Job ID = 6366953 SRX = SRX2576653 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:12:46 prefetch.2.10.7: 1) Downloading 'SRR5272610'... 2020-06-15T23:12:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:59 prefetch.2.10.7: 'SRR5272610' is valid 2020-06-15T23:13:59 prefetch.2.10.7: 1) 'SRR5272610' was downloaded successfully Read 16703865 spots for SRR5272610/SRR5272610.sra Written 16703865 spots for SRR5272610/SRR5272610.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: 00:03:08 16703865 reads; of these: 16703865 (100.00%) were unpaired; of these: 2311059 (13.84%) aligned 0 times 12118662 (72.55%) aligned exactly 1 time 2274144 (13.61%) aligned >1 times 86.16% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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_rmdupse_core] 4130692 / 14392806 = 0.2870 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 08:22:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.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 08:22:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:22: 1000000 INFO @ Tue, 16 Jun 2020 08:22:28: 2000000 INFO @ Tue, 16 Jun 2020 08:22:34: 3000000 INFO @ Tue, 16 Jun 2020 08:22:40: 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 08:22:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.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 08:22:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:46: 5000000 INFO @ Tue, 16 Jun 2020 08:22:52: 1000000 INFO @ Tue, 16 Jun 2020 08:22:52: 6000000 INFO @ Tue, 16 Jun 2020 08:22:58: 2000000 INFO @ Tue, 16 Jun 2020 08:22:58: 7000000 INFO @ Tue, 16 Jun 2020 08:23:05: 3000000 INFO @ Tue, 16 Jun 2020 08:23:05: 8000000 INFO @ Tue, 16 Jun 2020 08:23:11: 9000000 INFO @ Tue, 16 Jun 2020 08:23:11: 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 08:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.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 08:23:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:17: 10000000 INFO @ Tue, 16 Jun 2020 08:23:18: 5000000 INFO @ Tue, 16 Jun 2020 08:23:19: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:23:19: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:23:19: #1 total tags in treatment: 10262114 INFO @ Tue, 16 Jun 2020 08:23:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:19: #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 08:23:19: #1 tags after filtering in treatment: 10262114 INFO @ Tue, 16 Jun 2020 08:23:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:20: #2 number of paired peaks: 1029 INFO @ Tue, 16 Jun 2020 08:23:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:20: #2 predicted fragment length is 115 bps INFO @ Tue, 16 Jun 2020 08:23:20: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 16 Jun 2020 08:23:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.05_model.r INFO @ Tue, 16 Jun 2020 08:23:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:22: 1000000 INFO @ Tue, 16 Jun 2020 08:23:25: 6000000 INFO @ Tue, 16 Jun 2020 08:23:29: 2000000 INFO @ Tue, 16 Jun 2020 08:23:31: 7000000 INFO @ Tue, 16 Jun 2020 08:23:36: 3000000 INFO @ Tue, 16 Jun 2020 08:23:38: 8000000 INFO @ Tue, 16 Jun 2020 08:23:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:42: 4000000 INFO @ Tue, 16 Jun 2020 08:23:45: 9000000 INFO @ Tue, 16 Jun 2020 08:23:49: 5000000 INFO @ Tue, 16 Jun 2020 08:23:52: 10000000 INFO @ Tue, 16 Jun 2020 08:23:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.05_summits.bed INFO @ Tue, 16 Jun 2020 08:23:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4958 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:53: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:23:53: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:23:53: #1 total tags in treatment: 10262114 INFO @ Tue, 16 Jun 2020 08:23:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:53: #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 08:23:54: #1 tags after filtering in treatment: 10262114 INFO @ Tue, 16 Jun 2020 08:23:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:54: #2 number of paired peaks: 1029 INFO @ Tue, 16 Jun 2020 08:23:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:54: #2 predicted fragment length is 115 bps INFO @ Tue, 16 Jun 2020 08:23:54: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 16 Jun 2020 08:23:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.10_model.r INFO @ Tue, 16 Jun 2020 08:23:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:56: 6000000 INFO @ Tue, 16 Jun 2020 08:24:02: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:24:09: 8000000 INFO @ Tue, 16 Jun 2020 08:24:15: 9000000 INFO @ Tue, 16 Jun 2020 08:24:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:22: 10000000 INFO @ Tue, 16 Jun 2020 08:24:24: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:24:24: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:24:24: #1 total tags in treatment: 10262114 INFO @ Tue, 16 Jun 2020 08:24:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:24: #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 08:24:24: #1 tags after filtering in treatment: 10262114 INFO @ Tue, 16 Jun 2020 08:24:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:25: #2 number of paired peaks: 1029 INFO @ Tue, 16 Jun 2020 08:24:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:25: #2 predicted fragment length is 115 bps INFO @ Tue, 16 Jun 2020 08:24:25: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 16 Jun 2020 08:24:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.20_model.r INFO @ Tue, 16 Jun 2020 08:24:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.10_summits.bed INFO @ Tue, 16 Jun 2020 08:24:27: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3362 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:24:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576653/SRX2576653.20_summits.bed INFO @ Tue, 16 Jun 2020 08:24:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2159 records, 4 fields): 4 millis CompletedMACS2peakCalling