Job ID = 8184180 SRX = SRX8047572 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T02:46:00 prefetch.2.10.7: 1) Downloading 'SRR11471297'... 2020-08-10T02:46:00 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T02:50:55 prefetch.2.10.7: HTTPS download failed 2020-08-10T02:50:55 prefetch.2.10.7: 1) failed to download SRR11471297 2020-08-10T02:51:06 prefetch.2.10.7: 1) Downloading 'SRR11471297'... 2020-08-10T02:51:06 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T02:51:06 prefetch.2.10.7: Continue download of 'SRR11471297' from 2072985166 2020-08-10T02:51:14 prefetch.2.10.7: HTTPS download succeed 2020-08-10T02:51:14 prefetch.2.10.7: 1) 'SRR11471297' was downloaded successfully Read 62387827 spots for SRR11471297/SRR11471297.sra Written 62387827 spots for SRR11471297/SRR11471297.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: 00:00:01 Multiseed full-index search: 00:48:55 62387827 reads; of these: 62387827 (100.00%) were unpaired; of these: 1645177 (2.64%) aligned 0 times 47668454 (76.41%) aligned exactly 1 time 13074196 (20.96%) aligned >1 times 97.36% overall alignment rate Time searching: 00:48:59 Overall time: 00:48:59 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] 13171743 / 60742650 = 0.2168 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 12:58:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.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 12:58:14: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:58:14: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:58:21: 1000000 INFO @ Mon, 10 Aug 2020 12:58:27: 2000000 INFO @ Mon, 10 Aug 2020 12:58:33: 3000000 INFO @ Mon, 10 Aug 2020 12:58:39: 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 12:58:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.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 12:58:44: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:58:44: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:58:45: 5000000 INFO @ Mon, 10 Aug 2020 12:58:50: 1000000 INFO @ Mon, 10 Aug 2020 12:58:52: 6000000 INFO @ Mon, 10 Aug 2020 12:58:57: 2000000 INFO @ Mon, 10 Aug 2020 12:58:58: 7000000 INFO @ Mon, 10 Aug 2020 12:59:03: 3000000 INFO @ Mon, 10 Aug 2020 12:59:05: 8000000 INFO @ Mon, 10 Aug 2020 12:59:09: 4000000 INFO @ Mon, 10 Aug 2020 12:59:10: 9000000 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 12:59:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.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 12:59:14: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:59:14: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:59:16: 5000000 INFO @ Mon, 10 Aug 2020 12:59:17: 10000000 INFO @ Mon, 10 Aug 2020 12:59:21: 1000000 INFO @ Mon, 10 Aug 2020 12:59:23: 6000000 INFO @ Mon, 10 Aug 2020 12:59:23: 11000000 INFO @ Mon, 10 Aug 2020 12:59:27: 2000000 INFO @ Mon, 10 Aug 2020 12:59:29: 7000000 INFO @ Mon, 10 Aug 2020 12:59:30: 12000000 INFO @ Mon, 10 Aug 2020 12:59:34: 3000000 INFO @ Mon, 10 Aug 2020 12:59:35: 8000000 INFO @ Mon, 10 Aug 2020 12:59:36: 13000000 INFO @ Mon, 10 Aug 2020 12:59:40: 4000000 INFO @ Mon, 10 Aug 2020 12:59:41: 9000000 INFO @ Mon, 10 Aug 2020 12:59:42: 14000000 INFO @ Mon, 10 Aug 2020 12:59:46: 5000000 INFO @ Mon, 10 Aug 2020 12:59:48: 10000000 INFO @ Mon, 10 Aug 2020 12:59:48: 15000000 INFO @ Mon, 10 Aug 2020 12:59:53: 6000000 INFO @ Mon, 10 Aug 2020 12:59:54: 16000000 INFO @ Mon, 10 Aug 2020 12:59:54: 11000000 INFO @ Mon, 10 Aug 2020 12:59:59: 7000000 INFO @ Mon, 10 Aug 2020 13:00:01: 17000000 INFO @ Mon, 10 Aug 2020 13:00:01: 12000000 INFO @ Mon, 10 Aug 2020 13:00:05: 8000000 INFO @ Mon, 10 Aug 2020 13:00:07: 18000000 INFO @ Mon, 10 Aug 2020 13:00:07: 13000000 INFO @ Mon, 10 Aug 2020 13:00:12: 9000000 INFO @ Mon, 10 Aug 2020 13:00:13: 14000000 INFO @ Mon, 10 Aug 2020 13:00:13: 19000000 INFO @ Mon, 10 Aug 2020 13:00:18: 10000000 INFO @ Mon, 10 Aug 2020 13:00:20: 15000000 INFO @ Mon, 10 Aug 2020 13:00:20: 20000000 INFO @ Mon, 10 Aug 2020 13:00:25: 11000000 INFO @ Mon, 10 Aug 2020 13:00:26: 16000000 INFO @ Mon, 10 Aug 2020 13:00:26: 21000000 INFO @ Mon, 10 Aug 2020 13:00:31: 12000000 INFO @ Mon, 10 Aug 2020 13:00:32: 17000000 INFO @ Mon, 10 Aug 2020 13:00:33: 22000000 INFO @ Mon, 10 Aug 2020 13:00:38: 13000000 INFO @ Mon, 10 Aug 2020 13:00:39: 23000000 INFO @ Mon, 10 Aug 2020 13:00:39: 18000000 INFO @ Mon, 10 Aug 2020 13:00:44: 14000000 INFO @ Mon, 10 Aug 2020 13:00:46: 24000000 INFO @ Mon, 10 Aug 2020 13:00:46: 19000000 INFO @ Mon, 10 Aug 2020 13:00:50: 15000000 INFO @ Mon, 10 Aug 2020 13:00:52: 25000000 INFO @ Mon, 10 Aug 2020 13:00:52: 20000000 INFO @ Mon, 10 Aug 2020 13:00:57: 16000000 INFO @ Mon, 10 Aug 2020 13:00:59: 26000000 INFO @ Mon, 10 Aug 2020 13:00:59: 21000000 INFO @ Mon, 10 Aug 2020 13:01:03: 17000000 INFO @ Mon, 10 Aug 2020 13:01:05: 22000000 INFO @ Mon, 10 Aug 2020 13:01:05: 27000000 INFO @ Mon, 10 Aug 2020 13:01:10: 18000000 INFO @ Mon, 10 Aug 2020 13:01:11: 23000000 INFO @ Mon, 10 Aug 2020 13:01:12: 28000000 INFO @ Mon, 10 Aug 2020 13:01:17: 19000000 INFO @ Mon, 10 Aug 2020 13:01:18: 29000000 INFO @ Mon, 10 Aug 2020 13:01:18: 24000000 INFO @ Mon, 10 Aug 2020 13:01:23: 20000000 INFO @ Mon, 10 Aug 2020 13:01:24: 30000000 INFO @ Mon, 10 Aug 2020 13:01:25: 25000000 INFO @ Mon, 10 Aug 2020 13:01:29: 21000000 INFO @ Mon, 10 Aug 2020 13:01:31: 31000000 INFO @ Mon, 10 Aug 2020 13:01:31: 26000000 INFO @ Mon, 10 Aug 2020 13:01:36: 22000000 INFO @ Mon, 10 Aug 2020 13:01:37: 32000000 INFO @ Mon, 10 Aug 2020 13:01:38: 27000000 INFO @ Mon, 10 Aug 2020 13:01:42: 23000000 INFO @ Mon, 10 Aug 2020 13:01:44: 33000000 INFO @ Mon, 10 Aug 2020 13:01:44: 28000000 INFO @ Mon, 10 Aug 2020 13:01:49: 24000000 INFO @ Mon, 10 Aug 2020 13:01:50: 34000000 INFO @ Mon, 10 Aug 2020 13:01:51: 29000000 INFO @ Mon, 10 Aug 2020 13:01:56: 25000000 INFO @ Mon, 10 Aug 2020 13:01:57: 35000000 INFO @ Mon, 10 Aug 2020 13:01:57: 30000000 INFO @ Mon, 10 Aug 2020 13:02:02: 26000000 INFO @ Mon, 10 Aug 2020 13:02:03: 36000000 INFO @ Mon, 10 Aug 2020 13:02:04: 31000000 INFO @ Mon, 10 Aug 2020 13:02:09: 27000000 INFO @ Mon, 10 Aug 2020 13:02:10: 37000000 INFO @ Mon, 10 Aug 2020 13:02:10: 32000000 INFO @ Mon, 10 Aug 2020 13:02:15: 28000000 INFO @ Mon, 10 Aug 2020 13:02:16: 38000000 INFO @ Mon, 10 Aug 2020 13:02:17: 33000000 INFO @ Mon, 10 Aug 2020 13:02:22: 29000000 INFO @ Mon, 10 Aug 2020 13:02:23: 39000000 INFO @ Mon, 10 Aug 2020 13:02:24: 34000000 INFO @ Mon, 10 Aug 2020 13:02:28: 30000000 INFO @ Mon, 10 Aug 2020 13:02:30: 40000000 INFO @ Mon, 10 Aug 2020 13:02:30: 35000000 