Job ID = 8184517 SRX = SRX8047599 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:57:21 prefetch.2.10.7: 1) Downloading 'SRR11471323'... 2020-08-10T03:57:21 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:00:40 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:00:40 prefetch.2.10.7: 1) 'SRR11471323' was downloaded successfully Read 62217791 spots for SRR11471323/SRR11471323.sra Written 62217791 spots for SRR11471323/SRR11471323.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: 00:41:15 62217791 reads; of these: 62217791 (100.00%) were unpaired; of these: 1473635 (2.37%) aligned 0 times 50573923 (81.29%) aligned exactly 1 time 10170233 (16.35%) aligned >1 times 97.63% overall alignment rate Time searching: 00:41:17 Overall time: 00:41:17 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] 18754061 / 60744156 = 0.3087 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 @ Mon, 10 Aug 2020 13:58:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.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 @ Mon, 10 Aug 2020 13:58:55: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:58:55: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:59:00: 1000000 INFO @ Mon, 10 Aug 2020 13:59:05: 2000000 INFO @ Mon, 10 Aug 2020 13:59:10: 3000000 INFO @ Mon, 10 Aug 2020 13:59:15: 4000000 INFO @ Mon, 10 Aug 2020 13:59:20: 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 @ Mon, 10 Aug 2020 13:59:25: 6000000 INFO @ Mon, 10 Aug 2020 13:59:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.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 @ Mon, 10 Aug 2020 13:59:25: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:59:25: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:59:29: 7000000 INFO @ Mon, 10 Aug 2020 13:59:30: 1000000 INFO @ Mon, 10 Aug 2020 13:59:34: 8000000 INFO @ Mon, 10 Aug 2020 13:59:35: 2000000 INFO @ Mon, 10 Aug 2020 13:59:39: 9000000 INFO @ Mon, 10 Aug 2020 13:59:40: 3000000 INFO @ Mon, 10 Aug 2020 13:59:44: 10000000 INFO @ Mon, 10 Aug 2020 13:59:45: 4000000 INFO @ Mon, 10 Aug 2020 13:59:49: 11000000 INFO @ Mon, 10 Aug 2020 13:59:50: 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 @ Mon, 10 Aug 2020 13:59:54: 12000000 INFO @ Mon, 10 Aug 2020 13:59:55: 6000000 INFO @ Mon, 10 Aug 2020 13:59:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.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 @ Mon, 10 Aug 2020 13:59:55: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:59:55: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:59:59: 13000000 INFO @ Mon, 10 Aug 2020 14:00:00: 7000000 INFO @ Mon, 10 Aug 2020 14:00:01: 1000000 INFO @ Mon, 10 Aug 2020 14:00:04: 14000000 INFO @ Mon, 10 Aug 2020 14:00:05: 8000000 INFO @ Mon, 10 Aug 2020 14:00:06: 2000000 INFO @ Mon, 10 Aug 2020 14:00:09: 15000000 INFO @ Mon, 10 Aug 2020 14:00:10: 9000000 INFO @ Mon, 10 Aug 2020 14:00:11: 3000000 INFO @ Mon, 10 Aug 2020 14:00:14: 16000000 INFO @ Mon, 10 Aug 2020 14:00:15: 10000000 INFO @ Mon, 10 Aug 2020 14:00:16: 4000000 INFO @ Mon, 10 Aug 2020 14:00:19: 17000000 INFO @ Mon, 10 Aug 2020 14:00:20: 11000000 INFO @ Mon, 10 Aug 2020 14:00:21: 5000000 INFO @ Mon, 10 Aug 2020 14:00:24: 18000000 INFO @ Mon, 10 Aug 2020 14:00:25: 12000000 INFO @ Mon, 10 Aug 2020 14:00:27: 6000000 INFO @ Mon, 10 Aug 2020 14:00:29: 19000000 INFO @ Mon, 10 Aug 2020 14:00:31: 13000000 INFO @ Mon, 10 Aug 2020 14:00:32: 7000000 INFO @ Mon, 10 Aug 2020 14:00:34: 20000000 INFO @ Mon, 10 Aug 2020 14:00:36: 14000000 INFO @ Mon, 10 Aug 2020 14:00:37: 8000000 INFO @ Mon, 10 Aug 2020 14:00:39: 21000000 INFO @ Mon, 10 Aug 2020 14:00:41: 15000000 INFO @ Mon, 10 Aug 2020 14:00:42: 9000000 INFO @ Mon, 10 Aug 2020 14:00:44: 22000000 INFO @ Mon, 10 Aug 2020 14:00:46: 16000000 INFO @ Mon, 10 Aug 2020 14:00:47: 10000000 INFO @ Mon, 10 Aug 2020 14:00:49: 23000000 INFO @ Mon, 10 Aug 2020 14:00:51: 17000000 INFO @ Mon, 10 Aug 2020 14:00:52: 11000000 INFO @ Mon, 10 Aug 2020 14:00:54: 24000000 INFO @ Mon, 10 Aug 2020 14:00:56: 18000000 INFO @ Mon, 10 Aug 2020 14:00:57: 12000000 