Job ID = 6368709 SRX = SRX5402733 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:49 prefetch.2.10.7: 1) Downloading 'SRR8602967'... 2020-06-16T00:26:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:26 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:27 prefetch.2.10.7: 'SRR8602967' is valid 2020-06-16T00:27:27 prefetch.2.10.7: 1) 'SRR8602967' was downloaded successfully 2020-06-16T00:27:27 prefetch.2.10.7: 'SRR8602967' has 0 unresolved dependencies Read 6980982 spots for SRR8602967/SRR8602967.sra Written 6980982 spots for SRR8602967/SRR8602967.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: 00:01:20 6980982 reads; of these: 6980982 (100.00%) were unpaired; of these: 452467 (6.48%) aligned 0 times 5746796 (82.32%) aligned exactly 1 time 781719 (11.20%) aligned >1 times 93.52% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 1903093 / 6528515 = 0.2915 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 09:31:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.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 09:31:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:14: 1000000 INFO @ Tue, 16 Jun 2020 09:31:19: 2000000 INFO @ Tue, 16 Jun 2020 09:31:25: 3000000 INFO @ Tue, 16 Jun 2020 09:31:31: 4000000 INFO @ Tue, 16 Jun 2020 09:31:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:31:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:31:34: #1 total tags in treatment: 4625422 INFO @ Tue, 16 Jun 2020 09:31:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:34: #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 09:31:34: #1 tags after filtering in treatment: 4625422 INFO @ Tue, 16 Jun 2020 09:31:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:35: #2 number of paired peaks: 4437 INFO @ Tue, 16 Jun 2020 09:31:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:35: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 09:31:35: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 16 Jun 2020 09:31:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.05_model.r INFO @ Tue, 16 Jun 2020 09:31:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:35: #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 09:31:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.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 09:31:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:44: 1000000 INFO @ Tue, 16 Jun 2020 09:31:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:49: 2000000 INFO @ Tue, 16 Jun 2020 09:31:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.05_summits.bed INFO @ Tue, 16 Jun 2020 09:31:52: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5611 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:55: 3000000 INFO @ Tue, 16 Jun 2020 09:32:01: 4000000 INFO @ Tue, 16 Jun 2020 09:32:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:04: #1 total tags in treatment: 4625422 INFO @ Tue, 16 Jun 2020 09:32:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:04: #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 09:32:04: #1 tags after filtering in treatment: 4625422 INFO @ Tue, 16 Jun 2020 09:32:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:05: #2 number of paired peaks: 4437 INFO @ Tue, 16 Jun 2020 09:32:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:05: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 09:32:05: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 16 Jun 2020 09:32:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.10_model.r INFO @ Tue, 16 Jun 2020 09:32:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:05: #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 09:32:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.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 09:32:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:13: 1000000 INFO @ Tue, 16 Jun 2020 09:32:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:19: 2000000 INFO @ Tue, 16 Jun 2020 09:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:22: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4821 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:24: 3000000 INFO @ Tue, 16 Jun 2020 09:32:30: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:33: #1 total tags in treatment: 4625422 INFO @ Tue, 16 Jun 2020 09:32:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:33: #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 09:32:33: #1 tags after filtering in treatment: 4625422 INFO @ Tue, 16 Jun 2020 09:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:34: #2 number of paired peaks: 4437 INFO @ Tue, 16 Jun 2020 09:32:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:34: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 09:32:34: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 16 Jun 2020 09:32:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.20_model.r INFO @ Tue, 16 Jun 2020 09:32:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:32:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402733/SRX5402733.20_summits.bed INFO @ Tue, 16 Jun 2020 09:32:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3916 records, 4 fields): 6 millis CompletedMACS2peakCalling