Job ID = 6366333 SRX = SRX113607 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:40:06 prefetch.2.10.7: 1) Downloading 'SRR393707'... 2020-06-15T22:40:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:40:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:40:43 prefetch.2.10.7: 'SRR393707' is valid 2020-06-15T22:40:43 prefetch.2.10.7: 1) 'SRR393707' was downloaded successfully Read 8241670 spots for SRR393707/SRR393707.sra Written 8241670 spots for SRR393707/SRR393707.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: 00:01:52 8241670 reads; of these: 8241670 (100.00%) were unpaired; of these: 410199 (4.98%) aligned 0 times 5481261 (66.51%) aligned exactly 1 time 2350210 (28.52%) aligned >1 times 95.02% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 2857741 / 7831471 = 0.3649 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 07:44:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.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 07:44:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:04: 1000000 INFO @ Tue, 16 Jun 2020 07:45:09: 2000000 INFO @ Tue, 16 Jun 2020 07:45:14: 3000000 INFO @ Tue, 16 Jun 2020 07:45:19: 4000000 INFO @ Tue, 16 Jun 2020 07:45:24: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:45:24: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:45:24: #1 total tags in treatment: 4973730 INFO @ Tue, 16 Jun 2020 07:45:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:24: #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 07:45:24: #1 tags after filtering in treatment: 4973730 INFO @ Tue, 16 Jun 2020 07:45:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:24: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:25: #2 number of paired peaks: 3668 INFO @ Tue, 16 Jun 2020 07:45:25: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:25: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:25: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:25: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:25: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 07:45:25: #2 alternative fragment length(s) may be 1,168,227 bps INFO @ Tue, 16 Jun 2020 07:45:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.05_model.r INFO @ Tue, 16 Jun 2020 07:45:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:25: #3 Pre-compute pvalue-qvalue table... 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 07:45:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.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 07:45:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:35: 1000000 INFO @ Tue, 16 Jun 2020 07:45:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:40: 2000000 INFO @ Tue, 16 Jun 2020 07:45:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.05_summits.bed INFO @ Tue, 16 Jun 2020 07:45:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1225 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:45:45: 3000000 INFO @ Tue, 16 Jun 2020 07:45:50: 4000000 INFO @ Tue, 16 Jun 2020 07:45:55: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:45:55: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:45:55: #1 total tags in treatment: 4973730 INFO @ Tue, 16 Jun 2020 07:45:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:55: #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 07:45:55: #1 tags after filtering in treatment: 4973730 INFO @ Tue, 16 Jun 2020 07:45:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:55: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:55: #2 number of paired peaks: 3668 INFO @ Tue, 16 Jun 2020 07:45:55: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:55: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:55: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:55: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:55: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 07:45:55: #2 alternative fragment length(s) may be 1,168,227 bps INFO @ Tue, 16 Jun 2020 07:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.10_model.r INFO @ Tue, 16 Jun 2020 07:45:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:55: #3 Pre-compute pvalue-qvalue table... 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 07:46:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.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 07:46:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:46:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:46:05: 1000000 INFO @ Tue, 16 Jun 2020 07:46:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:46:10: 2000000 INFO @ Tue, 16 Jun 2020 07:46:15: 3000000 INFO @ Tue, 16 Jun 2020 07:46:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:46:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:46:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.10_summits.bed INFO @ Tue, 16 Jun 2020 07:46:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:46:20: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:46:25: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:46:25: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:46:25: #1 total tags in treatment: 4973730 INFO @ Tue, 16 Jun 2020 07:46:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:46:25: #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 07:46:25: #1 tags after filtering in treatment: 4973730 INFO @ Tue, 16 Jun 2020 07:46:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:46:25: #1 finished! INFO @ Tue, 16 Jun 2020 07:46:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:46:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:46:25: #2 number of paired peaks: 3668 INFO @ Tue, 16 Jun 2020 07:46:25: start model_add_line... INFO @ Tue, 16 Jun 2020 07:46:25: start X-correlation... INFO @ Tue, 16 Jun 2020 07:46:25: end of X-cor INFO @ Tue, 16 Jun 2020 07:46:25: #2 finished! INFO @ Tue, 16 Jun 2020 07:46:25: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 07:46:25: #2 alternative fragment length(s) may be 1,168,227 bps INFO @ Tue, 16 Jun 2020 07:46:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.20_model.r INFO @ Tue, 16 Jun 2020 07:46:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:46:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:46:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:46:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:46:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113607/SRX113607.20_summits.bed INFO @ Tue, 16 Jun 2020 07:46:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (106 records, 4 fields): 1 millis CompletedMACS2peakCalling