Job ID = 8184594 SRX = SRX8047615 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:49:09 prefetch.2.10.7: 1) Downloading 'SRR11471339'... 2020-08-10T04:49:09 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:51:53 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:51:53 prefetch.2.10.7: 1) 'SRR11471339' was downloaded successfully Read 55188152 spots for SRR11471339/SRR11471339.sra Written 55188152 spots for SRR11471339/SRR11471339.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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:26:07 55188152 reads; of these: 55188152 (100.00%) were unpaired; of these: 2355174 (4.27%) aligned 0 times 45958372 (83.28%) aligned exactly 1 time 6874606 (12.46%) aligned >1 times 95.73% overall alignment rate Time searching: 00:26:13 Overall time: 00:26:13 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] 18305477 / 52832978 = 0.3465 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 14:32:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.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 14:32:26: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:32:26: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:32:32: 1000000 INFO @ Mon, 10 Aug 2020 14:32:38: 2000000 INFO @ Mon, 10 Aug 2020 14:32:44: 3000000 INFO @ Mon, 10 Aug 2020 14:32:50: 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 14:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.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 14:32:55: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:32:55: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:32:56: 5000000 INFO @ Mon, 10 Aug 2020 14:33:02: 1000000 INFO @ Mon, 10 Aug 2020 14:33:03: 6000000 INFO @ Mon, 10 Aug 2020 14:33:09: 2000000 INFO @ Mon, 10 Aug 2020 14:33:10: 7000000 INFO @ Mon, 10 Aug 2020 14:33:16: 3000000 INFO @ Mon, 10 Aug 2020 14:33:17: 8000000 INFO @ Mon, 10 Aug 2020 14:33:23: 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 14:33:24: 9000000 INFO @ Mon, 10 Aug 2020 14:33:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.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 14:33:26: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:33:26: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:33:30: 5000000 INFO @ Mon, 10 Aug 2020 14:33:31: 10000000 INFO @ Mon, 10 Aug 2020 14:33:33: 1000000 INFO @ Mon, 10 Aug 2020 14:33:37: 6000000 INFO @ Mon, 10 Aug 2020 14:33:38: 11000000 INFO @ Mon, 10 Aug 2020 14:33:40: 2000000 INFO @ Mon, 10 Aug 2020 14:33:44: 7000000 INFO @ Mon, 10 Aug 2020 14:33:45: 12000000 INFO @ Mon, 10 Aug 2020 14:33:47: 3000000 INFO @ Mon, 10 Aug 2020 14:33:51: 8000000 INFO @ Mon, 10 Aug 2020 14:33:52: 13000000 INFO @ Mon, 10 Aug 2020 14:33:54: 4000000 INFO @ Mon, 10 Aug 2020 14:33:58: 9000000 INFO @ Mon, 10 Aug 2020 14:33:59: 14000000 INFO @ Mon, 10 Aug 2020 14:34:00: 5000000 INFO @ Mon, 10 Aug 2020 14:34:05: 10000000 INFO @ Mon, 10 Aug 2020 14:34:06: 15000000 INFO @ Mon, 10 Aug 2020 14:34:07: 6000000 INFO @ Mon, 10 Aug 2020 14:34:12: 11000000 INFO @ Mon, 10 Aug 2020 14:34:13: 16000000 INFO @ Mon, 10 Aug 2020 14:34:14: 7000000 INFO @ Mon, 10 Aug 2020 14:34:19: 12000000 INFO @ Mon, 10 Aug 2020 14:34:20: 17000000 INFO @ Mon, 10 Aug 2020 14:34:21: 8000000 INFO @ Mon, 10 Aug 2020 14:34:26: 13000000 INFO @ Mon, 10 Aug 2020 14:34:27: 18000000 INFO @ Mon, 10 Aug 2020 14:34:28: 9000000 INFO @ Mon, 10 Aug 2020 14:34:33: 14000000 INFO @ Mon, 10 Aug 2020 14:34:35: 19000000 INFO @ Mon, 10 Aug 2020 14:34:35: 10000000 INFO @ Mon, 10 Aug 2020 14:34:40: 15000000 INFO @ Mon, 10 Aug 2020 14:34:42: 20000000 INFO @ Mon, 10 Aug 2020 14:34:42: 11000000 INFO @ Mon, 10 Aug 2020 14:34:47: 16000000 INFO @ Mon, 10 Aug 2020 