Job ID = 8184520 SRX = SRX8047600 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:00:55 prefetch.2.10.7: 1) Downloading 'SRR11471324'... 2020-08-10T04:00:55 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:03:47 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:03:47 prefetch.2.10.7: 1) 'SRR11471324' was downloaded successfully Read 57784098 spots for SRR11471324/SRR11471324.sra Written 57784098 spots for SRR11471324/SRR11471324.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: 00:39:25 57784098 reads; of these: 57784098 (100.00%) were unpaired; of these: 1369634 (2.37%) aligned 0 times 46117379 (79.81%) aligned exactly 1 time 10297085 (17.82%) aligned >1 times 97.63% overall alignment rate Time searching: 00:39:27 Overall time: 00:39:27 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] 8839815 / 56414464 = 0.1567 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 13:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.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 13:59:52: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:59:52: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:59:58: 1000000 INFO @ Mon, 10 Aug 2020 14:00:03: 2000000 INFO @ Mon, 10 Aug 2020 14:00:09: 3000000 INFO @ Mon, 10 Aug 2020 14:00:14: 4000000 INFO @ Mon, 10 Aug 2020 14:00:20: 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 14:00:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.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 14:00:22: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:00:22: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:00:26: 6000000 INFO @ Mon, 10 Aug 2020 14:00:29: 1000000 INFO @ Mon, 10 Aug 2020 14:00:33: 7000000 INFO @ Mon, 10 Aug 2020 14:00:35: 2000000 INFO @ Mon, 10 Aug 2020 14:00:39: 8000000 INFO @ Mon, 10 Aug 2020 14:00:42: 3000000 INFO @ Mon, 10 Aug 2020 14:00:46: 9000000 INFO @ Mon, 10 Aug 2020 14:00:48: 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 14:00:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.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 14:00:52: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:00:52: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:00:53: 10000000 INFO @ Mon, 10 Aug 2020 14:00:55: 5000000 INFO @ Mon, 10 Aug 2020 14:01:00: 1000000 INFO @ Mon, 10 Aug 2020 14:01:00: 11000000 INFO @ Mon, 10 Aug 2020 14:01:02: 6000000 INFO @ Mon, 10 Aug 2020 14:01:07: 12000000 INFO @ Mon, 10 Aug 2020 14:01:07: 2000000 INFO @ Mon, 10 Aug 2020 14:01:09: 7000000 INFO @ Mon, 10 Aug 2020 14:01:14: 13000000 INFO @ Mon, 10 Aug 2020 14:01:15: 3000000 INFO @ Mon, 10 Aug 2020 14:01:16: 8000000 INFO @ Mon, 10 Aug 2020 14:01:20: 14000000 INFO @ Mon, 10 Aug 2020 14:01:22: 4000000 INFO @ Mon, 10 Aug 2020 14:01:23: 9000000 INFO @ Mon, 10 Aug 2020 14:01:27: 15000000 INFO @ Mon, 10 Aug 2020 14:01:30: 5000000 INFO @ Mon, 10 Aug 2020 14:01:30: 10000000 INFO @ Mon, 10 Aug 2020 14:01:34: 16000000 INFO @ Mon, 10 Aug 2020 14:01:37: 11000000 INFO @ Mon, 10 Aug 2020 14:01:37: 6000000 INFO @ Mon, 10 Aug 2020 14:01:41: 17000000 INFO @ Mon, 10 Aug 2020 14:01:44: 12000000 INFO @ Mon, 10 Aug 2020 14:01:45: 7000000 INFO @ Mon, 10 Aug 2020 14:01:48: 18000000 INFO @ Mon, 10 Aug 2020 14:01:51: 13000000 INFO @ Mon, 10 Aug 2020 14:01:52: 8000000 INFO @ Mon, 10 Aug 2020 14:01:55: 19000000 INFO @ Mon, 10 Aug 2020 14:01:58: 14000000 INFO @ Mon, 10 Aug 2020 14:02:00: 9000000 INFO @ Mon, 10 Aug 2020 14:02:02: 20000000 INFO @ Mon, 10 Aug 2020 14:02:05: 15000000 INFO @ Mon, 10 Aug 2020 14:02:07: 10000000 INFO @ Mon, 10 Aug 2020 14:02:09: 21000000 INFO @ Mon, 10 Aug 2020 14:02:12: 16000000 INFO @ Mon, 10 Aug 2020 14:02:15: 11000000 INFO @ Mon, 10 Aug 2020 14:02:16: 22000000 INFO @ Mon, 10 Aug 2020 14:02:19: 17000000 INFO @ Mon, 10 Aug 2020 14:02:22: 12000000 INFO @ Mon, 10 Aug 2020 14:02:23: 23000000 INFO @ Mon, 10 Aug 2020 14:02:26: 18000000 INFO @ Mon, 10 Aug 2020 14:02:30: 13000000 INFO @ Mon, 10 Aug 2020 14:02:30: 24000000 INFO @ Mon, 10 Aug 2020 14:02:32: 19000000 INFO @ Mon, 10 Aug 2020 14:02:37: 25000000 INFO @ Mon, 10 Aug 2020 14:02:37: 14000000 INFO @ Mon, 10 Aug 2020 14:02:39: 20000000 INFO @ Mon, 10 Aug 2020 14:02:44: 26000000 INFO @ Mon, 10 Aug 2020 14:02:45: 15000000 INFO @ Mon, 10 Aug 2020 14:02:46: 21000000 INFO @ Mon, 