INFO @ Mon, 10 Aug 2020 14:00:59: 25000000 INFO @ Mon, 10 Aug 2020 14:01:01: 19000000 INFO @ Mon, 10 Aug 2020 14:01:02: 13000000 INFO @ Mon, 10 Aug 2020 14:01:04: 26000000 INFO @ Mon, 10 Aug 2020 14:01:06: 20000000 INFO @ Mon, 10 Aug 2020 14:01:07: 14000000 INFO @ Mon, 10 Aug 2020 14:01:09: 27000000 INFO @ Mon, 10 Aug 2020 14:01:11: 21000000 INFO @ Mon, 10 Aug 2020 14:01:12: 15000000 INFO @ Mon, 10 Aug 2020 14:01:15: 28000000 INFO @ Mon, 10 Aug 2020 14:01:16: 22000000 INFO @ Mon, 10 Aug 2020 14:01:17: 16000000 INFO @ Mon, 10 Aug 2020 14:01:20: 29000000 INFO @ Mon, 10 Aug 2020 14:01:21: 23000000 INFO @ Mon, 10 Aug 2020 14:01:22: 17000000 INFO @ Mon, 10 Aug 2020 14:01:25: 30000000 INFO @ Mon, 10 Aug 2020 14:01:26: 24000000 INFO @ Mon, 10 Aug 2020 14:01:27: 18000000 INFO @ Mon, 10 Aug 2020 14:01:30: 31000000 INFO @ Mon, 10 Aug 2020 14:01:31: 25000000 INFO @ Mon, 10 Aug 2020 14:01:32: 19000000 INFO @ Mon, 10 Aug 2020 14:01:35: 32000000 INFO @ Mon, 10 Aug 2020 14:01:36: 26000000 INFO @ Mon, 10 Aug 2020 14:01:37: 20000000 INFO @ Mon, 10 Aug 2020 14:01:40: 33000000 INFO @ Mon, 10 Aug 2020 14:01:42: 27000000 INFO @ Mon, 10 Aug 2020 14:01:42: 21000000 INFO @ Mon, 10 Aug 2020 14:01:45: 34000000 INFO @ Mon, 10 Aug 2020 14:01:47: 28000000 INFO @ Mon, 10 Aug 2020 14:01:47: 22000000 INFO @ Mon, 10 Aug 2020 14:01:50: 35000000 INFO @ Mon, 10 Aug 2020 14:01:52: 29000000 INFO @ Mon, 10 Aug 2020 14:01:52: 23000000 INFO @ Mon, 10 Aug 2020 14:01:55: 36000000 INFO @ Mon, 10 Aug 2020 14:01:57: 24000000 INFO @ Mon, 10 Aug 2020 14:01:57: 30000000 INFO @ Mon, 10 Aug 2020 14:02:00: 37000000 INFO @ Mon, 10 Aug 2020 14:02:02: 25000000 INFO @ Mon, 10 Aug 2020 14:02:02: 31000000 INFO @ Mon, 10 Aug 2020 14:02:05: 38000000 INFO @ Mon, 10 Aug 2020 14:02:07: 26000000 INFO @ Mon, 10 Aug 2020 14:02:07: 32000000 INFO @ Mon, 10 Aug 2020 14:02:10: 39000000 INFO @ Mon, 10 Aug 2020 14:02:12: 27000000 INFO @ Mon, 10 Aug 2020 14:02:12: 33000000 INFO @ Mon, 10 Aug 2020 14:02:15: 40000000 INFO @ Mon, 10 Aug 2020 14:02:17: 28000000 INFO @ Mon, 10 Aug 2020 14:02:17: 34000000 INFO @ Mon, 10 Aug 2020 14:02:20: 41000000 INFO @ Mon, 10 Aug 2020 14:02:22: 29000000 INFO @ Mon, 10 Aug 2020 14:02:22: 35000000 INFO @ Mon, 10 Aug 2020 14:02:26: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:02:26: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:02:26: #1 total tags in treatment: 41990095 INFO @ Mon, 10 Aug 2020 14:02:26: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:02:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:02:26: #1 tags after filtering in treatment: 41989979 INFO @ Mon, 10 Aug 2020 14:02:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:02:26: #1 finished! INFO @ Mon, 10 Aug 2020 14:02:26: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:02:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:02:27: 30000000 INFO @ Mon, 10 Aug 2020 14:02:27: 36000000 INFO @ Mon, 10 Aug 2020 14:02:32: 31000000 INFO @ Mon, 10 Aug 2020 14:02:32: #2 number of paired peaks: 72324 INFO @ Mon, 10 Aug 2020 14:02:32: start model_add_line... INFO @ Mon, 10 Aug 2020 14:02:32: 37000000 INFO @ Mon, 10 Aug 2020 14:02:33: start X-correlation... INFO @ Mon, 10 Aug 2020 14:02:33: end of X-cor INFO @ Mon, 10 Aug 2020 14:02:33: #2 finished! INFO @ Mon, 10 Aug 2020 14:02:33: #2 predicted fragment length is 140 bps INFO @ Mon, 10 Aug 2020 14:02:33: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 10 Aug 2020 14:02:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.05_model.r INFO @ Mon, 10 Aug 2020 14:02:33: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:02:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:02:37: 32000000 INFO @ Mon, 10 Aug 2020 14:02:38: 38000000 INFO @ Mon, 10 Aug 2020 14:02:42: 33000000 INFO @ Mon, 10 Aug 2020 14:02:43: 39000000 INFO @ Mon, 10 Aug 2020 14:02:47: 34000000 INFO @ Mon, 10 Aug 2020 14:02:49: 40000000 INFO @ Mon, 10 Aug 2020 14:02:53: 35000000 INFO @ Mon, 10 Aug 2020 14:02:55: 41000000 INFO @ Mon, 10 Aug 2020 14:02:58: 36000000 INFO @ Mon, 10 Aug 2020 