Job ID = 6367170 SRX = SRX2965744 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:20:16 prefetch.2.10.7: 1) Downloading 'SRR5766329'... 2020-06-15T23:20:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:06 prefetch.2.10.7: 1) 'SRR5766329' was downloaded successfully Read 23051447 spots for SRR5766329/SRR5766329.sra Written 23051447 spots for SRR5766329/SRR5766329.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: 00:09:45 23051447 reads; of these: 23051447 (100.00%) were unpaired; of these: 2727870 (11.83%) aligned 0 times 17726010 (76.90%) aligned exactly 1 time 2597567 (11.27%) aligned >1 times 88.17% overall alignment rate Time searching: 00:09:45 Overall time: 00:09:45 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] 3154322 / 20323577 = 0.1552 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 08:40:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.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 08:40:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:52: 1000000 INFO @ Tue, 16 Jun 2020 08:40:58: 2000000 INFO @ Tue, 16 Jun 2020 08:41:05: 3000000 INFO @ Tue, 16 Jun 2020 08:41:11: 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 08:41:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.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 08:41:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:17: 5000000 INFO @ Tue, 16 Jun 2020 08:41:22: 1000000 INFO @ Tue, 16 Jun 2020 08:41:24: 6000000 INFO @ Tue, 16 Jun 2020 08:41:29: 2000000 INFO @ Tue, 16 Jun 2020 08:41:31: 7000000 INFO @ Tue, 16 Jun 2020 08:41:36: 3000000 INFO @ Tue, 16 Jun 2020 08:41:38: 8000000 INFO @ Tue, 16 Jun 2020 08:41:43: 4000000 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 08:41:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.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 08:41:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:45: 9000000 INFO @ Tue, 16 Jun 2020 08:41:50: 5000000 INFO @ Tue, 16 Jun 2020 08:41:52: 10000000 INFO @ Tue, 16 Jun 2020 08:41:52: 1000000 INFO @ Tue, 16 Jun 2020 08:41:57: 6000000 INFO @ Tue, 16 Jun 2020 08:41:59: 11000000 INFO @ Tue, 16 Jun 2020 08:42:00: 2000000 INFO @ Tue, 16 Jun 2020 08:42:05: 7000000 INFO @ Tue, 16 Jun 2020 08:42:07: 12000000 INFO @ Tue, 16 Jun 2020 08:42:07: 3000000 INFO @ Tue, 16 Jun 2020 08:42:12: 8000000 INFO @ Tue, 16 Jun 2020 08:42:14: 13000000 INFO @ Tue, 16 Jun 2020 08:42:14: 4000000 INFO @ Tue, 16 Jun 2020 08:42:19: 9000000 INFO @ Tue, 16 Jun 2020 08:42:21: 14000000 INFO @ Tue, 16 Jun 2020 08:42:21: 5000000 INFO @ Tue, 16 Jun 2020 08:42:26: 10000000 INFO @ Tue, 16 Jun 2020 08:42:28: 15000000 INFO @ Tue, 16 Jun 2020 08:42:28: 6000000 INFO @ Tue, 16 Jun 2020 08:42:33: 11000000 INFO @ Tue, 16 Jun 2020 08:42:36: 7000000 INFO @ Tue, 16 Jun 2020 08:42:36: 16000000 INFO @ Tue, 16 Jun 2020 08:42:40: 12000000 INFO @ Tue, 16 Jun 2020 08:42:43: 8000000 INFO @ Tue, 16 Jun 2020 08:42:43: 17000000 INFO @ Tue, 16 Jun 2020 08:42:44: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:42:44: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:42:44: #1 total tags in treatment: 17169255 INFO @ Tue, 16 Jun 2020 08:42:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:44: #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 08:42:45: #1 tags after filtering in treatment: 17169255 INFO @ Tue, 16 Jun 2020 08:42:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:46: #2 number of paired peaks: 1243 INFO @ Tue, 16 Jun 2020 08:42:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:46: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:42:46: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 16 Jun 2020 08:42:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.05_model.r WARNING @ Tue, 16 Jun 2020 08:42:46: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:46: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Tue, 16 Jun 2020 08:42:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:42:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:47: 13000000 INFO @ Tue, 16 Jun 2020 08:42:50: 9000000 INFO @ Tue, 16 Jun 2020 08:42:54: 14000000 INFO @ Tue, 16 Jun 2020 08:42:57: 10000000 INFO @ Tue, 16 Jun 2020 08:43:02: 15000000 INFO @ Tue, 16 Jun 2020 08:43:04: 11000000 INFO @ Tue, 16 Jun 2020 08:43:09: 16000000 INFO @ Tue, 16 Jun 2020 08:43:11: 12000000 INFO @ Tue, 16 Jun 2020 08:43:16: 17000000 INFO @ Tue, 16 Jun 2020 08:43:18: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:43:18: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:43:18: #1 total tags in treatment: 17169255 INFO @ Tue, 16 Jun 2020 08:43:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:18: #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 08:43:18: #1 tags after filtering in treatment: 17169255 INFO @ Tue, 16 Jun 2020 08:43:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:19: 13000000 INFO @ Tue, 16 Jun 2020 08:43:19: #2 number of paired peaks: 1243 INFO @ Tue, 16 Jun 2020 08:43:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:19: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:43:19: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 16 Jun 2020 08:43:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.10_model.r WARNING @ Tue, 16 Jun 2020 08:43:19: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:43:19: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Tue, 16 Jun 2020 08:43:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:43:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:43:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:26: 14000000 INFO @ Tue, 16 Jun 2020 08:43:32: 15000000 INFO @ Tue, 16 Jun 2020 08:43:39: 16000000 INFO @ Tue, 16 Jun 2020 08:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.05_summits.bed INFO @ Tue, 16 Jun 2020 08:43:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5400 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:43:46: 17000000 INFO @ Tue, 16 Jun 2020 08:43:47: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:43:47: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:43:47: #1 total tags in treatment: 17169255 INFO @ Tue, 16 Jun 2020 08:43:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:47: #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 08:43:48: #1 tags after filtering in treatment: 17169255 INFO @ Tue, 16 Jun 2020 08:43:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:49: #2 number of paired peaks: 1243 INFO @ Tue, 16 Jun 2020 08:43:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:49: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:43:49: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 16 Jun 2020 08:43:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.20_model.r WARNING @ Tue, 16 Jun 2020 08:43:49: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:43:49: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Tue, 16 Jun 2020 08:43:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:43:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:43:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:44:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.10_summits.bed INFO @ Tue, 16 Jun 2020 08:44:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3910 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:44:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965744/SRX2965744.20_summits.bed INFO @ Tue, 16 Jun 2020 08:44:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2683 records, 4 fields): 4 millis CompletedMACS2peakCalling