INFO @ Mon, 10 Aug 2020 13:02:35: 31000000 INFO @ Mon, 10 Aug 2020 13:02:36: 41000000 INFO @ Mon, 10 Aug 2020 13:02:37: 36000000 INFO @ Mon, 10 Aug 2020 13:02:41: 32000000 INFO @ Mon, 10 Aug 2020 13:02:43: 42000000 INFO @ Mon, 10 Aug 2020 13:02:44: 37000000 INFO @ Mon, 10 Aug 2020 13:02:48: 33000000 INFO @ Mon, 10 Aug 2020 13:02:49: 43000000 INFO @ Mon, 10 Aug 2020 13:02:50: 38000000 INFO @ Mon, 10 Aug 2020 13:02:54: 34000000 INFO @ Mon, 10 Aug 2020 13:02:56: 44000000 INFO @ Mon, 10 Aug 2020 13:02:57: 39000000 INFO @ Mon, 10 Aug 2020 13:03:01: 35000000 INFO @ Mon, 10 Aug 2020 13:03:02: 45000000 INFO @ Mon, 10 Aug 2020 13:03:04: 40000000 INFO @ Mon, 10 Aug 2020 13:03:08: 36000000 INFO @ Mon, 10 Aug 2020 13:03:08: 46000000 INFO @ Mon, 10 Aug 2020 13:03:10: 41000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:03:14: 37000000 INFO @ Mon, 10 Aug 2020 13:03:15: 47000000 INFO @ Mon, 10 Aug 2020 13:03:17: 42000000 INFO @ Mon, 10 Aug 2020 13:03:19: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:03:19: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:03:19: #1 total tags in treatment: 47570907 INFO @ Mon, 10 Aug 2020 13:03:19: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:03:19: #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 13:03:20: #1 tags after filtering in treatment: 47570838 INFO @ Mon, 10 Aug 2020 13:03:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:03:20: #1 finished! INFO @ Mon, 10 Aug 2020 13:03:20: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:03:21: 38000000 INFO @ Mon, 10 Aug 2020 13:03:24: 43000000 INFO @ Mon, 10 Aug 2020 13:03:24: #2 number of paired peaks: 35251 INFO @ Mon, 10 Aug 2020 13:03:24: start model_add_line... INFO @ Mon, 10 Aug 2020 13:03:25: start X-correlation... INFO @ Mon, 10 Aug 2020 13:03:25: end of X-cor INFO @ Mon, 10 Aug 2020 13:03:25: #2 finished! INFO @ Mon, 10 Aug 2020 13:03:25: #2 predicted fragment length is 122 bps INFO @ Mon, 10 Aug 2020 13:03:25: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 10 Aug 2020 13:03:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.05_model.r INFO @ Mon, 10 Aug 2020 13:03:25: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:03:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:03:27: 39000000 INFO @ Mon, 10 Aug 2020 13:03:30: 44000000 INFO @ Mon, 10 Aug 2020 13:03:34: 40000000 INFO @ Mon, 10 Aug 2020 13:03:37: 45000000 INFO @ Mon, 10 Aug 2020 13:03:40: 41000000 INFO @ Mon, 10 Aug 2020 13:03:43: 46000000 INFO @ Mon, 10 Aug 2020 13:03:47: 42000000 INFO @ Mon, 10 Aug 2020 13:03:50: 47000000 INFO @ Mon, 10 Aug 2020 13:03:53: 43000000 INFO @ Mon, 10 Aug 2020 13:03:53: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:03:53: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:03:53: #1 total tags in treatment: 47570907 INFO @ Mon, 10 Aug 2020 13:03:53: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:03:53: #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 13:03:54: #1 tags after filtering in treatment: 47570838 INFO @ Mon, 10 Aug 2020 13:03:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:03:54: #1 finished! INFO @ Mon, 10 Aug 2020 13:03:54: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:03:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:03:59: #2 number