14:34:49: 21000000 INFO @ Mon, 10 Aug 2020 14:34:49: 12000000 INFO @ Mon, 10 Aug 2020 14:34:54: 17000000 INFO @ Mon, 10 Aug 2020 14:34:56: 22000000 INFO @ Mon, 10 Aug 2020 14:34:56: 13000000 INFO @ Mon, 10 Aug 2020 14:35:01: 18000000 INFO @ Mon, 10 Aug 2020 14:35:03: 23000000 INFO @ Mon, 10 Aug 2020 14:35:03: 14000000 INFO @ Mon, 10 Aug 2020 14:35:08: 19000000 INFO @ Mon, 10 Aug 2020 14:35:10: 24000000 INFO @ Mon, 10 Aug 2020 14:35:10: 15000000 INFO @ Mon, 10 Aug 2020 14:35:15: 20000000 INFO @ Mon, 10 Aug 2020 14:35:17: 25000000 INFO @ Mon, 10 Aug 2020 14:35:17: 16000000 INFO @ Mon, 10 Aug 2020 14:35:22: 21000000 INFO @ Mon, 10 Aug 2020 14:35:24: 26000000 INFO @ Mon, 10 Aug 2020 14:35:25: 17000000 INFO @ Mon, 10 Aug 2020 14:35:29: 22000000 INFO @ Mon, 10 Aug 2020 14:35:31: 27000000 INFO @ Mon, 10 Aug 2020 14:35:32: 18000000 INFO @ Mon, 10 Aug 2020 14:35:36: 23000000 INFO @ Mon, 10 Aug 2020 14:35:38: 28000000 INFO @ Mon, 10 Aug 2020 14:35:39: 19000000 INFO @ Mon, 10 Aug 2020 14:35:43: 24000000 INFO @ Mon, 10 Aug 2020 14:35:45: 29000000 INFO @ Mon, 10 Aug 2020 14:35:46: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:35:50: 25000000 INFO @ Mon, 10 Aug 2020 14:35:52: 30000000 INFO @ Mon, 10 Aug 2020 14:35:53: 21000000 INFO @ Mon, 10 Aug 2020 14:35:57: 26000000 INFO @ Mon, 10 Aug 2020 14:36:00: 31000000 INFO @ Mon, 10 Aug 2020 14:36:00: 22000000 INFO @ Mon, 10 Aug 2020 14:36:04: 27000000 INFO @ Mon, 10 Aug 2020 14:36:07: 32000000 INFO @ Mon, 10 Aug 2020 14:36:07: 23000000 INFO @ Mon, 10 Aug 2020 14:36:11: 28000000 INFO @ Mon, 10 Aug 2020 14:36:14: 33000000 INFO @ Mon, 10 Aug 2020 14:36:14: 24000000 INFO @ Mon, 10 Aug 2020 14:36:18: 29000000 INFO @ Mon, 10 Aug 2020 14:36:21: 25000000 INFO @ Mon, 10 Aug 2020 14:36:21: 34000000 INFO @ Mon, 10 Aug 2020 14:36:25: 30000000 INFO @ Mon, 10 Aug 2020 14:36:25: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:36:25: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:36:25: #1 total tags in treatment: 34527501 INFO @ Mon, 10 Aug 2020 14:36:25: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:36:25: #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 14:36:26: #1 tags after filtering in treatment: 34527339 INFO @ Mon, 10 Aug 2020 14:36:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:36:26: #1 finished! INFO @ Mon, 10 Aug 2020 14:36:26: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:36:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:36:28: 26000000 INFO @ Mon, 10 Aug 2020 14:36:31: #2 number of paired peaks: 43496 INFO @ Mon, 10 Aug 2020 14:36:31: start model_add_line... INFO @ Mon, 10 Aug 2020 14:36:31: start X-correlation... INFO @ Mon, 10 Aug 2020 14:36:31: end of X-cor INFO @ Mon, 10 Aug 2020 14:36:31: #2 finished! INFO @ Mon, 10 Aug 2020 14:36:31: #2 predicted fragment length is 119 bps INFO @ Mon, 10 Aug 2020 14:36:31: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 10 Aug 2020 14:36:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.05_model.r INFO @ Mon, 10 Aug 2020 14:36:31: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:36:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:36:32: 31000000 INFO @ Mon, 10 Aug 2020 14:36:35: 27000000 BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:36:40: 32000000 INFO @ Mon, 10 Aug 2020 14:36:42: 28000000 INFO @ Mon, 10 Aug 2020 14:36:47: 33000000 INFO @ Mon, 10 Aug 2020 14:36:50: 29000000 INFO @ Mon, 10 Aug 2020 14:36:54: 34000000 INFO @ Mon, 10 Aug 2020 14:36:57: 30000000 INFO @ Mon, 10 Aug 2020 14:36:58: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:36:58: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:36:58: #1 total tags in treatment: 34527501 INFO @ Mon, 10 Aug 2020 