Job ID = 8184514 SRX = SRX8047598 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:53:51 prefetch.2.10.7: 1) Downloading 'SRR11471322'... 2020-08-10T03:53:51 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:56:08 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:56:08 prefetch.2.10.7: 1) 'SRR11471322' was downloaded successfully Read 58852396 spots for SRR11471322/SRR11471322.sra Written 58852396 spots for SRR11471322/SRR11471322.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: 00:00:01 Multiseed full-index search: 00:45:55 58852396 reads; of these: 58852396 (100.00%) were unpaired; of these: 2514333 (4.27%) aligned 0 times 43994694 (74.75%) aligned exactly 1 time 12343369 (20.97%) aligned >1 times 95.73% overall alignment rate Time searching: 00:45:57 Overall time: 00:45:57 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] 17471867 / 56338063 = 0.3101 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 13:57:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.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 13:57:59: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:57:59: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:58:04: 1000000 INFO @ Mon, 10 Aug 2020 13:58:09: 2000000 INFO @ Mon, 10 Aug 2020 13:58:14: 3000000 INFO @ Mon, 10 Aug 2020 13:58:19: 4000000 INFO @ Mon, 10 Aug 2020 13:58:24: 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 13:58:29: 6000000 INFO @ Mon, 10 Aug 2020 13:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.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 13:58:29: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:58:29: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:58:34: 7000000 INFO @ Mon, 10 Aug 2020 13:58:34: 1000000 INFO @ Mon, 10 Aug 2020 13:58:39: 8000000 INFO @ Mon, 10 Aug 2020 13:58:39: 2000000 INFO @ Mon, 10 Aug 2020 13:58:44: 9000000 INFO @ Mon, 10 Aug 2020 13:58:44: 3000000 INFO @ Mon, 10 Aug 2020 13:58:49: 10000000 INFO @ Mon, 10 Aug 2020 13:58:49: 4000000 INFO @ Mon, 10 Aug 2020 13:58:54: 11000000 INFO @ Mon, 10 Aug 2020 13:58:55: 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 13:58:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.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 13:58:59: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:58:59: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:59:00: 12000000 INFO @ Mon, 10 Aug 2020 13:59:00: 6000000 INFO @ Mon, 10 Aug 2020 13:59:05: 1000000 INFO @ Mon, 10 Aug 2020 13:59:05: 13000000 INFO @ Mon, 10 Aug 2020 13:59:05: 7000000 INFO @ Mon, 10 Aug 2020 13:59:10: 2000000 INFO @ Mon, 10 Aug 2020 13:59:10: 14000000 INFO @ Mon, 10 Aug 2020 13:59:10: 8000000 INFO @ Mon, 10 Aug 2020 13:59:15: 3000000 INFO @ Mon, 10 Aug 2020 13:59:16: 15000000 INFO @ Mon, 10 Aug 2020 13:59:16: 9000000 INFO @ Mon, 10 Aug 2020 13:59:20: 4000000 INFO @ Mon, 10 Aug 2020 13:59:21: 16000000 INFO @ Mon, 10 Aug 2020 13:59:21: 10000000 INFO @ Mon, 10 Aug 2020 13:59:26: 5000000 INFO @ Mon, 10 Aug 2020 13:59:26: 11000000 INFO @ Mon, 10 Aug 2020 13:59:26: 17000000 INFO @ Mon, 10 Aug 2020 13:59:31: 6000000 INFO @ Mon, 10 Aug 2020 13:59:31: 12000000 INFO @ Mon, 10 Aug 2020 13:59:32: 18000000 INFO @ Mon, 10 Aug 2020 13:59:36: 7000000 INFO @ Mon, 10 Aug 2020 13:59:36: 13000000 INFO @ Mon, 10 Aug 2020 13:59:37: 19000000 INFO @ Mon, 10 Aug 2020 13:59:41: 8000000 INFO @ Mon, 10 Aug 2020 13:59:42: 14000000 INFO @ Mon, 10 Aug 2020 13:59:43: 20000000 INFO @ Mon, 10 Aug 2020 13:59:47: 9000000 INFO @ Mon, 10 Aug 2020 13:59:47: 15000000 INFO @ Mon, 10 Aug 2020 13:59:48: 21000000 INFO @ Mon, 10 Aug 2020 13:59:52: 10000000 INFO @ Mon, 10 Aug 2020 13:59:53: 16000000 INFO @ Mon, 10 Aug 2020 13:59:54: 22000000 INFO @ Mon, 10 Aug 2020 13:59:57: 11000000 INFO @ Mon, 10 Aug 2020 13:59:58: 17000000 INFO @ Mon, 10 Aug 2020 13:59:59: 23000000 INFO @ Mon, 10 Aug 