10 Aug 2020 14:02:51: 27000000 INFO @ Mon, 10 Aug 2020 14:02:53: 16000000 INFO @ Mon, 10 Aug 2020 14:02:53: 22000000 INFO @ Mon, 10 Aug 2020 14:02:58: 28000000 INFO @ Mon, 10 Aug 2020 14:03:00: 17000000 INFO @ Mon, 10 Aug 2020 14:03:00: 23000000 INFO @ Mon, 10 Aug 2020 14:03:05: 29000000 INFO @ Mon, 10 Aug 2020 14:03:07: 24000000 INFO @ Mon, 10 Aug 2020 14:03:07: 18000000 INFO @ Mon, 10 Aug 2020 14:03:12: 30000000 INFO @ Mon, 10 Aug 2020 14:03:14: 25000000 INFO @ Mon, 10 Aug 2020 14:03:15: 19000000 INFO @ Mon, 10 Aug 2020 14:03:19: 31000000 INFO @ Mon, 10 Aug 2020 14:03:21: 26000000 INFO @ Mon, 10 Aug 2020 14:03:23: 20000000 INFO @ Mon, 10 Aug 2020 14:03:25: 32000000 INFO @ Mon, 10 Aug 2020 14:03:28: 27000000 INFO @ Mon, 10 Aug 2020 14:03:30: 21000000 INFO @ Mon, 10 Aug 2020 14:03:32: 33000000 INFO @ Mon, 10 Aug 2020 14:03:35: 28000000 INFO @ Mon, 10 Aug 2020 14:03:38: 22000000 INFO @ Mon, 10 Aug 2020 14:03:39: 34000000 INFO @ Mon, 10 Aug 2020 14:03:42: 29000000 INFO @ Mon, 10 Aug 2020 14:03:45: 23000000 INFO @ Mon, 10 Aug 2020 14:03:46: 35000000 INFO @ Mon, 10 Aug 2020 14:03:49: 30000000 INFO @ Mon, 10 Aug 2020 14:03:53: 24000000 INFO @ Mon, 10 Aug 2020 14:03:53: 36000000 INFO @ Mon, 10 Aug 2020 14:03:56: 31000000 INFO @ Mon, 10 Aug 2020 14:04:00: 37000000 INFO @ Mon, 10 Aug 2020 14:04:00: 25000000 INFO @ Mon, 10 Aug 2020 14:04:03: 32000000 INFO @ Mon, 10 Aug 2020 14:04:07: 38000000 INFO @ Mon, 10 Aug 2020 14:04:08: 26000000 INFO @ Mon, 10 Aug 2020 14:04:10: 33000000 INFO @ Mon, 10 Aug 2020 14:04:14: 39000000 INFO @ Mon, 10 Aug 2020 14:04:16: 27000000 INFO @ Mon, 10 Aug 2020 14:04:17: 34000000 INFO @ Mon, 10 Aug 2020 14:04:21: 40000000 INFO @ Mon, 10 Aug 2020 14:04:23: 28000000 INFO @ Mon, 10 Aug 2020 14:04:24: 35000000 INFO @ Mon, 10 Aug 2020 14:04:28: 41000000 INFO @ Mon, 10 Aug 2020 14:04:30: 36000000 INFO @ Mon, 10 Aug 2020 14:04:31: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:04:35: 42000000 INFO @ Mon, 10 Aug 2020 14:04:37: 37000000 INFO @ Mon, 10 Aug 2020 14:04:38: 30000000 INFO @ Mon, 10 Aug 2020 14:04:42: 43000000 INFO @ Mon, 10 Aug 2020 14:04:44: 38000000 INFO @ Mon, 10 Aug 2020 14:04:45: 31000000 INFO @ Mon, 10 Aug 2020 14:04:49: 44000000 INFO @ Mon, 10 Aug 2020 14:04:51: 39000000 INFO @ Mon, 10 Aug 2020 14:04:52: 32000000 INFO @ Mon, 10 Aug 2020 14:04:56: 45000000 INFO @ Mon, 10 Aug 2020 14:04:58: 40000000 INFO @ Mon, 10 Aug 2020 14:05:00: 33000000 INFO @ Mon, 10 Aug 2020 14:05:03: 46000000 INFO @ Mon, 10 Aug 2020 14:05:05: 41000000 INFO @ Mon, 10 Aug 2020 14:05:07: 34000000 INFO @ Mon, 10 Aug 2020 14:05:10: 47000000 INFO @ Mon, 10 Aug 2020 14:05:12: 42000000 INFO @ Mon, 10 Aug 2020 14:05:14: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:05:14: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:05:14: #1 total tags in treatment: 47574649 INFO @ Mon, 10 Aug 2020 14:05:14: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:05:14: #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 14:05:14: 35000000 INFO @ Mon, 10 Aug 2020 14:05:15: #1 tags after filtering in treatment: 47574550 INFO @ Mon, 10 Aug 2020 14:05:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:05:15: #1 finished! INFO @ Mon, 10 Aug 2020 14:05:15: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:05:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:05:19: 43000000 INFO @ Mon, 10 Aug 2020 14:05:21: #2 number of paired peaks: 60218 INFO @ Mon, 10 Aug 2020 14:05:21: start model_add_line... INFO @ Mon, 10 Aug 2020 14:05:21: start X-correlation... INFO @ Mon, 10 Aug 2020 14:05:21: end of X-cor INFO @ Mon, 10 Aug 2020 14:05:21: #2 finished! INFO @ Mon, 10 Aug 2020 14:05:21: #2 predicted fragment length is 129 bps INFO @ Mon, 10 Aug 2020 14:05:21: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 10 Aug 2020 14:05:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.05_model.r INFO @ Mon, 10 Aug 2020 14:05:21: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:05:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:05:22: 36000000 INFO @ Mon, 10 Aug 2020 14:05:25: 44000000 INFO @ Mon, 10 Aug 2020 14:05:29: 37000000 INFO @ Mon, 10 Aug 2020 14:05:32: 45000000 INFO @ Mon, 10 Aug 2020 14:05:36: 38000000 INFO @ Mon, 10 Aug 2020 14:05:39: 46000000 INFO @ Mon, 10 Aug 2020 14:05:44: 39000000 