Job ID = 6368712 SRX = SRX5402736 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:21:55 prefetch.2.10.7: 1) Downloading 'SRR8602970'... 2020-06-16T00:21:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:32 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:32 prefetch.2.10.7: 1) 'SRR8602970' was downloaded successfully Read 22553583 spots for SRR8602970/SRR8602970.sra Written 22553583 spots for SRR8602970/SRR8602970.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: 00:05:01 22553583 reads; of these: 22553583 (100.00%) were unpaired; of these: 2520888 (11.18%) aligned 0 times 17168418 (76.12%) aligned exactly 1 time 2864277 (12.70%) aligned >1 times 88.82% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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_sort_core] merging from 12 files... [bam_rmdupse_core] 5679444 / 20032695 = 0.2835 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 09:36:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.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 09:36:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:07: 1000000 INFO @ Tue, 16 Jun 2020 09:37:16: 2000000 INFO @ Tue, 16 Jun 2020 09:37:24: 3000000 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 09:37:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.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 09:37:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:32: 4000000 INFO @ Tue, 16 Jun 2020 09:37:35: 1000000 INFO @ Tue, 16 Jun 2020 09:37:39: 5000000 INFO @ Tue, 16 Jun 2020 09:37:43: 2000000 INFO @ Tue, 16 Jun 2020 09:37:47: 6000000 INFO @ Tue, 16 Jun 2020 09:37:50: 3000000 INFO @ Tue, 16 Jun 2020 09:37:56: 7000000 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 09:37:58: 4000000 INFO @ Tue, 16 Jun 2020 09:37:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.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 09:37:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:04: 8000000 INFO @ Tue, 16 Jun 2020 09:38:06: 5000000 INFO @ Tue, 16 Jun 2020 09:38:07: 1000000 INFO @ Tue, 16 Jun 2020 09:38:12: 9000000 INFO @ Tue, 16 Jun 2020 09:38:14: 6000000 INFO @ Tue, 16 Jun 2020 09:38:15: 2000000 INFO @ Tue, 16 Jun 2020 09:38:21: 10000000 INFO @ Tue, 16 Jun 2020 09:38:23: 7000000 INFO @ Tue, 16 Jun 2020 09:38:24: 3000000 INFO @ Tue, 16 Jun 2020 09:38:29: 11000000 INFO @ Tue, 16 Jun 2020 09:38:32: 4000000 INFO @ Tue, 16 Jun 2020 09:38:32: 8000000 INFO @ Tue, 16 Jun 2020 09:38:38: 12000000 INFO @ Tue, 16 Jun 2020 09:38:41: 5000000 INFO @ Tue, 16 Jun 2020 09:38:41: 9000000 INFO @ Tue, 16 Jun 2020 09:38:46: 13000000 INFO @ Tue, 16 Jun 2020 09:38:49: 6000000 INFO @ Tue, 16 Jun 2020 09:38:50: 10000000 INFO @ Tue, 16 Jun 2020 09:38:54: 14000000 INFO @ Tue, 16 Jun 2020 09:38:57: 7000000 INFO @ Tue, 16 Jun 2020 09:38:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:38:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:38:57: #1 total tags in treatment: 14353251 INFO @ Tue, 16 Jun 2020 09:38:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:57: #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 09:38:57: #1 tags after filtering in treatment: 14353251 INFO @ Tue, 16 Jun 2020 09:38:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:58: #2 number of paired peaks: 1799 INFO @ Tue, 16 Jun 2020 09:38:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:58: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 09:38:58: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 09:38:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.05_model.r INFO @ Tue, 16 Jun 2020 09:38:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:59: 11000000 INFO @ Tue, 16 Jun 2020 09:39:03: 8000000 INFO @ Tue, 16 Jun 2020 09:39:07: 12000000 INFO @ Tue, 16 Jun 2020 09:39:10: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:39:16: 13000000 INFO @ Tue, 16 Jun 2020 09:39:16: 10000000 INFO @ Tue, 16 Jun 2020 09:39:23: 11000000 INFO @ Tue, 16 Jun 2020 09:39:25: 14000000 INFO @ Tue, 16 Jun 2020 09:39:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:39:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:39:28: #1 total tags in treatment: 14353251 INFO @ Tue, 16 Jun 2020 09:39:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:28: #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 09:39:28: #1 tags after filtering in treatment: 14353251 INFO @ Tue, 16 Jun 2020 09:39:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:29: 12000000 INFO @ Tue, 16 Jun 2020 09:39:30: #2 number of paired peaks: 1799 INFO @ Tue, 16 Jun 2020 09:39:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:30: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 09:39:30: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 09:39:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.10_model.r INFO @ Tue, 16 Jun 2020 09:39:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:36: 13000000 INFO @ Tue, 16 Jun 2020 09:39:42: 14000000 INFO @ Tue, 16 Jun 2020 09:39:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.05_summits.bed INFO @ Tue, 16 Jun 2020 09:39:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5365 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:39:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:39:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:39:45: #1 total tags in treatment: 14353251 INFO @ Tue, 16 Jun 2020 09:39:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:45: #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 09:39:45: #1 tags after filtering in treatment: 14353251 INFO @ Tue, 16 Jun 2020 09:39:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:46: #2 number of paired peaks: 1799 INFO @ Tue, 16 Jun 2020 09:39:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:46: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 09:39:46: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 09:39:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.20_model.r INFO @ Tue, 16 Jun 2020 09:39:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:40:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.10_summits.bed INFO @ Tue, 16 Jun 2020 09:40:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4421 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402736/SRX5402736.20_summits.bed INFO @ Tue, 16 Jun 2020 09:40:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3642 records, 4 fields): 8 millis CompletedMACS2peakCalling