Job ID = 6368699 SRX = SRX5402724 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:35:35 prefetch.2.10.7: 1) Downloading 'SRR8602958'... 2020-06-16T00:35:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:39:20 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:39:20 prefetch.2.10.7: 1) 'SRR8602958' was downloaded successfully Read 23857285 spots for SRR8602958/SRR8602958.sra Written 23857285 spots for SRR8602958/SRR8602958.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: 00:04:51 23857285 reads; of these: 23857285 (100.00%) were unpaired; of these: 2658424 (11.14%) aligned 0 times 18263449 (76.55%) aligned exactly 1 time 2935412 (12.30%) aligned >1 times 88.86% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 7655593 / 21198861 = 0.3611 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 09:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.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 09:50:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:29: 1000000 INFO @ Tue, 16 Jun 2020 09:50:35: 2000000 INFO @ Tue, 16 Jun 2020 09:50:42: 3000000 INFO @ Tue, 16 Jun 2020 09:50:48: 4000000 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 09:50:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.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 09:50:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:54: 5000000 INFO @ Tue, 16 Jun 2020 09:50:59: 1000000 INFO @ Tue, 16 Jun 2020 09:51:00: 6000000 INFO @ Tue, 16 Jun 2020 09:51:06: 2000000 INFO @ Tue, 16 Jun 2020 09:51:07: 7000000 INFO @ Tue, 16 Jun 2020 09:51:12: 3000000 INFO @ Tue, 16 Jun 2020 09:51:13: 8000000 INFO @ Tue, 16 Jun 2020 09:51:19: 4000000 INFO @ Tue, 16 Jun 2020 09:51:19: 9000000 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 09:51:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.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 09:51:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:25: 5000000 INFO @ Tue, 16 Jun 2020 09:51:26: 10000000 INFO @ Tue, 16 Jun 2020 09:51:29: 1000000 INFO @ Tue, 16 Jun 2020 09:51:32: 6000000 INFO @ Tue, 16 Jun 2020 09:51:32: 11000000 INFO @ Tue, 16 Jun 2020 09:51:34: 2000000 INFO @ Tue, 16 Jun 2020 09:51:38: 7000000 INFO @ Tue, 16 Jun 2020 09:51:38: 12000000 INFO @ Tue, 16 Jun 2020 09:51:40: 3000000 INFO @ Tue, 16 Jun 2020 09:51:45: 13000000 INFO @ Tue, 16 Jun 2020 09:51:45: 8000000 INFO @ Tue, 16 Jun 2020 09:51:46: 4000000 INFO @ Tue, 16 Jun 2020 09:51:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:48: #1 total tags in treatment: 13543268 INFO @ Tue, 16 Jun 2020 09:51:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:48: #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 09:51:48: #1 tags after filtering in treatment: 13543268 INFO @ Tue, 16 Jun 2020 09:51:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:50: #2 number of paired peaks: 2570 INFO @ Tue, 16 Jun 2020 09:51:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:50: #2 predicted fragment length is 186 bps INFO @ Tue, 16 Jun 2020 09:51:50: #2 alternative fragment length(s) may be 186 bps INFO @ Tue, 16 Jun 2020 09:51:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.05_model.r INFO @ Tue, 16 Jun 2020 09:51:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:51: 9000000 INFO @ Tue, 16 Jun 2020 09:51:52: 5000000 INFO @ Tue, 16 Jun 2020 09:51:57: 6000000 INFO @ Tue, 16 Jun 2020 09:51:58: 10000000 INFO @ Tue, 16 Jun 2020 09:52:03: 7000000 INFO @ Tue, 16 Jun 2020 09:52:04: 11000000 INFO @ Tue, 16 Jun 2020 09:52:09: 8000000 INFO @ Tue, 16 Jun 2020 09:52:11: 12000000 INFO @ Tue, 16 Jun 2020 09:52:15: 9000000 INFO @ Tue, 16 Jun 2020 09:52:17: 13000000 INFO @ Tue, 16 Jun 2020 09:52:21: 10000000 INFO @ Tue, 16 Jun 2020 09:52:21: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:21: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:21: #1 total tags in treatment: 13543268 INFO @ Tue, 16 Jun 2020 09:52:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:21: #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 09:52:21: #1 tags after filtering in treatment: 13543268 INFO @ Tue, 16 Jun 2020 09:52:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:22: #2 number of paired peaks: 2570 INFO @ Tue, 16 Jun 2020 09:52:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:22: #2 predicted fragment length is 186 bps INFO @ Tue, 16 Jun 2020 09:52:22: #2 alternative fragment length(s) may be 186 bps INFO @ Tue, 16 Jun 2020 09:52:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.10_model.r INFO @ Tue, 16 Jun 2020 09:52:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:26: 11000000 INFO @ Tue, 16 Jun 2020 09:52:32: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:52:37: 13000000 INFO @ Tue, 16 Jun 2020 09:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.05_summits.bed INFO @ Tue, 16 Jun 2020 09:52:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5259 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:40: #1 total tags in treatment: 13543268 INFO @ Tue, 16 Jun 2020 09:52:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:40: #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 09:52:40: #1 tags after filtering in treatment: 13543268 INFO @ Tue, 16 Jun 2020 09:52:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:41: #2 number of paired peaks: 2570 INFO @ Tue, 16 Jun 2020 09:52:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:42: #2 predicted fragment length is 186 bps INFO @ Tue, 16 Jun 2020 09:52:42: #2 alternative fragment length(s) may be 186 bps INFO @ Tue, 16 Jun 2020 09:52:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.20_model.r INFO @ Tue, 16 Jun 2020 09:52:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4365 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402724/SRX5402724.20_summits.bed INFO @ Tue, 16 Jun 2020 09:53:29: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3617 records, 4 fields): 5 millis CompletedMACS2peakCalling