Job ID = 6367940 SRX = SRX4344456 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:44:59 prefetch.2.10.7: 1) Downloading 'SRR7474923'... 2020-06-15T23:44:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:58 prefetch.2.10.7: 'SRR7474923' is valid 2020-06-15T23:45:58 prefetch.2.10.7: 1) 'SRR7474923' was downloaded successfully 2020-06-15T23:45:58 prefetch.2.10.7: 'SRR7474923' has 0 unresolved dependencies Read 6890646 spots for SRR7474923/SRR7474923.sra Written 6890646 spots for SRR7474923/SRR7474923.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: 00:01:14 6890646 reads; of these: 6890646 (100.00%) were unpaired; of these: 2320604 (33.68%) aligned 0 times 3919537 (56.88%) aligned exactly 1 time 650505 (9.44%) aligned >1 times 66.32% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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] 1474102 / 4570042 = 0.3226 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 08:49:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.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 08:49:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:28: 1000000 INFO @ Tue, 16 Jun 2020 08:49:36: 2000000 INFO @ Tue, 16 Jun 2020 08:49:44: 3000000 INFO @ Tue, 16 Jun 2020 08:49:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:49:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:49:44: #1 total tags in treatment: 3095940 INFO @ Tue, 16 Jun 2020 08:49:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:44: #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 08:49:44: #1 tags after filtering in treatment: 3095940 INFO @ Tue, 16 Jun 2020 08:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:45: #2 number of paired peaks: 1166 INFO @ Tue, 16 Jun 2020 08:49:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:45: #2 predicted fragment length is 155 bps INFO @ Tue, 16 Jun 2020 08:49:45: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 16 Jun 2020 08:49:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.05_model.r INFO @ Tue, 16 Jun 2020 08:49:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:45: #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 08:49:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.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 08:49:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.05_summits.bed INFO @ Tue, 16 Jun 2020 08:49:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2571 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:49:58: 1000000 INFO @ Tue, 16 Jun 2020 08:50:06: 2000000 INFO @ Tue, 16 Jun 2020 08:50:14: 3000000 INFO @ Tue, 16 Jun 2020 08:50:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:50:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:50:14: #1 total tags in treatment: 3095940 INFO @ Tue, 16 Jun 2020 08:50:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:14: #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 08:50:14: #1 tags after filtering in treatment: 3095940 INFO @ Tue, 16 Jun 2020 08:50:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:14: #2 number of paired peaks: 1166 INFO @ Tue, 16 Jun 2020 08:50:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:14: #2 predicted fragment length is 155 bps INFO @ Tue, 16 Jun 2020 08:50:14: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 16 Jun 2020 08:50:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.10_model.r INFO @ Tue, 16 Jun 2020 08:50:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:14: #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 08:50:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.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 08:50:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.10_summits.bed INFO @ Tue, 16 Jun 2020 08:50:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1501 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:28: 1000000 INFO @ Tue, 16 Jun 2020 08:50:36: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:43: 3000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:50:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:50:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:50:44: #1 total tags in treatment: 3095940 INFO @ Tue, 16 Jun 2020 08:50:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:44: #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 08:50:44: #1 tags after filtering in treatment: 3095940 INFO @ Tue, 16 Jun 2020 08:50:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:44: #2 number of paired peaks: 1166 INFO @ Tue, 16 Jun 2020 08:50:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:44: #2 predicted fragment length is 155 bps INFO @ Tue, 16 Jun 2020 08:50:44: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 16 Jun 2020 08:50:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.20_model.r INFO @ Tue, 16 Jun 2020 08:50:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4344456/SRX4344456.20_summits.bed INFO @ Tue, 16 Jun 2020 08:50:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (769 records, 4 fields): 2 millis CompletedMACS2peakCalling