Job ID = 6368701 SRX = SRX5402726 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:36 prefetch.2.10.7: 1) Downloading 'SRR8602960'... 2020-06-16T00:24:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:08 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:08 prefetch.2.10.7: 'SRR8602960' is valid 2020-06-16T00:25:08 prefetch.2.10.7: 1) 'SRR8602960' was downloaded successfully 2020-06-16T00:25:08 prefetch.2.10.7: 'SRR8602960' has 0 unresolved dependencies Read 4541733 spots for SRR8602960/SRR8602960.sra Written 4541733 spots for SRR8602960/SRR8602960.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: 00:00:59 4541733 reads; of these: 4541733 (100.00%) were unpaired; of these: 44122 (0.97%) aligned 0 times 4069505 (89.60%) aligned exactly 1 time 428106 (9.43%) aligned >1 times 99.03% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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] 1735077 / 4497611 = 0.3858 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 09:27:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.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 09:27:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:39: 1000000 INFO @ Tue, 16 Jun 2020 09:27:45: 2000000 INFO @ Tue, 16 Jun 2020 09:27:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:27:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:27:48: #1 total tags in treatment: 2762534 INFO @ Tue, 16 Jun 2020 09:27:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:48: #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 09:27:48: #1 tags after filtering in treatment: 2762534 INFO @ Tue, 16 Jun 2020 09:27:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:49: #2 number of paired peaks: 5017 INFO @ Tue, 16 Jun 2020 09:27:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:49: #2 predicted fragment length is 185 bps INFO @ Tue, 16 Jun 2020 09:27:49: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 16 Jun 2020 09:27:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.05_model.r INFO @ Tue, 16 Jun 2020 09:27:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.05_summits.bed INFO @ Tue, 16 Jun 2020 09:28:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4772 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 09:28:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.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 09:28:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:10: 1000000 INFO @ Tue, 16 Jun 2020 09:28:16: 2000000 INFO @ Tue, 16 Jun 2020 09:28:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:28:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:28:20: #1 total tags in treatment: 2762534 INFO @ Tue, 16 Jun 2020 09:28:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:20: #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 09:28:20: #1 tags after filtering in treatment: 2762534 INFO @ Tue, 16 Jun 2020 09:28:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:20: #2 number of paired peaks: 5017 INFO @ Tue, 16 Jun 2020 09:28:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:20: #2 predicted fragment length is 185 bps INFO @ Tue, 16 Jun 2020 09:28:20: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 16 Jun 2020 09:28:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.10_model.r INFO @ Tue, 16 Jun 2020 09:28:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.10_summits.bed INFO @ Tue, 16 Jun 2020 09:28:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3973 records, 4 fields): 5 millis CompletedMACS2peakCalling 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 09:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.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 09:28:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:40: 1000000 INFO @ Tue, 16 Jun 2020 09:28:46: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:28:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:28:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:28:50: #1 total tags in treatment: 2762534 INFO @ Tue, 16 Jun 2020 09:28:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:50: #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 09:28:50: #1 tags after filtering in treatment: 2762534 INFO @ Tue, 16 Jun 2020 09:28:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:50: #2 number of paired peaks: 5017 INFO @ Tue, 16 Jun 2020 09:28:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:51: #2 predicted fragment length is 185 bps INFO @ Tue, 16 Jun 2020 09:28:51: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 16 Jun 2020 09:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.20_model.r INFO @ Tue, 16 Jun 2020 09:28:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:28:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402726/SRX5402726.20_summits.bed INFO @ Tue, 16 Jun 2020 09:29:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3258 records, 4 fields): 4 millis CompletedMACS2peakCalling