of paired peaks: 35251 INFO @ Mon, 10 Aug 2020 13:03:59: start model_add_line... INFO @ Mon, 10 Aug 2020 13:04:00: start X-correlation... INFO @ Mon, 10 Aug 2020 13:04:00: end of X-cor INFO @ Mon, 10 Aug 2020 13:04:00: #2 finished! INFO @ Mon, 10 Aug 2020 13:04:00: #2 predicted fragment length is 122 bps INFO @ Mon, 10 Aug 2020 13:04:00: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 10 Aug 2020 13:04:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.10_model.r INFO @ Mon, 10 Aug 2020 13:04:00: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:04:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:04:00: 44000000 INFO @ Mon, 10 Aug 2020 13:04:06: 45000000 INFO @ Mon, 10 Aug 2020 13:04:12: 46000000 INFO @ Mon, 10 Aug 2020 13:04:18: 47000000 INFO @ Mon, 10 Aug 2020 13:04:22: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:04:22: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:04:22: #1 total tags in treatment: 47570907 INFO @ Mon, 10 Aug 2020 13:04:22: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:04:22: #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 13:04:23: #1 tags after filtering in treatment: 47570838 INFO @ Mon, 10 Aug 2020 13:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:04:23: #1 finished! INFO @ Mon, 10 Aug 2020 13:04:23: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:04:28: #2 number of paired peaks: 35251 INFO @ Mon, 10 Aug 2020 13:04:28: start model_add_line... INFO @ Mon, 10 Aug 2020 13:04:28: start X-correlation... INFO @ Mon, 10 Aug 2020 13:04:28: end of X-cor INFO @ Mon, 10 Aug 2020 13:04:28: #2 finished! INFO @ Mon, 10 Aug 2020 13:04:28: #2 predicted fragment length is 122 bps INFO @ Mon, 10 Aug 2020 13:04:28: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 10 Aug 2020 13:04:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.20_model.r INFO @ Mon, 10 Aug 2020 13:04:28: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:04:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:05:09: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:05:42: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:06:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:06:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:06:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.05_summits.bed INFO @ Mon, 10 Aug 2020 13:06:05: Done! pass1 - making usageList (114 chroms): 4 millis pass2 - checking and writing primary data (24806 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:06:17: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:06:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:06:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:06:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.10_summits.bed INFO @ Mon, 10 Aug 2020 13:06:38: Done! pass1 - making usageList (86 chroms): 2 millis pass2 - checking and writing primary data (14905 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:07:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:07:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047572/SRX8047572.20_summits.bed INFO @ Mon, 10 Aug 2020 13:07:20: Done! pass1 - making usageList (61 chroms): 2 millis pass2 - checking and writing primary data (7189 records, 4 fields): 8 millis CompletedMACS2peakCalling