Job ID = 6368989 SRX = SRX958294 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:33:40 prefetch.2.10.7: 1) Downloading 'SRR1917667'... 2020-06-16T00:33:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:43:25 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:43:25 prefetch.2.10.7: 1) 'SRR1917667' was downloaded successfully Read 73597677 spots for SRR1917667/SRR1917667.sra Written 73597677 spots for SRR1917667/SRR1917667.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: 00:16:30 73597677 reads; of these: 73597677 (100.00%) were unpaired; of these: 19632604 (26.68%) aligned 0 times 31667625 (43.03%) aligned exactly 1 time 22297448 (30.30%) aligned >1 times 73.32% overall alignment rate Time searching: 00:16:30 Overall time: 00:16:30 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 24 files... [bam_rmdupse_core] 38324723 / 53965073 = 0.7102 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 10:13:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.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 10:13:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:13:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:13:59: 1000000 INFO @ Tue, 16 Jun 2020 10:14:07: 2000000 INFO @ Tue, 16 Jun 2020 10:14:14: 3000000 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 10:14:21: 4000000 INFO @ Tue, 16 Jun 2020 10:14:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.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 10:14:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:14:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:14:29: 5000000 INFO @ Tue, 16 Jun 2020 10:14:30: 1000000 INFO @ Tue, 16 Jun 2020 10:14:37: 6000000 INFO @ Tue, 16 Jun 2020 10:14:37: 2000000 INFO @ Tue, 16 Jun 2020 10:14:45: 7000000 INFO @ Tue, 16 Jun 2020 10:14:45: 3000000 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 10:14:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.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 10:14:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:14:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:14:52: 4000000 INFO @ Tue, 16 Jun 2020 10:14:53: 8000000 INFO @ Tue, 16 Jun 2020 10:15:00: 1000000 INFO @ Tue, 16 Jun 2020 10:15:00: 5000000 INFO @ Tue, 16 Jun 2020 10:15:01: 9000000 INFO @ Tue, 16 Jun 2020 10:15:08: 2000000 INFO @ Tue, 16 Jun 2020 10:15:08: 6000000 INFO @ Tue, 16 Jun 2020 10:15:09: 10000000 INFO @ Tue, 16 Jun 2020 10:15:16: 3000000 INFO @ Tue, 16 Jun 2020 10:15:16: 7000000 INFO @ Tue, 16 Jun 2020 10:15:17: 11000000 INFO @ Tue, 16 Jun 2020 10:15:24: 4000000 INFO @ Tue, 16 Jun 2020 10:15:24: 8000000 INFO @ Tue, 16 Jun 2020 10:15:25: 12000000 INFO @ Tue, 16 Jun 2020 10:15:31: 5000000 INFO @ Tue, 16 Jun 2020 10:15:31: 9000000 INFO @ Tue, 16 Jun 2020 10:15:33: 13000000 INFO @ Tue, 16 Jun 2020 10:15:39: 6000000 INFO @ Tue, 16 Jun 2020 10:15:39: 10000000 INFO @ Tue, 16 Jun 2020 10:15:41: 14000000 INFO @ Tue, 16 Jun 2020 10:15:47: 7000000 INFO @ Tue, 16 Jun 2020 10:15:47: 11000000 INFO @ Tue, 16 Jun 2020 10:15:48: 15000000 INFO @ Tue, 16 Jun 2020 10:15:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:15:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:15:53: #1 total tags in treatment: 15640350 INFO @ Tue, 16 Jun 2020 10:15:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:15:53: #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 10:15:53: #1 tags after filtering in treatment: 15640350 INFO @ Tue, 16 Jun 2020 10:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:15:53: #1 finished! INFO @ Tue, 16 Jun 2020 10:15:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:15:55: 8000000 INFO @ Tue, 16 Jun 2020 10:15:55: 12000000 INFO @ Tue, 16 Jun 2020 10:15:55: #2 number of paired peaks: 2733 INFO @ Tue, 16 Jun 2020 10:15:55: start model_add_line... INFO @ Tue, 16 Jun 2020 10:15:55: start X-correlation... INFO @ Tue, 16 Jun 2020 10:15:55: end of X-cor INFO @ Tue, 16 Jun 2020 10:15:55: #2 finished! INFO @ Tue, 16 Jun 2020 10:15:55: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 10:15:55: #2 alternative fragment length(s) may be 4,148 bps INFO @ Tue, 16 Jun 2020 10:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.05_model.r INFO @ Tue, 16 Jun 2020 10:15:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:16:02: 9000000 INFO @ Tue, 16 Jun 2020 10:16:02: 13000000 INFO @ Tue, 16 Jun 2020 10:16:09: 10000000 INFO @ Tue, 16 Jun 2020 10:16:10: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:16:16: 11000000 INFO @ Tue, 16 Jun 2020 10:16:17: 15000000 INFO @ Tue, 16 Jun 2020 10:16:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:16:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:16:22: #1 total tags in treatment: 15640350 INFO @ Tue, 16 Jun 2020 10:16:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:16:22: #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 10:16:22: #1 tags after filtering in treatment: 15640350 INFO @ Tue, 16 Jun 2020 10:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:16:22: #1 finished! INFO @ Tue, 16 Jun 2020 10:16:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:16:23: 12000000 INFO @ Tue, 16 Jun 2020 10:16:23: #2 number of paired peaks: 2733 INFO @ Tue, 16 Jun 2020 10:16:23: start model_add_line... INFO @ Tue, 16 Jun 2020 10:16:24: start X-correlation... INFO @ Tue, 16 Jun 2020 10:16:24: end of X-cor INFO @ Tue, 16 Jun 2020 10:16:24: #2 finished! INFO @ Tue, 16 Jun 2020 10:16:24: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 10:16:24: #2 alternative fragment length(s) may be 4,148 bps INFO @ Tue, 16 Jun 2020 10:16:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.10_model.r INFO @ Tue, 16 Jun 2020 10:16:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:16:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:16:30: 13000000 INFO @ Tue, 16 Jun 2020 10:16:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:16:36: 14000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:16:42: 15000000 INFO @ Tue, 16 Jun 2020 10:16:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:16:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:16:47: #1 total tags in treatment: 15640350 INFO @ Tue, 16 Jun 2020 10:16:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:16:47: #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 10:16:47: #1 tags after filtering in treatment: 15640350 INFO @ Tue, 16 Jun 2020 10:16:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:16:47: #1 finished! INFO @ Tue, 16 Jun 2020 10:16:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:16:48: #2 number of paired peaks: 2733 INFO @ Tue, 16 Jun 2020 10:16:48: start model_add_line... INFO @ Tue, 16 Jun 2020 10:16:48: start X-correlation... INFO @ Tue, 16 Jun 2020 10:16:48: end of X-cor INFO @ Tue, 16 Jun 2020 10:16:48: #2 finished! INFO @ Tue, 16 Jun 2020 10:16:48: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 10:16:48: #2 alternative fragment length(s) may be 4,148 bps INFO @ Tue, 16 Jun 2020 10:16:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.20_model.r INFO @ Tue, 16 Jun 2020 10:16:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:16:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:16:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:16:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:16:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.05_summits.bed INFO @ Tue, 16 Jun 2020 10:16:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9537 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:17:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:17:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:17:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:17:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.10_summits.bed INFO @ Tue, 16 Jun 2020 10:17:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6868 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:17:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:17:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:17:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:17:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX958294/SRX958294.20_summits.bed INFO @ Tue, 16 Jun 2020 10:17:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4005 records, 4 fields): 5 millis CompletedMACS2peakCalling