INFO @ Mon, 10 Aug 2020 14:05:46: 47000000 INFO @ Mon, 10 Aug 2020 14:05:50: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:05:50: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:05:50: #1 total tags in treatment: 47574649 INFO @ Mon, 10 Aug 2020 14:05:50: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:05:50: #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 14:05:51: 40000000 INFO @ Mon, 10 Aug 2020 14:05:51: #1 tags after filtering in treatment: 47574550 INFO @ Mon, 10 Aug 2020 14:05:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:05:51: #1 finished! INFO @ Mon, 10 Aug 2020 14:05:51: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:05:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:05:57: #2 number of paired peaks: 60218 INFO @ Mon, 10 Aug 2020 14:05:57: start model_add_line... INFO @ Mon, 10 Aug 2020 14:05:57: start X-correlation... INFO @ Mon, 10 Aug 2020 14:05:57: end of X-cor INFO @ Mon, 10 Aug 2020 14:05:57: #2 finished! INFO @ Mon, 10 Aug 2020 14:05:57: #2 predicted fragment length is 129 bps INFO @ Mon, 10 Aug 2020 14:05:57: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 10 Aug 2020 14:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.10_model.r INFO @ Mon, 10 Aug 2020 14:05:57: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:05:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:05:57: 41000000 INFO @ Mon, 10 Aug 2020 14:06:04: 42000000 INFO @ Mon, 10 Aug 2020 14:06:11: 43000000 INFO @ Mon, 10 Aug 2020 14:06:18: 44000000 BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:06:25: 45000000 INFO @ Mon, 10 Aug 2020 14:06:31: 46000000 INFO @ Mon, 10 Aug 2020 14:06:38: 47000000 INFO @ Mon, 10 Aug 2020 14:06:43: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:06:43: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:06:43: #1 total tags in treatment: 47574649 INFO @ Mon, 10 Aug 2020 14:06:43: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:06:43: #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 14:06:43: #1 tags after filtering in treatment: 47574550 INFO @ Mon, 10 Aug 2020 14:06:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:06:43: #1 finished! INFO @ Mon, 10 Aug 2020 14:06:43: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:06:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:06:49: #2 number of paired peaks: 60218 INFO @ Mon, 10 Aug 2020 14:06:49: start model_add_line... INFO @ Mon, 10 Aug 2020 14:06:50: start X-correlation... INFO @ Mon, 10 Aug 2020 14:06:50: end of X-cor INFO @ Mon, 10 Aug 2020 14:06:50: #2 finished! INFO @ Mon, 10 Aug 2020 14:06:50: #2 predicted fragment length is 129 bps INFO @ Mon, 10 Aug 2020 14:06:50: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 10 Aug 2020 14:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.20_model.r INFO @ Mon, 10 Aug 2020 14:06:50: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:06:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:07:05: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:07:42: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:08:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:08:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:08:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.05_summits.bed INFO @ Mon, 10 Aug 2020 14:08:04: Done! pass1 - making usageList (116 chroms): 5 millis pass2 - checking and writing primary data (35929 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:08:35: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:08:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:08:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:08:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.10_summits.bed INFO @ Mon, 10 Aug 2020 14:08:41: Done! pass1 - making usageList (99 chroms): 4 millis pass2 - checking and writing primary data (22968 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:09:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:09:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:09:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047600/SRX8047600.20_summits.bed INFO @ Mon, 10 Aug 2020 14:09:33: Done! pass1 - making usageList (79 chroms): 3 millis pass2 - checking and writing primary data (14155 records, 4 fields): 15 millis CompletedMACS2peakCalling