Job ID = 6366884 SRX = SRX2543052 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:35 prefetch.2.10.7: 1) Downloading 'SRR5235988'... 2020-06-15T23:31:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:35 prefetch.2.10.7: 'SRR5235988' is valid 2020-06-15T23:33:35 prefetch.2.10.7: 1) 'SRR5235988' was downloaded successfully 2020-06-15T23:33:35 prefetch.2.10.7: 'SRR5235988' has 0 unresolved dependencies Read 17696870 spots for SRR5235988/SRR5235988.sra Written 17696870 spots for SRR5235988/SRR5235988.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: 00:05:36 17696870 reads; of these: 17696870 (100.00%) were unpaired; of these: 2159915 (12.21%) aligned 0 times 13455757 (76.03%) aligned exactly 1 time 2081198 (11.76%) aligned >1 times 87.79% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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 8 files... [bam_rmdupse_core] 4064896 / 15536955 = 0.2616 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 08:43:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.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 08:43:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:55: 1000000 INFO @ Tue, 16 Jun 2020 08:44:01: 2000000 INFO @ Tue, 16 Jun 2020 08:44:07: 3000000 INFO @ Tue, 16 Jun 2020 08:44:13: 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 08:44:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.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 08:44:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:19: 5000000 INFO @ Tue, 16 Jun 2020 08:44:25: 1000000 INFO @ Tue, 16 Jun 2020 08:44:26: 6000000 INFO @ Tue, 16 Jun 2020 08:44:33: 2000000 INFO @ Tue, 16 Jun 2020 08:44:34: 7000000 INFO @ Tue, 16 Jun 2020 08:44:40: 3000000 INFO @ Tue, 16 Jun 2020 08:44:41: 8000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 08:44:47: 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 08:44:48: 9000000 INFO @ Tue, 16 Jun 2020 08:44:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.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 08:44:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:54: 5000000 INFO @ Tue, 16 Jun 2020 08:44:55: 10000000 INFO @ Tue, 16 Jun 2020 08:44:56: 1000000 INFO @ Tue, 16 Jun 2020 08:45:01: 6000000 INFO @ Tue, 16 Jun 2020 08:45:02: 11000000 INFO @ Tue, 16 Jun 2020 08:45:03: 2000000 INFO @ Tue, 16 Jun 2020 08:45:05: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:45:05: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:45:05: #1 total tags in treatment: 11472059 INFO @ Tue, 16 Jun 2020 08:45:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:05: #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 08:45:05: #1 tags after filtering in treatment: 11472059 INFO @ Tue, 16 Jun 2020 08:45:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:06: #2 number of paired peaks: 3241 INFO @ Tue, 16 Jun 2020 08:45:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:06: #2 predicted fragment length is 228 bps INFO @ Tue, 16 Jun 2020 08:45:06: #2 alternative fragment length(s) may be 4,228 bps INFO @ Tue, 16 Jun 2020 08:45:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.05_model.r INFO @ Tue, 16 Jun 2020 08:45:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:08: 7000000 INFO @ Tue, 16 Jun 2020 08:45:10: 3000000 INFO @ Tue, 16 Jun 2020 08:45:15: 8000000 INFO @ Tue, 16 Jun 2020 08:45:17: 4000000 INFO @ Tue, 16 Jun 2020 08:45:22: 9000000 INFO @ Tue, 16 Jun 2020 08:45:24: 5000000 INFO @ Tue, 16 Jun 2020 08:45:29: 10000000 INFO @ Tue, 16 Jun 2020 08:45:31: 6000000 INFO @ Tue, 16 Jun 2020 08:45:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:36: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:38: 7000000 INFO @ Tue, 16 Jun 2020 08:45:40: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:45:40: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:45:40: #1 total tags in treatment: 11472059 INFO @ Tue, 16 Jun 2020 08:45:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:40: #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 08:45:40: #1 tags after filtering in treatment: 11472059 INFO @ Tue, 16 Jun 2020 08:45:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:41: #2 number of paired peaks: 3241 INFO @ Tue, 16 Jun 2020 08:45:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:41: #2 predicted fragment length is 228 bps INFO @ Tue, 16 Jun 2020 08:45:41: #2 alternative fragment length(s) may be 4,228 bps INFO @ Tue, 16 Jun 2020 08:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.10_model.r INFO @ Tue, 16 Jun 2020 08:45:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:45: 8000000 INFO @ Tue, 16 Jun 2020 08:45:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.05_summits.bed INFO @ Tue, 16 Jun 2020 08:45:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4878 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:45:51: 9000000 INFO @ Tue, 16 Jun 2020 08:45:57: 10000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:46:04: 11000000 INFO @ Tue, 16 Jun 2020 08:46:06: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:46:06: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:46:06: #1 total tags in treatment: 11472059 INFO @ Tue, 16 Jun 2020 08:46:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:06: #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 08:46:07: #1 tags after filtering in treatment: 11472059 INFO @ Tue, 16 Jun 2020 08:46:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:08: #2 number of paired peaks: 3241 INFO @ Tue, 16 Jun 2020 08:46:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:08: #2 predicted fragment length is 228 bps INFO @ Tue, 16 Jun 2020 08:46:08: #2 alternative fragment length(s) may be 4,228 bps INFO @ Tue, 16 Jun 2020 08:46:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.20_model.r INFO @ Tue, 16 Jun 2020 08:46:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.10_summits.bed INFO @ Tue, 16 Jun 2020 08:46:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3895 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543052/SRX2543052.20_summits.bed INFO @ Tue, 16 Jun 2020 08:46:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2968 records, 4 fields): 4 millis CompletedMACS2peakCalling