Job ID = 6368725 SRX = SRX5402749 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:34 prefetch.2.10.7: 1) Downloading 'SRR8602983'... 2020-06-16T00:26:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:46 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:46 prefetch.2.10.7: 1) 'SRR8602983' was downloaded successfully Read 25026804 spots for SRR8602983/SRR8602983.sra Written 25026804 spots for SRR8602983/SRR8602983.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: 00:05:47 25026804 reads; of these: 25026804 (100.00%) were unpaired; of these: 4239549 (16.94%) aligned 0 times 10917917 (43.62%) aligned exactly 1 time 9869338 (39.44%) aligned >1 times 83.06% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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_sort_core] merging from 12 files... [bam_rmdupse_core] 9697797 / 20787255 = 0.4665 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 09:43:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.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 09:43:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:03: 1000000 INFO @ Tue, 16 Jun 2020 09:44:10: 2000000 INFO @ Tue, 16 Jun 2020 09:44:16: 3000000 INFO @ Tue, 16 Jun 2020 09:44:22: 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 09:44:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.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 09:44:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:28: 5000000 INFO @ Tue, 16 Jun 2020 09:44:34: 1000000 INFO @ Tue, 16 Jun 2020 09:44:35: 6000000 INFO @ Tue, 16 Jun 2020 09:44:41: 2000000 INFO @ Tue, 16 Jun 2020 09:44:42: 7000000 INFO @ Tue, 16 Jun 2020 09:44:47: 3000000 INFO @ Tue, 16 Jun 2020 09:44:48: 8000000 INFO @ Tue, 16 Jun 2020 09:44:54: 4000000 INFO @ Tue, 16 Jun 2020 09:44:55: 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 09:44:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.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 09:44:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:01: 5000000 INFO @ Tue, 16 Jun 2020 09:45:02: 10000000 INFO @ Tue, 16 Jun 2020 09:45:04: 1000000 INFO @ Tue, 16 Jun 2020 09:45:08: 6000000 INFO @ Tue, 16 Jun 2020 09:45:09: 11000000 INFO @ Tue, 16 Jun 2020 09:45:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:09: #1 total tags in treatment: 11089458 INFO @ Tue, 16 Jun 2020 09:45:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:09: #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 09:45:09: #1 tags after filtering in treatment: 11089458 INFO @ Tue, 16 Jun 2020 09:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:10: #2 number of paired peaks: 3504 INFO @ Tue, 16 Jun 2020 09:45:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:10: #2 predicted fragment length is 109 bps INFO @ Tue, 16 Jun 2020 09:45:10: #2 alternative fragment length(s) may be 109 bps INFO @ Tue, 16 Jun 2020 09:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.05_model.r INFO @ Tue, 16 Jun 2020 09:45:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:11: 2000000 INFO @ Tue, 16 Jun 2020 09:45:15: 7000000 INFO @ Tue, 16 Jun 2020 09:45:18: 3000000 INFO @ Tue, 16 Jun 2020 09:45:22: 8000000 INFO @ Tue, 16 Jun 2020 09:45:24: 4000000 INFO @ Tue, 16 Jun 2020 09:45:29: 9000000 INFO @ Tue, 16 Jun 2020 09:45:31: 5000000 INFO @ Tue, 16 Jun 2020 09:45:36: 10000000 INFO @ Tue, 16 Jun 2020 09:45:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:38: 6000000 INFO @ Tue, 16 Jun 2020 09:45:43: 11000000 INFO @ Tue, 16 Jun 2020 09:45:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:44: #1 total tags in treatment: 11089458 INFO @ Tue, 16 Jun 2020 09:45:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:44: #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 09:45:44: #1 tags after filtering in treatment: 11089458 INFO @ Tue, 16 Jun 2020 09:45:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:44: 7000000 INFO @ Tue, 16 Jun 2020 09:45:45: #2 number of paired peaks: 3504 INFO @ Tue, 16 Jun 2020 09:45:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:45: #2 predicted fragment length is 109 bps INFO @ Tue, 16 Jun 2020 09:45:45: #2 alternative fragment length(s) may be 109 bps INFO @ Tue, 16 Jun 2020 09:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.10_model.r INFO @ Tue, 16 Jun 2020 09:45:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.05_summits.bed INFO @ Tue, 16 Jun 2020 09:45:49: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9427 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:45:51: 8000000 INFO @ Tue, 16 Jun 2020 09:45:57: 9000000 INFO @ Tue, 16 Jun 2020 09:46:04: 10000000 INFO @ Tue, 16 Jun 2020 09:46:10: 11000000 INFO @ Tue, 16 Jun 2020 09:46:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:46:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:46:11: #1 total tags in treatment: 11089458 INFO @ Tue, 16 Jun 2020 09:46:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:11: #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 09:46:11: #1 tags after filtering in treatment: 11089458 INFO @ Tue, 16 Jun 2020 09:46:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:11: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:46:12: #2 number of paired peaks: 3504 INFO @ Tue, 16 Jun 2020 09:46:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:12: #2 predicted fragment length is 109 bps INFO @ Tue, 16 Jun 2020 09:46:12: #2 alternative fragment length(s) may be 109 bps INFO @ Tue, 16 Jun 2020 09:46:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.20_model.r INFO @ Tue, 16 Jun 2020 09:46:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.10_summits.bed INFO @ Tue, 16 Jun 2020 09:46:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6668 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:46:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402749/SRX5402749.20_summits.bed INFO @ Tue, 16 Jun 2020 09:46:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3695 records, 4 fields): 5 millis CompletedMACS2peakCalling