2020 14:00:02: 12000000 INFO @ Mon, 10 Aug 2020 14:00:03: 18000000 INFO @ Mon, 10 Aug 2020 14:00:04: 24000000 INFO @ Mon, 10 Aug 2020 14:00:08: 13000000 INFO @ Mon, 10 Aug 2020 14:00:08: 19000000 INFO @ Mon, 10 Aug 2020 14:00:10: 25000000 INFO @ Mon, 10 Aug 2020 14:00:13: 14000000 INFO @ Mon, 10 Aug 2020 14:00:14: 20000000 INFO @ Mon, 10 Aug 2020 14:00:15: 26000000 INFO @ Mon, 10 Aug 2020 14:00:18: 15000000 INFO @ Mon, 10 Aug 2020 14:00:19: 21000000 INFO @ Mon, 10 Aug 2020 14:00:20: 27000000 INFO @ Mon, 10 Aug 2020 14:00:23: 16000000 INFO @ Mon, 10 Aug 2020 14:00:24: 22000000 INFO @ Mon, 10 Aug 2020 14:00:25: 28000000 INFO @ Mon, 10 Aug 2020 14:00:28: 17000000 INFO @ Mon, 10 Aug 2020 14:00:29: 23000000 INFO @ Mon, 10 Aug 2020 14:00:31: 29000000 INFO @ Mon, 10 Aug 2020 14:00:34: 18000000 INFO @ Mon, 10 Aug 2020 14:00:35: 24000000 INFO @ Mon, 10 Aug 2020 14:00:36: 30000000 INFO @ Mon, 10 Aug 2020 14:00:39: 19000000 INFO @ Mon, 10 Aug 2020 14:00:40: 25000000 INFO @ Mon, 10 Aug 2020 14:00:41: 31000000 INFO @ Mon, 10 Aug 2020 14:00:44: 20000000 INFO @ Mon, 10 Aug 2020 14:00:45: 26000000 INFO @ Mon, 10 Aug 2020 14:00:46: 32000000 INFO @ Mon, 10 Aug 2020 14:00:49: 21000000 INFO @ Mon, 10 Aug 2020 14:00:50: 27000000 INFO @ Mon, 10 Aug 2020 14:00:51: 33000000 INFO @ Mon, 10 Aug 2020 14:00:54: 22000000 INFO @ Mon, 10 Aug 2020 14:00:55: 28000000 INFO @ Mon, 10 Aug 2020 14:00:57: 34000000 INFO @ Mon, 10 Aug 2020 14:01:00: 23000000 INFO @ Mon, 10 Aug 2020 14:01:01: 29000000 INFO @ Mon, 10 Aug 2020 14:01:02: 35000000 INFO @ Mon, 10 Aug 2020 14:01:05: 24000000 INFO @ Mon, 10 Aug 2020 14:01:06: 30000000 INFO @ Mon, 10 Aug 2020 14:01:08: 36000000 INFO @ Mon, 10 Aug 2020 14:01:10: 25000000 INFO @ Mon, 10 Aug 2020 14:01:11: 31000000 INFO @ Mon, 10 Aug 2020 14:01:13: 37000000 INFO @ Mon, 10 Aug 2020 14:01:16: 26000000 INFO @ Mon, 10 Aug 2020 14:01:17: 32000000 INFO @ Mon, 10 Aug 2020 14:01:19: 38000000 INFO @ Mon, 10 Aug 2020 14:01:21: 27000000 INFO @ Mon, 10 Aug 2020 14:01:22: 33000000 INFO @ Mon, 10 Aug 2020 14:01:24: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:01:24: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:01:24: #1 total tags in treatment: 38866196 INFO @ Mon, 10 Aug 2020 14:01:24: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:01:24: #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 14:01:24: #1 tags after filtering in treatment: 38866108 INFO @ Mon, 10 Aug 2020 14:01:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:01:24: #1 finished! INFO @ Mon, 10 Aug 2020 14:01:24: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:01:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:01:26: 28000000 INFO @ Mon, 10 Aug 2020 14:01:27: 34000000 INFO @ Mon, 10 Aug 2020 14:01:29: #2 number of paired peaks: 37388 INFO @ Mon, 10 Aug 2020 14:01:29: start model_add_line... INFO @ Mon, 10 Aug 2020 14:01:29: start X-correlation... INFO @ Mon, 10 Aug 2020 14:01:29: end of X-cor INFO @ Mon, 10 Aug 2020 14:01:29: #2 finished! INFO @ Mon, 10 Aug 2020 14:01:29: #2 predicted fragment length is 120 bps INFO @ Mon, 10 Aug 2020 14:01:29: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 10 Aug 2020 14:01:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.05_model.r INFO @ Mon, 10 Aug 2020 14:01:29: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:01:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:01:32: 29000000 INFO @ Mon, 10 Aug 2020 14:01:33: 35000000 INFO @ Mon, 10 Aug 2020 14:01:37: 30000000 INFO @ Mon, 10 Aug 2020 14:01:38: 36000000 INFO @ Mon, 10 Aug 2020 14:01:42: 31000000 INFO @ Mon, 10 Aug 2020 14:01:43: 37000000 INFO @ Mon, 10 Aug 2020 14:01:47: 32000000 INFO @ Mon, 10 Aug 2020 14:01:49: 38000000 INFO @ Mon, 10 Aug 2020 14:01:53: 33000000 INFO @ Mon, 10 Aug 2020 14:01:54: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:01:54: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:01:54: #1 total tags in treatment: 38866196 INFO @ Mon, 10 Aug 2020 14:01:54: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:01:54: #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 14:01:54: #1 tags after filtering in treatment: 38866108 INFO @ Mon, 10 Aug 2020 14:01:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:01:54: #1 finished! INFO @ Mon, 10 Aug 2020 14:01:54: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:01:58: 34000000 INFO @ Mon, 10 Aug 2020 14:01:59: #2 number of paired peaks: 37388 INFO @ Mon, 10 Aug 2020 14:01:59: start model_add_line... INFO @ Mon, 10 Aug 2020 14:01:59: start X-correlation... INFO @ Mon, 10 Aug 2020 14:01:59: end of X-cor INFO @ Mon, 10 Aug 2020 14:01:59: #2 finished! INFO @ Mon, 10 Aug 2020 14:01:59: #2 predicted fragment length is 120 bps INFO @ Mon, 10 Aug 2020 14:01:59: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 10 Aug 2020 14:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.10_model.r INFO @ Mon, 10 Aug 2020 14:01:59: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:01:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:02:03: 35000000 INFO @ Mon, 10 Aug 2020 14:02:08: 36000000 INFO @ Mon, 10 Aug 2020 14:02:13: 37000000 INFO @ Mon, 10 Aug 2020 14:02:18: 38000000 INFO @ Mon, 10 Aug 2020 14:02:23: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:02:23: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:02:23: #1 total tags in treatment: 38866196 INFO @ Mon, 10 Aug 2020 14:02:23: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:02:23: #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 14:02:24: #1 tags after filtering in treatment: 38866108 INFO @ Mon, 10 Aug 2020 14:02:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:02:24: #1 finished! INFO @ Mon, 10 Aug 2020 14:02:24: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:02:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:02:28: #2 number of paired peaks: 37388 INFO @ Mon, 10 Aug 2020 14:02:28: start model_add_line... INFO @ Mon, 10 Aug 2020 14:02:28: start X-correlation... INFO @ Mon, 10 Aug 2020 14:02:28: end of X-cor INFO @ Mon, 10 Aug 2020 14:02:28: #2 finished! INFO @ Mon, 10 Aug 2020 14:02:28: #2 predicted fragment length is 120 bps INFO @ Mon, 10 Aug 2020 14:02:28: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 10 Aug 2020 14:02:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.20_model.r INFO @ Mon, 10 Aug 2020 14:02:28: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:02:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:02:56: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:03:23: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:03:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:03:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:03:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.05_summits.bed INFO @ Mon, 10 Aug 2020 14:03:42: Done! pass1 - making usageList (113 chroms): 3 millis pass2 - checking and writing primary data (19778 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:03:50: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:04:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:04:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:04:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.10_summits.bed INFO @ Mon, 10 Aug 2020 14:04:08: Done! pass1 - making usageList (88 chroms): 2 millis pass2 - checking and writing primary data (9452 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:04:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:04:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:04:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047598/SRX8047598.20_summits.bed INFO @ Mon, 10 Aug 2020 14:04:34: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (2761 records, 4 fields): 5 millis CompletedMACS2peakCalling