14:36:58: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:36:58: #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 14:36:58: #1 tags after filtering in treatment: 34527339 INFO @ Mon, 10 Aug 2020 14:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:36:58: #1 finished! INFO @ Mon, 10 Aug 2020 14:36:58: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:37:03: #2 number of paired peaks: 43496 INFO @ Mon, 10 Aug 2020 14:37:03: start model_add_line... INFO @ Mon, 10 Aug 2020 14:37:03: 31000000 INFO @ Mon, 10 Aug 2020 14:37:03: start X-correlation... INFO @ Mon, 10 Aug 2020 14:37:03: end of X-cor INFO @ Mon, 10 Aug 2020 14:37:03: #2 finished! INFO @ Mon, 10 Aug 2020 14:37:03: #2 predicted fragment length is 119 bps INFO @ Mon, 10 Aug 2020 14:37:03: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 10 Aug 2020 14:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.10_model.r INFO @ Mon, 10 Aug 2020 14:37:03: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:37:09: 32000000 INFO @ Mon, 10 Aug 2020 14:37:15: 33000000 INFO @ Mon, 10 Aug 2020 14:37:21: 34000000 INFO @ Mon, 10 Aug 2020 14:37:25: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:37:25: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:37:25: #1 total tags in treatment: 34527501 INFO @ Mon, 10 Aug 2020 14:37:25: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:37:25: #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 14:37:25: #1 tags after filtering in treatment: 34527339 INFO @ Mon, 10 Aug 2020 14:37:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:37:25: #1 finished! INFO @ Mon, 10 Aug 2020 14:37:25: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:37:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:37:30: #2 number of paired peaks: 43496 INFO @ Mon, 10 Aug 2020 14:37:30: start model_add_line... INFO @ Mon, 10 Aug 2020 14:37:30: start X-correlation... INFO @ Mon, 10 Aug 2020 14:37:30: end of X-cor INFO @ Mon, 10 Aug 2020 14:37:30: #2 finished! INFO @ Mon, 10 Aug 2020 14:37:30: #2 predicted fragment length is 119 bps INFO @ Mon, 10 Aug 2020 14:37:30: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 10 Aug 2020 14:37:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.20_model.r INFO @ Mon, 10 Aug 2020 14:37:30: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:37:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:37:40: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:38:14: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:38:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:38:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:38:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.05_summits.bed INFO @ Mon, 10 Aug 2020 14:38:18: Done! pass1 - making usageList (149 chroms): 6 millis pass2 - checking and writing primary data (39390 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:38:39: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:38:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:38:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:38:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.10_summits.bed INFO @ Mon, 10 Aug 2020 14:38:53: Done! pass1 - making usageList (133 chroms): 5 millis pass2 - checking and writing primary data (33639 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:39:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:39:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:39:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047615/SRX8047615.20_summits.bed INFO @ Mon, 10 Aug 2020 14:39:16: Done! pass1 - making usageList (114 chroms): 5 millis pass2 - checking and writing primary data (27698 records, 4 fields): 29 millis CompletedMACS2peakCalling