Job ID = 6366973 SRX = SRX257672 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:05 prefetch.2.10.7: 1) Downloading 'SRR800683'... 2020-06-15T23:33:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:12 prefetch.2.10.7: 1) 'SRR800683' was downloaded successfully Read 22304749 spots for SRR800683/SRR800683.sra Written 22304749 spots for SRR800683/SRR800683.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: 00:04:55 22304749 reads; of these: 22304749 (100.00%) were unpaired; of these: 432164 (1.94%) aligned 0 times 18752306 (84.07%) aligned exactly 1 time 3120279 (13.99%) aligned >1 times 98.06% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 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] 13244628 / 21872585 = 0.6055 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 08:46:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.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 08:46:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:46:41: 1000000 INFO @ Tue, 16 Jun 2020 08:46:47: 2000000 INFO @ Tue, 16 Jun 2020 08:46:52: 3000000 INFO @ Tue, 16 Jun 2020 08:46:58: 4000000 INFO @ Tue, 16 Jun 2020 08:47:03: 5000000 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 08:47:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.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 08:47:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:09: 6000000 INFO @ Tue, 16 Jun 2020 08:47:12: 1000000 INFO @ Tue, 16 Jun 2020 08:47:14: 7000000 INFO @ Tue, 16 Jun 2020 08:47:17: 2000000 INFO @ Tue, 16 Jun 2020 08:47:20: 8000000 INFO @ Tue, 16 Jun 2020 08:47:23: 3000000 INFO @ Tue, 16 Jun 2020 08:47:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:47:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:47:24: #1 total tags in treatment: 8627957 INFO @ Tue, 16 Jun 2020 08:47:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:24: #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 08:47:24: #1 tags after filtering in treatment: 8627957 INFO @ Tue, 16 Jun 2020 08:47:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:25: #2 number of paired peaks: 2700 INFO @ Tue, 16 Jun 2020 08:47:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:25: #2 predicted fragment length is 312 bps INFO @ Tue, 16 Jun 2020 08:47:25: #2 alternative fragment length(s) may be 4,312 bps INFO @ Tue, 16 Jun 2020 08:47:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.05_model.r INFO @ Tue, 16 Jun 2020 08:47:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:47:29: 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 08:47:35: 5000000 INFO @ Tue, 16 Jun 2020 08:47:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.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 08:47:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:41: 6000000 INFO @ Tue, 16 Jun 2020 08:47:42: 1000000 INFO @ Tue, 16 Jun 2020 08:47:47: 7000000 INFO @ Tue, 16 Jun 2020 08:47:48: 2000000 INFO @ Tue, 16 Jun 2020 08:47:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:53: 8000000 INFO @ Tue, 16 Jun 2020 08:47:54: 3000000 INFO @ Tue, 16 Jun 2020 08:47:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:47:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:47:57: #1 total tags in treatment: 8627957 INFO @ Tue, 16 Jun 2020 08:47:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:57: #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 08:47:57: #1 tags after filtering in treatment: 8627957 INFO @ Tue, 16 Jun 2020 08:47:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:58: #2 number of paired peaks: 2700 INFO @ Tue, 16 Jun 2020 08:47:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:58: #2 predicted fragment length is 312 bps INFO @ Tue, 16 Jun 2020 08:47:58: #2 alternative fragment length(s) may be 4,312 bps INFO @ Tue, 16 Jun 2020 08:47:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.10_model.r INFO @ Tue, 16 Jun 2020 08:47:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:00: 4000000 INFO @ Tue, 16 Jun 2020 08:48:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.05_summits.bed INFO @ Tue, 16 Jun 2020 08:48:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5138 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:06: 5000000 INFO @ Tue, 16 Jun 2020 08:48:12: 6000000 INFO @ Tue, 16 Jun 2020 08:48:18: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:48:23: 8000000 INFO @ Tue, 16 Jun 2020 08:48:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:27: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:48:27: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:48:27: #1 total tags in treatment: 8627957 INFO @ Tue, 16 Jun 2020 08:48:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:27: #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 08:48:27: #1 tags after filtering in treatment: 8627957 INFO @ Tue, 16 Jun 2020 08:48:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:28: #2 number of paired peaks: 2700 INFO @ Tue, 16 Jun 2020 08:48:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:28: #2 predicted fragment length is 312 bps INFO @ Tue, 16 Jun 2020 08:48:28: #2 alternative fragment length(s) may be 4,312 bps INFO @ Tue, 16 Jun 2020 08:48:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.20_model.r INFO @ Tue, 16 Jun 2020 08:48:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.10_summits.bed INFO @ Tue, 16 Jun 2020 08:48:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3833 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:48:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257672/SRX257672.20_summits.bed INFO @ Tue, 16 Jun 2020 08:49:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2321 records, 4 fields): 3 millis CompletedMACS2peakCalling