Job ID = 8184544 SRX = SRX8047603 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:23:08 prefetch.2.10.7: 1) Downloading 'SRR11471327'... 2020-08-10T04:23:08 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:26:10 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:26:10 prefetch.2.10.7: 1) 'SRR11471327' was downloaded successfully Read 60331323 spots for SRR11471327/SRR11471327.sra Written 60331323 spots for SRR11471327/SRR11471327.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: 00:38:13 60331323 reads; of these: 60331323 (100.00%) were unpaired; of these: 1733304 (2.87%) aligned 0 times 49985569 (82.85%) aligned exactly 1 time 8612450 (14.28%) aligned >1 times 97.13% overall alignment rate Time searching: 00:38:15 Overall time: 00:38:15 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 24 files... [bam_rmdupse_core] 18417177 / 58598019 = 0.3143 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 14:20:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.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 14:20:37: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:20:37: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:20:43: 1000000 INFO @ Mon, 10 Aug 2020 14:20:48: 2000000 INFO @ Mon, 10 Aug 2020 14:20:54: 3000000 INFO @ Mon, 10 Aug 2020 14:21:00: 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 @ Mon, 10 Aug 2020 14:21:05: 5000000 INFO @ Mon, 10 Aug 2020 14:21:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.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 14:21:07: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:21:07: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:21:12: 6000000 INFO @ Mon, 10 Aug 2020 14:21:13: 1000000 INFO @ Mon, 10 Aug 2020 14:21:18: 7000000 INFO @ Mon, 10 Aug 2020 14:21:20: 2000000 INFO @ Mon, 10 Aug 2020 14:21:25: 8000000 INFO @ Mon, 10 Aug 2020 14:21:26: 3000000 INFO @ Mon, 10 Aug 2020 14:21:31: 9000000 INFO @ Mon, 10 Aug 2020 14:21:33: 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 @ Mon, 10 Aug 2020 14:21:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.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 14:21:37: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:21:37: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:21:38: 10000000 INFO @ Mon, 10 Aug 2020 14:21:39: 5000000 INFO @ Mon, 10 Aug 2020 14:21:44: 1000000 INFO @ Mon, 10 Aug 2020 14:21:44: 11000000 INFO @ Mon, 10 Aug 2020 14:21:46: 6000000 INFO @ Mon, 10 Aug 2020 14:21:50: 2000000 INFO @ Mon, 10 Aug 2020 14:21:51: 12000000 INFO @ Mon, 10 Aug 2020 14:21:52: 7000000 INFO @ Mon, 10 Aug 2020 14:21:56: 3000000 INFO @ Mon, 10 Aug 2020 14:21:57: 13000000 INFO @ Mon, 10 Aug 2020 14:21:59: 8000000 INFO @ Mon, 10 Aug 2020 14:22:03: 4000000 INFO @ Mon, 10 Aug 2020 14:22:04: 14000000 INFO @ Mon, 10 Aug 2020 14:22:05: 9000000 INFO @ Mon, 10 Aug 2020 14:22:09: 5000000 INFO @ Mon, 10 Aug 2020 14:22:10: 15000000 INFO @ Mon, 10 Aug 2020 14:22:12: 10000000 INFO @ Mon, 10 Aug 2020 14:22:16: 6000000 INFO @ Mon, 10 Aug 2020 14:22:17: 16000000 INFO @ Mon, 10 Aug 2020 14:22:18: 11000000 INFO @ Mon, 10 Aug 2020 14:22:22: 7000000 INFO @ Mon, 10 Aug 2020 14:22:23: 17000000 INFO @ Mon, 10 Aug 2020 14:22:25: 12000000 INFO @ Mon, 10 Aug 2020 14:22:29: 8000000 INFO @ Mon, 10 Aug 2020 14:22:30: 18000000 INFO @ Mon, 10 Aug 2020 14:22:31: 13000000 INFO @ Mon, 10 Aug 2020 14:22:35: 9000000 INFO @ Mon, 10 Aug 2020 14:22:36: 19000000 INFO @ Mon, 10 Aug 2020 14:22:38: 14000000 INFO @ Mon, 10 Aug 2020 14:22:42: 10000000 INFO @ Mon, 10 Aug 2020 14:22:43: 20000000 INFO @ Mon, 10 Aug 2020 14:22:44: 15000000 INFO @ Mon, 10 Aug 2020 14:22:49: 11000000 INFO @ Mon, 10 Aug 2020 14:22:49: 21000000 INFO @ Mon, 10 Aug 2020 14:22:51: 16000000 INFO @ Mon, 10 Aug 2020 14:22:55: 12000000 INFO @ Mon, 10 Aug 2020 14:22:56: 22000000 INFO @ Mon, 10 Aug 2020 14:22:57: 17000000 INFO @ Mon, 10 Aug 2020 14:23:01: 13000000 INFO @ Mon, 10 Aug 2020 14:23:02: 23000000 INFO @ Mon, 10 Aug 2020 14:23:04: 18000000 INFO @ Mon, 10 Aug 2020 14:23:08: 14000000 INFO @ Mon, 10 Aug 2020 14:23:09: 24000000 INFO @ Mon, 10 Aug 2020 14:23:10: 19000000 INFO @ Mon, 10 Aug 2020 14:23:14: 15000000 INFO @ Mon, 10 Aug 2020 14:23:15: 25000000 INFO @ Mon, 10 Aug 2020 14:23:17: 20000000 INFO @ Mon, 10 Aug 2020 14:23:21: 16000000 INFO @ Mon, 10 Aug 2020 14:23:22: 26000000 INFO @ Mon, 10 Aug 2020 14:23:23: 21000000 INFO @ Mon, 10 Aug 2020 14:23:27: 17000000 INFO @ Mon, 10 Aug 2020 14:23:28: 27000000 INFO @ Mon, 10 Aug 2020 14:23:29: 22000000 INFO @ Mon, 10 Aug 2020 14:23:34: 18000000 INFO @ Mon, 10 Aug 2020 14:23:35: 28000000 INFO @ Mon, 10 Aug 2020 14:23:36: 23000000 INFO @ Mon, 10 Aug 2020 14:23:40: 19000000 INFO @ Mon, 10 Aug 2020 14:23:41: 29000000 INFO @ Mon, 10 Aug 2020 14:23:43: 24000000 INFO @ Mon, 10 Aug 2020 14:23:47: 20000000 INFO @ Mon, 10 Aug 2020 14:23:48: 30000000 INFO @ Mon, 10 Aug 2020 14:23:50: 25000000 INFO @ Mon, 10 Aug 2020 14:23:54: 21000000 INFO @ Mon, 10 Aug 2020 14:23:55: 31000000 INFO @ Mon, 10 Aug 2020 14:23:57: 26000000 INFO @ Mon, 10 Aug 2020 14:24:01: 22000000 INFO @ Mon, 10 Aug 2020 14:24:02: 32000000 INFO @ Mon, 10 Aug 2020 14:24:04: 27000000 INFO @ Mon, 10 Aug 2020 14:24:08: 23000000 INFO @ Mon, 10 Aug 2020 14:24:09: 33000000 INFO @ Mon, 10 Aug 2020 14:24:11: 28000000 INFO @ Mon, 10 Aug 2020 14:24:15: 24000000 INFO @ Mon, 10 Aug 2020 14:24:16: 34000000 INFO @ Mon, 10 Aug 2020 14:24:17: 29000000 INFO @ Mon, 10 Aug 2020 14:24:22: 25000000 INFO @ Mon, 10 Aug 2020 14:24:22: 35000000 INFO @ Mon, 10 Aug 2020 14:24:24: 30000000 INFO @ Mon, 10 Aug 2020 14:24:29: 26000000 INFO @ Mon, 10 Aug 2020 14:24:29: 36000000 INFO @ Mon, 10 Aug 2020 14:24:31: 31000000 INFO @ Mon, 10 Aug 2020 14:24:35: 27000000 INFO @ Mon, 10 Aug 2020 14:24:36: 37000000 INFO @ Mon, 10 Aug 2020 14:24:38: 32000000 INFO @ Mon, 10 Aug 2020 14:24:42: 28000000 INFO @ Mon, 10 Aug 2020 14:24:42: 38000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:24:44: 33000000 INFO @ Mon, 10 Aug 2020 14:24:49: 29000000 INFO @ Mon, 10 Aug 2020 14:24:49: 39000000 INFO @ Mon, 10 Aug 2020 14:24:51: 34000000 INFO @ Mon, 10 Aug 2020 14:24:56: 30000000 INFO @ Mon, 10 Aug 2020 14:24:56: 40000000 INFO @ Mon, 10 Aug 2020 14:24:57: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:24:57: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:24:57: #1 total tags in treatment: 40180842 INFO @ Mon, 10 Aug 2020 14:24:57: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:24:57: #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 14:24:58: 35000000 INFO @ Mon, 10 Aug 2020 14:24:58: #1 tags after filtering in treatment: 40180687 INFO @ Mon, 10 Aug 2020 14:24:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:24:58: #1 finished! INFO @ Mon, 10 Aug 2020 14:24:58: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:24:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:25:03: 31000000 INFO @ Mon, 10 Aug 2020 14:25:04: #2 number of paired peaks: 86992 INFO @ Mon, 10 Aug 2020 14:25:04: start model_add_line... INFO @ Mon, 10 Aug 2020 14:25:05: 36000000 INFO @ Mon, 10 Aug 2020 14:25:05: start X-correlation... INFO @ Mon, 10 Aug 2020 14:25:05: end of X-cor INFO @ Mon, 10 Aug 2020 14:25:05: #2 finished! INFO @ Mon, 10 Aug 2020 14:25:05: #2 predicted fragment length is 120 bps INFO @ Mon, 10 Aug 2020 14:25:05: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 10 Aug 2020 14:25:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.05_model.r INFO @ Mon, 10 Aug 2020 14:25:05: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:25:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:25:09: 32000000 INFO @ Mon, 10 Aug 2020 14:25:11: 37000000 INFO @ Mon, 10 Aug 2020 14:25:16: 33000000 INFO @ Mon, 10 Aug 2020 14:25:18: 38000000 INFO @ Mon, 10 Aug 2020 14:25:23: 34000000 INFO @ Mon, 10 Aug 2020 14:25:24: 39000000 INFO @ Mon, 10 Aug 2020 14:25:29: 35000000 INFO @ Mon, 10 Aug 2020 14:25:31: 40000000 INFO @ Mon, 10 