Job ID = 6368108 SRX = SRX466571 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:58:50 prefetch.2.10.7: 1) Downloading 'SRR1163637'... 2020-06-15T23:58:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:27 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:27 prefetch.2.10.7: 1) 'SRR1163637' was downloaded successfully Read 23677270 spots for SRR1163637/SRR1163637.sra Written 23677270 spots for SRR1163637/SRR1163637.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: 00:04:49 23677270 reads; of these: 23677270 (100.00%) were unpaired; of these: 1783031 (7.53%) aligned 0 times 19272882 (81.40%) aligned exactly 1 time 2621357 (11.07%) aligned >1 times 92.47% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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 12 files... [bam_rmdupse_core] 7418977 / 21894239 = 0.3389 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 09:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.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 09:12:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:45: 1000000 INFO @ Tue, 16 Jun 2020 09:12:52: 2000000 INFO @ Tue, 16 Jun 2020 09:12:58: 3000000 INFO @ Tue, 16 Jun 2020 09:13:05: 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 09:13:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.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 09:13:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:12: 5000000 INFO @ Tue, 16 Jun 2020 09:13:15: 1000000 INFO @ Tue, 16 Jun 2020 09:13:19: 6000000 INFO @ Tue, 16 Jun 2020 09:13:22: 2000000 INFO @ Tue, 16 Jun 2020 09:13:26: 7000000 INFO @ Tue, 16 Jun 2020 09:13:29: 3000000 INFO @ Tue, 16 Jun 2020 09:13:33: 8000000 INFO @ Tue, 16 Jun 2020 09:13:36: 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 09:13:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.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 09:13:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:40: 9000000 INFO @ Tue, 16 Jun 2020 09:13:43: 5000000 INFO @ Tue, 16 Jun 2020 09:13:45: 1000000 INFO @ Tue, 16 Jun 2020 09:13:47: 10000000 INFO @ Tue, 16 Jun 2020 09:13:50: 6000000 INFO @ Tue, 16 Jun 2020 09:13:52: 2000000 INFO @ Tue, 16 Jun 2020 09:13:54: 11000000 INFO @ Tue, 16 Jun 2020 09:13:57: 7000000 INFO @ Tue, 16 Jun 2020 09:13:59: 3000000 INFO @ Tue, 16 Jun 2020 09:14:01: 12000000 INFO @ Tue, 16 Jun 2020 09:14:04: 8000000 INFO @ Tue, 16 Jun 2020 09:14:06: 4000000 INFO @ Tue, 16 Jun 2020 09:14:08: 13000000 INFO @ Tue, 16 Jun 2020 09:14:11: 9000000 INFO @ Tue, 16 Jun 2020 09:14:13: 5000000 INFO @ Tue, 16 Jun 2020 09:14:15: 14000000 INFO @ Tue, 16 Jun 2020 09:14:18: 10000000 INFO @ Tue, 16 Jun 2020 09:14:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:14:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:14:19: #1 total tags in treatment: 14475262 INFO @ Tue, 16 Jun 2020 09:14:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:19: #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 09:14:19: #1 tags after filtering in treatment: 14475262 INFO @ Tue, 16 Jun 2020 09:14:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:20: #2 number of paired peaks: 1049 INFO @ Tue, 16 Jun 2020 09:14:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:20: #2 predicted fragment length is 113 bps INFO @ Tue, 16 Jun 2020 09:14:20: #2 alternative fragment length(s) may be 4,113 bps INFO @ Tue, 16 Jun 2020 09:14:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.05_model.r INFO @ Tue, 16 Jun 2020 09:14:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:20: 6000000 INFO @ Tue, 16 Jun 2020 09:14:24: 11000000 INFO @ Tue, 16 Jun 2020 09:14:27: 7000000 INFO @ Tue, 16 Jun 2020 09:14:31: 12000000 INFO @ Tue, 16 Jun 2020 09:14:34: 8000000 INFO @ Tue, 16 Jun 2020 09:14:38: 13000000 INFO @ Tue, 16 Jun 2020 09:14:41: 9000000 INFO @ Tue, 16 Jun 2020 09:14:45: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:14:48: 10000000 INFO @ Tue, 16 Jun 2020 09:14:49: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:14:49: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:14:49: #1 total tags in treatment: 14475262 INFO @ Tue, 16 Jun 2020 09:14:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:49: #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 09:14:49: #1 tags after filtering in treatment: 14475262 INFO @ Tue, 16 Jun 2020 09:14:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:50: #2 number of paired peaks: 1049 INFO @ Tue, 16 Jun 2020 09:14:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:50: #2 predicted fragment length is 113 bps INFO @ Tue, 16 Jun 2020 09:14:50: #2 alternative fragment length(s) may be 4,113 bps INFO @ Tue, 16 Jun 2020 09:14:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.10_model.r INFO @ Tue, 16 Jun 2020 09:14:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:55: 11000000 INFO @ Tue, 16 Jun 2020 09:15:01: 12000000 INFO @ Tue, 16 Jun 2020 09:15:08: 13000000 INFO @ Tue, 16 Jun 2020 09:15:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.05_summits.bed INFO @ Tue, 16 Jun 2020 09:15:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4610 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:15:14: 14000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:15:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:15:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:15:17: #1 total tags in treatment: 14475262 INFO @ Tue, 16 Jun 2020 09:15:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:17: #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 09:15:17: #1 tags after filtering in treatment: 14475262 INFO @ Tue, 16 Jun 2020 09:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:18: #2 number of paired peaks: 1049 INFO @ Tue, 16 Jun 2020 09:15:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:18: #2 predicted fragment length is 113 bps INFO @ Tue, 16 Jun 2020 09:15:18: #2 alternative fragment length(s) may be 4,113 bps INFO @ Tue, 16 Jun 2020 09:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.20_model.r INFO @ Tue, 16 Jun 2020 09:15:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.10_summits.bed INFO @ Tue, 16 Jun 2020 09:15:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2294 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:15:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466571/SRX466571.20_summits.bed INFO @ Tue, 16 Jun 2020 09:16:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (693 records, 4 fields): 2 millis CompletedMACS2peakCalling