Job ID = 6507973 SRX = SRX514729 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:25:48 prefetch.2.10.7: 1) Downloading 'SRR1231450'... 2020-06-26T13:25:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:26:33 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:26:33 prefetch.2.10.7: 'SRR1231450' is valid 2020-06-26T13:26:33 prefetch.2.10.7: 1) 'SRR1231450' was downloaded successfully Read 4104181 spots for SRR1231450/SRR1231450.sra Written 4104181 spots for SRR1231450/SRR1231450.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: 00:00:47 4104181 reads; of these: 4104181 (100.00%) were unpaired; of these: 67063 (1.63%) aligned 0 times 3570298 (86.99%) aligned exactly 1 time 466820 (11.37%) aligned >1 times 98.37% overall alignment rate Time searching: 00:00:47 Overall time: 00:00:47 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] 302536 / 4037118 = 0.0749 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 @ Fri, 26 Jun 2020 22:28:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.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 @ Fri, 26 Jun 2020 22:28:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:28:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:02: 1000000 INFO @ Fri, 26 Jun 2020 22:29:08: 2000000 INFO @ Fri, 26 Jun 2020 22:29:14: 3000000 INFO @ Fri, 26 Jun 2020 22:29:19: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:29:19: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:29:19: #1 total tags in treatment: 3734582 INFO @ Fri, 26 Jun 2020 22:29:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:29:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:29:19: #1 tags after filtering in treatment: 3734582 INFO @ Fri, 26 Jun 2020 22:29:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:29:19: #1 finished! INFO @ Fri, 26 Jun 2020 22:29:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:29:19: #2 number of paired peaks: 2450 INFO @ Fri, 26 Jun 2020 22:29:19: start model_add_line... INFO @ Fri, 26 Jun 2020 22:29:19: start X-correlation... INFO @ Fri, 26 Jun 2020 22:29:19: end of X-cor INFO @ Fri, 26 Jun 2020 22:29:19: #2 finished! INFO @ Fri, 26 Jun 2020 22:29:19: #2 predicted fragment length is 234 bps INFO @ Fri, 26 Jun 2020 22:29:19: #2 alternative fragment length(s) may be 234 bps INFO @ Fri, 26 Jun 2020 22:29:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.05_model.r INFO @ Fri, 26 Jun 2020 22:29:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:29:19: #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 @ Fri, 26 Jun 2020 22:29:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.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 @ Fri, 26 Jun 2020 22:29:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:29:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:29:32: 1000000 INFO @ Fri, 26 Jun 2020 22:29:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:29:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:29:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.05_summits.bed INFO @ Fri, 26 Jun 2020 22:29:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5369 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:29:38: 2000000 INFO @ Fri, 26 Jun 2020 22:29:44: 3000000 INFO @ Fri, 26 Jun 2020 22:29:48: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:29:48: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:29:48: #1 total tags in treatment: 3734582 INFO @ Fri, 26 Jun 2020 22:29:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:29:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:29:48: #1 tags after filtering in treatment: 3734582 INFO @ Fri, 26 Jun 2020 22:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:29:48: #1 finished! INFO @ Fri, 26 Jun 2020 22:29:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:29:48: #2 number of paired peaks: 2450 INFO @ Fri, 26 Jun 2020 22:29:48: start model_add_line... INFO @ Fri, 26 Jun 2020 22:29:49: start X-correlation... INFO @ Fri, 26 Jun 2020 22:29:49: end of X-cor INFO @ Fri, 26 Jun 2020 22:29:49: #2 finished! INFO @ Fri, 26 Jun 2020 22:29:49: #2 predicted fragment length is 234 bps INFO @ Fri, 26 Jun 2020 22:29:49: #2 alternative fragment length(s) may be 234 bps INFO @ Fri, 26 Jun 2020 22:29:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.10_model.r INFO @ Fri, 26 Jun 2020 22:29:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:29:49: #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 @ Fri, 26 Jun 2020 22:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.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 @ Fri, 26 Jun 2020 22:29:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:29:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:30:02: 1000000 INFO @ Fri, 26 Jun 2020 22:30:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:30:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:30:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.10_summits.bed INFO @ Fri, 26 Jun 2020 22:30:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3105 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:30:08: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:30:14: 3000000 INFO @ Fri, 26 Jun 2020 22:30:18: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:30:18: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:30:18: #1 total tags in treatment: 3734582 INFO @ Fri, 26 Jun 2020 22:30:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:30:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:30:18: #1 tags after filtering in treatment: 3734582 INFO @ Fri, 26 Jun 2020 22:30:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:30:18: #1 finished! INFO @ Fri, 26 Jun 2020 22:30:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:30:18: #2 number of paired peaks: 2450 INFO @ Fri, 26 Jun 2020 22:30:18: start model_add_line... INFO @ Fri, 26 Jun 2020 22:30:18: start X-correlation... INFO @ Fri, 26 Jun 2020 22:30:18: end of X-cor INFO @ Fri, 26 Jun 2020 22:30:18: #2 finished! INFO @ Fri, 26 Jun 2020 22:30:18: #2 predicted fragment length is 234 bps INFO @ Fri, 26 Jun 2020 22:30:18: #2 alternative fragment length(s) may be 234 bps INFO @ Fri, 26 Jun 2020 22:30:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.20_model.r INFO @ Fri, 26 Jun 2020 22:30:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:30:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:30:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:30:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:30:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:30:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX514729/SRX514729.20_summits.bed INFO @ Fri, 26 Jun 2020 22:30:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1020 records, 4 fields): 7 millis CompletedMACS2peakCalling