14:03:01: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:03:01: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:03:01: #1 total tags in treatment: 41990095 INFO @ Mon, 10 Aug 2020 14:03:01: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:03:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:03:02: #1 tags after filtering in treatment: 41989979 INFO @ Mon, 10 Aug 2020 14:03:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:03:02: #1 finished! INFO @ Mon, 10 Aug 2020 14:03:02: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:03:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:03:04: 37000000 INFO @ Mon, 10 Aug 2020 14:03:08: #2 number of paired peaks: 72324 INFO @ Mon, 10 Aug 2020 14:03:08: start model_add_line... INFO @ Mon, 10 Aug 2020 14:03:08: start X-correlation... INFO @ Mon, 10 Aug 2020 14:03:08: end of X-cor INFO @ Mon, 10 Aug 2020 14:03:08: #2 finished! INFO @ Mon, 10 Aug 2020 14:03:08: #2 predicted fragment length is 140 bps INFO @ Mon, 10 Aug 2020 14:03:08: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 10 Aug 2020 14:03:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.10_model.r INFO @ Mon, 10 Aug 2020 14:03:08: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:03:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:03:09: 38000000 INFO @ Mon, 10 Aug 2020 14:03:14: 39000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:03:19: 40000000 INFO @ Mon, 10 Aug 2020 14:03:24: 41000000 INFO @ Mon, 10 Aug 2020 14:03:29: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:03:29: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:03:29: #1 total tags in treatment: 41990095 INFO @ Mon, 10 Aug 2020 14:03:29: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:03:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:03:30: #1 tags after filtering in treatment: 41989979 INFO @ Mon, 10 Aug 2020 14:03:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:03:30: #1 finished! INFO @ Mon, 10 Aug 2020 14:03:30: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:03:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:03:36: #2 number of paired peaks: 72324 INFO @ Mon, 10 Aug 2020 14:03:36: start model_add_line... INFO @ Mon, 10 Aug 2020 14:03:36: start X-correlation... INFO @ Mon, 10 Aug 2020 14:03:36: end of X-cor INFO @ Mon, 10 Aug 2020 14:03:36: #2 finished! INFO @ Mon, 10 Aug 2020 14:03:36: #2 predicted fragment length is 140 bps INFO @ Mon, 10 Aug 2020 14:03:36: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 10 Aug 2020 14:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.20_model.r INFO @ Mon, 10 Aug 2020 14:03:36: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:03:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:04:15: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:04:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:05:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:05:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:05:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.05_summits.bed INFO @ Mon, 10 Aug 2020 14:05:11: Done! pass1 - making usageList (122 chroms): 6 millis pass2 - checking and writing primary data (37244 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:05:15: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:05:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:05:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:05:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.10_summits.bed INFO @ Mon, 10 Aug 2020 14:05:37: Done! pass1 - making usageList (103 chroms): 4 millis pass2 - checking and writing primary data (22942 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:06:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:06:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:06:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047599/SRX8047599.20_summits.bed INFO @ Mon, 10 Aug 2020 14:06:04: Done! pass1 - making usageList (78 chroms): 2 millis pass2 - checking and writing primary data (13543 records, 4 fields): 15 millis CompletedMACS2peakCalling