Job ID = 6367744 SRX = SRX4082358 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:35 prefetch.2.10.7: 1) Downloading 'SRR7164176'... 2020-06-15T23:33:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:12 prefetch.2.10.7: 'SRR7164176' is valid 2020-06-15T23:35:12 prefetch.2.10.7: 1) 'SRR7164176' was downloaded successfully 2020-06-15T23:35:12 prefetch.2.10.7: 'SRR7164176' has 0 unresolved dependencies Read 14511367 spots for SRR7164176/SRR7164176.sra Written 14511367 spots for SRR7164176/SRR7164176.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: 00:01:27 14511367 reads; of these: 14511367 (100.00%) were unpaired; of these: 5469104 (37.69%) aligned 0 times 8054759 (55.51%) aligned exactly 1 time 987504 (6.81%) aligned >1 times 62.31% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 1705409 / 9042263 = 0.1886 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 08:39:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.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 08:39:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:21: 1000000 INFO @ Tue, 16 Jun 2020 08:39:26: 2000000 INFO @ Tue, 16 Jun 2020 08:39:31: 3000000 INFO @ Tue, 16 Jun 2020 08:39:36: 4000000 INFO @ Tue, 16 Jun 2020 08:39:41: 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 08:39:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.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 08:39:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:46: 6000000 INFO @ Tue, 16 Jun 2020 08:39:51: 1000000 INFO @ Tue, 16 Jun 2020 08:39:52: 7000000 INFO @ Tue, 16 Jun 2020 08:39:54: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:39:54: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:39:54: #1 total tags in treatment: 7336854 INFO @ Tue, 16 Jun 2020 08:39:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:54: #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 08:39:54: #1 tags after filtering in treatment: 7336854 INFO @ Tue, 16 Jun 2020 08:39:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:54: #2 number of paired peaks: 3083 INFO @ Tue, 16 Jun 2020 08:39:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:55: #2 predicted fragment length is 185 bps INFO @ Tue, 16 Jun 2020 08:39:55: #2 alternative fragment length(s) may be 3,185 bps INFO @ Tue, 16 Jun 2020 08:39:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.05_model.r INFO @ Tue, 16 Jun 2020 08:39:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:57: 2000000 INFO @ Tue, 16 Jun 2020 08:40:03: 3000000 INFO @ Tue, 16 Jun 2020 08:40:08: 4000000 INFO @ Tue, 16 Jun 2020 08:40:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:13: 5000000 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 08:40:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.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 08:40:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:19: 6000000 INFO @ Tue, 16 Jun 2020 08:40:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.05_summits.bed INFO @ Tue, 16 Jun 2020 08:40:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6364 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:21: 1000000 INFO @ Tue, 16 Jun 2020 08:40:24: 7000000 INFO @ Tue, 16 Jun 2020 08:40:26: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:26: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:26: #1 total tags in treatment: 7336854 INFO @ Tue, 16 Jun 2020 08:40:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:26: #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 08:40:26: #1 tags after filtering in treatment: 7336854 INFO @ Tue, 16 Jun 2020 08:40:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:26: 2000000 INFO @ Tue, 16 Jun 2020 08:40:27: #2 number of paired peaks: 3083 INFO @ Tue, 16 Jun 2020 08:40:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:27: #2 predicted fragment length is 185 bps INFO @ Tue, 16 Jun 2020 08:40:27: #2 alternative fragment length(s) may be 3,185 bps INFO @ Tue, 16 Jun 2020 08:40:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.10_model.r INFO @ Tue, 16 Jun 2020 08:40:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:32: 3000000 INFO @ Tue, 16 Jun 2020 08:40:37: 4000000 INFO @ Tue, 16 Jun 2020 08:40:42: 5000000 INFO @ Tue, 16 Jun 2020 08:40:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:47: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:40:52: 7000000 INFO @ Tue, 16 Jun 2020 08:40:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.10_summits.bed INFO @ Tue, 16 Jun 2020 08:40:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3282 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:54: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:54: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:54: #1 total tags in treatment: 7336854 INFO @ Tue, 16 Jun 2020 08:40:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:54: #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 08:40:54: #1 tags after filtering in treatment: 7336854 INFO @ Tue, 16 Jun 2020 08:40:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:55: #2 number of paired peaks: 3083 INFO @ Tue, 16 Jun 2020 08:40:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:55: #2 predicted fragment length is 185 bps INFO @ Tue, 16 Jun 2020 08:40:55: #2 alternative fragment length(s) may be 3,185 bps INFO @ Tue, 16 Jun 2020 08:40:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.20_model.r INFO @ Tue, 16 Jun 2020 08:40:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:41:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082358/SRX4082358.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (901 records, 4 fields): 2 millis CompletedMACS2peakCalling