Aug 2020 14:25:32: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:25:32: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:25:32: #1 total tags in treatment: 40180842 INFO @ Mon, 10 Aug 2020 14:25:32: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:25:32: #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 14:25:33: #1 tags after filtering in treatment: 40180687 INFO @ Mon, 10 Aug 2020 14:25:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:25:33: #1 finished! INFO @ Mon, 10 Aug 2020 14:25:33: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:25:35: 36000000 INFO @ Mon, 10 Aug 2020 14:25:39: #2 number of paired peaks: 86992 INFO @ Mon, 10 Aug 2020 14:25:39: start model_add_line... INFO @ Mon, 10 Aug 2020 14:25:40: start X-correlation... INFO @ Mon, 10 Aug 2020 14:25:40: end of X-cor INFO @ Mon, 10 Aug 2020 14:25:40: #2 finished! INFO @ Mon, 10 Aug 2020 14:25:40: #2 predicted fragment length is 120 bps INFO @ Mon, 10 Aug 2020 14:25:40: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 10 Aug 2020 14:25:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.10_model.r INFO @ Mon, 10 Aug 2020 14:25:40: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:25:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:25:41: 37000000 INFO @ Mon, 10 Aug 2020 14:25:46: 38000000 INFO @ Mon, 10 Aug 2020 14:25:52: 39000000 INFO @ Mon, 10 Aug 2020 14:25:57: 40000000 INFO @ Mon, 10 Aug 2020 14:25:59: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:25:59: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:25:59: #1 total tags in treatment: 40180842 INFO @ Mon, 10 Aug 2020 14:25:59: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:25:59: #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 14:25:59: #1 tags after filtering in treatment: 40180687 INFO @ Mon, 10 Aug 2020 14:25:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:25:59: #1 finished! INFO @ Mon, 10 Aug 2020 14:25:59: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:26:05: #2 number of paired peaks: 86992 INFO @ Mon, 10 Aug 2020 14:26:05: start model_add_line... INFO @ Mon, 10 Aug 2020 14:26:06: start X-correlation... INFO @ Mon, 10 Aug 2020 14:26:06: end of X-cor INFO @ Mon, 10 Aug 2020 14:26:06: #2 finished! INFO @ Mon, 10 Aug 2020 14:26:06: #2 predicted fragment length is 120 bps INFO @ Mon, 10 Aug 2020 14:26:06: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 10 Aug 2020 14:26:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.20_model.r INFO @ Mon, 10 Aug 2020 14:26:06: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:26:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:26:37: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:27:12: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:27:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:27:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:27:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.05_summits.bed INFO @ Mon, 10 Aug 2020 14:27:28: Done! pass1 - making usageList (129 chroms): 6 millis pass2 - checking and writing primary data (44846 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:27:37: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:28:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:28:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:28:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.10_summits.bed INFO @ Mon, 10 Aug 2020 14:28:03: Done! pass1 - making usageList (102 chroms): 4 millis pass2 - checking and writing primary data (25988 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:28:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:28:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:28:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047603/SRX8047603.20_summits.bed INFO @ Mon, 10 Aug 2020 14:28:27: Done! pass1 - making usageList (81 chroms): 2 millis pass2 - checking and writing primary data (14683 records, 4 fields): 16 millis CompletedMACS2peakCalling