Job ID = 6368707 SRX = SRX5402731 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:31:15 prefetch.2.10.7: 1) Downloading 'SRR8602965'... 2020-06-16T00:31:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:20 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:20 prefetch.2.10.7: 1) 'SRR8602965' was downloaded successfully Read 31280312 spots for SRR8602965/SRR8602965.sra Written 31280312 spots for SRR8602965/SRR8602965.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: 00:06:37 31280312 reads; of these: 31280312 (100.00%) were unpaired; of these: 3534296 (11.30%) aligned 0 times 23663219 (75.65%) aligned exactly 1 time 4082797 (13.05%) aligned >1 times 88.70% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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] 8951563 / 27746016 = 0.3226 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 09:49:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.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 09:49:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:54: 1000000 INFO @ Tue, 16 Jun 2020 09:50:00: 2000000 INFO @ Tue, 16 Jun 2020 09:50:05: 3000000 INFO @ Tue, 16 Jun 2020 09:50:11: 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 09:50:17: 5000000 INFO @ Tue, 16 Jun 2020 09:50:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.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 09:50:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:22: 6000000 INFO @ Tue, 16 Jun 2020 09:50:25: 1000000 INFO @ Tue, 16 Jun 2020 09:50:28: 7000000 INFO @ Tue, 16 Jun 2020 09:50:31: 2000000 INFO @ Tue, 16 Jun 2020 09:50:34: 8000000 INFO @ Tue, 16 Jun 2020 09:50:36: 3000000 INFO @ Tue, 16 Jun 2020 09:50:40: 9000000 INFO @ Tue, 16 Jun 2020 09:50:43: 4000000 INFO @ Tue, 16 Jun 2020 09:50:46: 10000000 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 09:50:48: 5000000 INFO @ Tue, 16 Jun 2020 09:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.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 09:50:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:52: 11000000 INFO @ Tue, 16 Jun 2020 09:50:54: 6000000 INFO @ Tue, 16 Jun 2020 09:50:54: 1000000 INFO @ Tue, 16 Jun 2020 09:50:58: 12000000 INFO @ Tue, 16 Jun 2020 09:51:00: 2000000 INFO @ Tue, 16 Jun 2020 09:51:00: 7000000 INFO @ Tue, 16 Jun 2020 09:51:04: 13000000 INFO @ Tue, 16 Jun 2020 09:51:06: 3000000 INFO @ Tue, 16 Jun 2020 09:51:06: 8000000 INFO @ Tue, 16 Jun 2020 09:51:09: 14000000 INFO @ Tue, 16 Jun 2020 09:51:12: 4000000 INFO @ Tue, 16 Jun 2020 09:51:13: 9000000 INFO @ Tue, 16 Jun 2020 09:51:15: 15000000 INFO @ Tue, 16 Jun 2020 09:51:18: 5000000 INFO @ Tue, 16 Jun 2020 09:51:19: 10000000 INFO @ Tue, 16 Jun 2020 09:51:22: 16000000 INFO @ Tue, 16 Jun 2020 09:51:24: 6000000 INFO @ Tue, 16 Jun 2020 09:51:25: 11000000 INFO @ Tue, 16 Jun 2020 09:51:28: 17000000 INFO @ Tue, 16 Jun 2020 09:51:31: 7000000 INFO @ Tue, 16 Jun 2020 09:51:31: 12000000 INFO @ Tue, 16 Jun 2020 09:51:34: 18000000 INFO @ Tue, 16 Jun 2020 09:51:37: 8000000 INFO @ Tue, 16 Jun 2020 09:51:37: 13000000 INFO @ Tue, 16 Jun 2020 09:51:39: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:39: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:39: #1 total tags in treatment: 18794453 INFO @ Tue, 16 Jun 2020 09:51:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:39: #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 09:51:39: #1 tags after filtering in treatment: 18794453 INFO @ Tue, 16 Jun 2020 09:51:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:41: #2 number of paired peaks: 2319 INFO @ Tue, 16 Jun 2020 09:51:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:41: #2 predicted fragment length is 159 bps INFO @ Tue, 16 Jun 2020 09:51:41: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 16 Jun 2020 09:51:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.05_model.r INFO @ Tue, 16 Jun 2020 09:51:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:43: 9000000 INFO @ Tue, 16 Jun 2020 09:51:44: 14000000 INFO @ Tue, 16 Jun 2020 09:51:49: 10000000 INFO @ Tue, 16 Jun 2020 09:51:50: 15000000 INFO @ Tue, 16 Jun 2020 09:51:55: 11000000 INFO @ Tue, 16 Jun 2020 09:51:57: 16000000 INFO @ Tue, 16 Jun 2020 09:52:01: 12000000 INFO @ Tue, 16 Jun 2020 09:52:03: 17000000 INFO @ Tue, 16 Jun 2020 09:52:07: 13000000 INFO @ Tue, 16 Jun 2020 09:52:10: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:52:13: 14000000 INFO @ Tue, 16 Jun 2020 09:52:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:15: #1 total tags in treatment: 18794453 INFO @ Tue, 16 Jun 2020 09:52:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:15: #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 09:52:15: #1 tags after filtering in treatment: 18794453 INFO @ Tue, 16 Jun 2020 09:52:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:17: #2 number of paired peaks: 2319 INFO @ Tue, 16 Jun 2020 09:52:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:17: #2 predicted fragment length is 159 bps INFO @ Tue, 16 Jun 2020 09:52:17: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 16 Jun 2020 09:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.10_model.r INFO @ Tue, 16 Jun 2020 09:52:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:19: 15000000 INFO @ Tue, 16 Jun 2020 09:52:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:25: 16000000 INFO @ Tue, 16 Jun 2020 09:52:31: 17000000 INFO @ Tue, 16 Jun 2020 09:52:37: 18000000 INFO @ Tue, 16 Jun 2020 09:52:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:42: #1 total tags in treatment: 18794453 INFO @ Tue, 16 Jun 2020 09:52:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:42: #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 09:52:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:42: #1 tags after filtering in treatment: 18794453 INFO @ Tue, 16 Jun 2020 09:52:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.05_summits.bed INFO @ Tue, 16 Jun 2020 09:52:42: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7179 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:43: #2 number of paired peaks: 2319 INFO @ Tue, 16 Jun 2020 09:52:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:44: #2 predicted fragment length is 159 bps INFO @ Tue, 16 Jun 2020 09:52:44: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 16 Jun 2020 09:52:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.20_model.r INFO @ Tue, 16 Jun 2020 09:52:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:52:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:17: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5705 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402731/SRX5402731.20_summits.bed INFO @ Tue, 16 Jun 2020 09:53:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4639 records, 4 fields): 6 millis CompletedMACS2peakCalling