Job ID = 6366522 SRX = SRX1674102 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:59 prefetch.2.10.7: 1) Downloading 'SRR3320148'... 2020-06-15T22:54:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:18 prefetch.2.10.7: 1) 'SRR3320148' was downloaded successfully Read 36972865 spots for SRR3320148/SRR3320148.sra Written 36972865 spots for SRR3320148/SRR3320148.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:16 36972865 reads; of these: 36972865 (100.00%) were unpaired; of these: 5432972 (14.69%) aligned 0 times 20610106 (55.74%) aligned exactly 1 time 10929787 (29.56%) aligned >1 times 85.31% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 12318728 / 31539893 = 0.3906 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 @ Tue, 16 Jun 2020 08:14:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:14:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:34: 1000000 INFO @ Tue, 16 Jun 2020 08:14:41: 2000000 INFO @ Tue, 16 Jun 2020 08:14:47: 3000000 INFO @ Tue, 16 Jun 2020 08:14:53: 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 @ Tue, 16 Jun 2020 08:14:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:14:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:00: 5000000 INFO @ Tue, 16 Jun 2020 08:15:04: 1000000 INFO @ Tue, 16 Jun 2020 08:15:06: 6000000 INFO @ Tue, 16 Jun 2020 08:15:11: 2000000 INFO @ Tue, 16 Jun 2020 08:15:13: 7000000 INFO @ Tue, 16 Jun 2020 08:15:17: 3000000 INFO @ Tue, 16 Jun 2020 08:15:20: 8000000 INFO @ Tue, 16 Jun 2020 08:15:24: 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 @ Tue, 16 Jun 2020 08:15:26: 9000000 INFO @ Tue, 16 Jun 2020 08:15:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:15:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:30: 5000000 INFO @ Tue, 16 Jun 2020 08:15:33: 10000000 INFO @ Tue, 16 Jun 2020 08:15:34: 1000000 INFO @ Tue, 16 Jun 2020 08:15:37: 6000000 INFO @ Tue, 16 Jun 2020 08:15:39: 11000000 INFO @ Tue, 16 Jun 2020 08:15:41: 2000000 INFO @ Tue, 16 Jun 2020 08:15:43: 7000000 INFO @ Tue, 16 Jun 2020 08:15:46: 12000000 INFO @ Tue, 16 Jun 2020 08:15:47: 3000000 INFO @ Tue, 16 Jun 2020 08:15:50: 8000000 INFO @ Tue, 16 Jun 2020 08:15:53: 13000000 INFO @ Tue, 16 Jun 2020 08:15:53: 4000000 INFO @ Tue, 16 Jun 2020 08:15:57: 9000000 INFO @ Tue, 16 Jun 2020 08:15:59: 14000000 INFO @ Tue, 16 Jun 2020 08:16:00: 5000000 INFO @ Tue, 16 Jun 2020 08:16:03: 10000000 INFO @ Tue, 16 Jun 2020 08:16:06: 15000000 INFO @ Tue, 16 Jun 2020 08:16:06: 6000000 INFO @ Tue, 16 Jun 2020 08:16:10: 11000000 INFO @ Tue, 16 Jun 2020 08:16:13: 16000000 INFO @ Tue, 16 Jun 2020 08:16:13: 7000000 INFO @ Tue, 16 Jun 2020 08:16:16: 12000000 INFO @ Tue, 16 Jun 2020 08:16:19: 17000000 INFO @ Tue, 16 Jun 2020 08:16:19: 8000000 INFO @ Tue, 16 Jun 2020 08:16:23: 13000000 INFO @ Tue, 16 Jun 2020 08:16:26: 9000000 INFO @ Tue, 16 Jun 2020 08:16:26: 18000000 INFO @ Tue, 16 Jun 2020 08:16:29: 14000000 INFO @ Tue, 16 Jun 2020 08:16:32: 10000000 INFO @ Tue, 16 Jun 2020 08:16:33: 19000000 INFO @ Tue, 16 Jun 2020 08:16:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:16:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:16:34: #1 total tags in treatment: 19221165 INFO @ Tue, 16 Jun 2020 08:16:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:16:35: #1 tags after filtering in treatment: 19221165 INFO @ Tue, 16 Jun 2020 08:16:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:36: 15000000 INFO @ Tue, 16 Jun 2020 08:16:36: #2 number of paired peaks: 4482 INFO @ Tue, 16 Jun 2020 08:16:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:37: #2 predicted fragment length is 238 bps INFO @ Tue, 16 Jun 2020 08:16:37: #2 alternative fragment length(s) may be 1,208,238 bps INFO @ Tue, 16 Jun 2020 08:16:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.05_model.r INFO @ Tue, 16 Jun 2020 08:16:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:39: 11000000 INFO @ Tue, 16 Jun 2020 08:16:42: 16000000 INFO @ Tue, 16 Jun 2020 08:16:45: 12000000 INFO @ Tue, 16 Jun 2020 08:16:49: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:52: 13000000 INFO @ Tue, 16 Jun 2020 08:16:55: 18000000 INFO @ Tue, 16 Jun 2020 08:16:58: 14000000 INFO @ Tue, 16 Jun 2020 08:17:02: 19000000 INFO @ Tue, 16 Jun 2020 08:17:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:17:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:17:04: #1 total tags in treatment: 19221165 INFO @ Tue, 16 Jun 2020 08:17:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:17:04: #1 tags after filtering in treatment: 19221165 INFO @ Tue, 16 Jun 2020 08:17:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:05: 15000000 INFO @ Tue, 16 Jun 2020 08:17:06: #2 number of paired peaks: 4482 INFO @ Tue, 16 Jun 2020 08:17:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:06: #2 predicted fragment length is 238 bps INFO @ Tue, 16 Jun 2020 08:17:06: #2 alternative fragment length(s) may be 1,208,238 bps INFO @ Tue, 16 Jun 2020 08:17:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.10_model.r INFO @ Tue, 16 Jun 2020 08:17:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:11: 16000000 INFO @ Tue, 16 Jun 2020 08:17:17: 17000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:17:23: 18000000 INFO @ Tue, 16 Jun 2020 08:17:29: 19000000 INFO @ Tue, 16 Jun 2020 08:17:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:17:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:17:31: #1 total tags in treatment: 19221165 INFO @ Tue, 16 Jun 2020 08:17:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:17:31: #1 tags after filtering in treatment: 19221165 INFO @ Tue, 16 Jun 2020 08:17:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:33: #2 number of paired peaks: 4482 INFO @ Tue, 16 Jun 2020 08:17:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:33: #2 predicted fragment length is 238 bps INFO @ Tue, 16 Jun 2020 08:17:33: #2 alternative fragment length(s) may be 1,208,238 bps INFO @ Tue, 16 Jun 2020 08:17:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.20_model.r INFO @ Tue, 16 Jun 2020 08:17:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.05_summits.bed INFO @ Tue, 16 Jun 2020 08:18:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5345 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.10_summits.bed INFO @ Tue, 16 Jun 2020 08:18:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3152 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674102/SRX1674102.20_summits.bed INFO @ Tue, 16 Jun 2020 08:18:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1462 records, 4 fields): 3 millis CompletedMACS2peakCalling