 06:17:08: 31000000 INFO @ Fri, 16 Oct 2020 06:17:09: 38000000 INFO @ Fri, 16 Oct 2020 06:17:10: 24000000 INFO @ Fri, 16 Oct 2020 06:17:13: 32000000 INFO @ Fri, 16 Oct 2020 06:17:14: 39000000 INFO @ Fri, 16 Oct 2020 06:17:15: 25000000 INFO @ Fri, 16 Oct 2020 06:17:19: 33000000 INFO @ Fri, 16 Oct 2020 06:17:19: 40000000 INFO @ Fri, 16 Oct 2020 06:17:21: 26000000 INFO @ Fri, 16 Oct 2020 06:17:24: 34000000 INFO @ Fri, 16 Oct 2020 06:17:25: 41000000 INFO @ Fri, 16 Oct 2020 06:17:26: 27000000 INFO @ Fri, 16 Oct 2020 06:17:29: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 06:17:29: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 06:17:29: #1 total tags in treatment: 41758974 INFO @ Fri, 16 Oct 2020 06:17:29: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 06:17:29: #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 06:17:30: 35000000 INFO @ Fri, 16 Oct 2020 06:17:30: #1 tags after filtering in treatment: 41758798 INFO @ Fri, 16 Oct 2020 06:17:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 06:17:30: #1 finished! INFO @ Fri, 16 Oct 2020 06:17:30: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 06:17:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 06:17:31: 28000000 INFO @ Fri, 16 Oct 2020 06:17:35: 36000000 INFO @ Fri, 16 Oct 2020 06:17:35: #2 number of paired peaks: 46510 INFO @ Fri, 16 Oct 2020 06:17:35: start model_add_line... INFO @ Fri, 16 Oct 2020 06:17:36: start X-correlation... INFO @ Fri, 16 Oct 2020 06:17:36: end of X-cor INFO @ Fri, 16 Oct 2020 06:17:36: #2 finished! INFO @ Fri, 16 Oct 2020 06:17:36: #2 predicted fragment length is 254 bps INFO @ Fri, 16 Oct 2020 06:17:36: #2 alternative fragment length(s) may be 4,254 bps INFO @ Fri, 16 Oct 2020 06:17:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.05_model.r INFO @ Fri, 16 Oct 2020 06:17:36: #3 Call peaks... INFO @ Fri, 16 Oct 2020 06:17:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 06:17:37: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 06:17:40: 37000000 INFO @ Fri, 16 Oct 2020 06:17:43: 30000000 INFO @ Fri, 16 Oct 2020 06:17:46: 38000000 INFO @ Fri, 16 Oct 2020 06:17:48: 31000000 INFO @ Fri, 16 Oct 2020 06:17:51: 39000000 INFO @ Fri, 16 Oct 2020 06:17:53: 32000000 INFO @ Fri, 16 Oct 2020 06:17:57: 40000000 INFO @ Fri, 16 Oct 2020 06:17:59: 33000000 INFO @ Fri, 16 Oct 2020 06:18:02: 41000000 INFO @ Fri, 16 Oct 2020 06:18:04: 34000000 INFO @ Fri, 16 Oct 2020 06:18:07: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 06:18:07: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 06:18:07: #1 total tags in treatment: 41758974 INFO @ Fri, 16 Oct 2020 06:18:07: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 06:18:07: #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 06:18:07: #1 tags after filtering in treatment: 41758798 INFO @ Fri, 16 Oct 2020 06:18:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 06:18:07: #1 finished! INFO @ Fri, 16 Oct 2020 06:18:07: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 06:18:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 06:18:09: 35000000 INFO @ Fri, 16 Oct 2020 06:18:13: #2 number of paired peaks: 46510 INFO @ Fri, 16 Oct 2020 06:18:13: start model_add_line... INFO @ Fri, 16 Oct 2020 06:18:13: start X-correlation... INFO @ Fri, 16 Oct 2020 06:18:13: end of X-cor INFO @ Fri, 16 Oct 2020 06:18:13: #2 finished! INFO @ Fri, 16 Oct 2020 06:18:13: #2 predicted fragment length is 254 bps INFO @ Fri, 16 Oct 2020 06:18:13: #2 alternative fragment length(s) may be 4,254 bps INFO @ Fri, 16 Oct 2020 06:18:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.10_model.r INFO @ Fri, 16 Oct 2020 06:18:13: #3 Call peaks... INFO @ Fri, 16 Oct 2020 06:18:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 06:18:14: 36000000 INFO @ Fri, 16 Oct 2020 06:18:19: 37000000 INFO @ Fri, 16 Oct 2020 06:18:24: 38000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 06:18:29: 39000000 INFO @ Fri, 16 Oct 2020 06:18:34: 40000000 INFO @ Fri, 16 Oct 2020 06:18:39: 41000000 INFO @ Fri, 16 Oct 2020 06:18:43: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 06:18:43: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 06:18:43: #1 total tags in treatment: 41758974 INFO @ Fri, 16 Oct 2020 06:18:43: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 06:18:43: #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: #1 tags after filtering in treatment: 41758798 INFO @ Fri, 16 Oct 2020 06:18:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 06:18:44: #1 finished! INFO @ Fri, 16 Oct 2020 06:18:44: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 06:18:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 06:18:49: #2 number of paired peaks: 46510 INFO @ Fri, 16 Oct 2020 06:18:49: start model_add_line... INFO @ Fri, 16 Oct 2020 06:18:50: start X-correlation... INFO @ Fri, 16 Oct 2020 06:18:50: end of X-cor INFO @ Fri, 16 Oct 2020 06:18:50: #2 finished! INFO @ Fri, 16 Oct 2020 06:18:50: #2 predicted fragment length is 254 bps INFO @ Fri, 16 Oct 2020 06:18:50: #2 alternative fragment length(s) may be 4,254 bps INFO @ Fri, 16 Oct 2020 06:18:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.20_model.r INFO @ Fri, 16 Oct 2020 06:18:50: #3 Call peaks... INFO @ Fri, 16 Oct 2020 06:18:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 06:19:24: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 06:20:01: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 06:20:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.05_peaks.xls INFO @ Fri, 16 Oct 2020 06:20:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 06:20:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.05_summits.bed INFO @ Fri, 16 Oct 2020 06:20:14: Done! pass1 - making usageList (148 chroms): 4 millis pass2 - checking and writing primary data (27046 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 06:20:39: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 06:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.10_peaks.xls INFO @ Fri, 16 Oct 2020 06:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 06:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.10_summits.bed INFO @ Fri, 16 Oct 2020 06:20:50: Done! pass1 - making usageList (135 chroms): 4 millis pass2 - checking and writing primary data (24218 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 06:21:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.20_peaks.xls INFO @ Fri, 16 Oct 2020 06:21:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 06:21:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745131/ERX2745131.20_summits.bed INFO @ Fri, 16 Oct 2020 06:21:27: Done! pass1 - making usageList (119 chroms): 4 millis pass2 - checking and writing primary data (21605 records, 4 fields): 23 millis CompletedMACS2peakCalling