Job ID = 6368724 SRX = SRX5402748 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:31:30 prefetch.2.10.7: 1) Downloading 'SRR8602982'... 2020-06-16T00:31:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:26 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:26 prefetch.2.10.7: 1) 'SRR8602982' was downloaded successfully Read 36790196 spots for SRR8602982/SRR8602982.sra Written 36790196 spots for SRR8602982/SRR8602982.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: 00:08:00 36790196 reads; of these: 36790196 (100.00%) were unpaired; of these: 10093328 (27.43%) aligned 0 times 15503760 (42.14%) aligned exactly 1 time 11193108 (30.42%) aligned >1 times 72.57% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 10238069 / 26696868 = 0.3835 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 09:51:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.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 09:51:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:23: 1000000 INFO @ Tue, 16 Jun 2020 09:51:28: 2000000 INFO @ Tue, 16 Jun 2020 09:51:33: 3000000 INFO @ Tue, 16 Jun 2020 09:51:39: 4000000 INFO @ Tue, 16 Jun 2020 09:51:44: 5000000 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 09:51:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.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 09:51:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:50: 6000000 INFO @ Tue, 16 Jun 2020 09:51:53: 1000000 INFO @ Tue, 16 Jun 2020 09:51:56: 7000000 INFO @ Tue, 16 Jun 2020 09:51:58: 2000000 INFO @ Tue, 16 Jun 2020 09:52:02: 8000000 INFO @ Tue, 16 Jun 2020 09:52:04: 3000000 INFO @ Tue, 16 Jun 2020 09:52:08: 9000000 INFO @ Tue, 16 Jun 2020 09:52:09: 4000000 INFO @ Tue, 16 Jun 2020 09:52:14: 10000000 INFO @ Tue, 16 Jun 2020 09:52:15: 5000000 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 09:52:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.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 09:52:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:20: 11000000 INFO @ Tue, 16 Jun 2020 09:52:20: 6000000 INFO @ Tue, 16 Jun 2020 09:52:23: 1000000 INFO @ Tue, 16 Jun 2020 09:52:25: 12000000 INFO @ Tue, 16 Jun 2020 09:52:26: 7000000 INFO @ Tue, 16 Jun 2020 09:52:28: 2000000 INFO @ Tue, 16 Jun 2020 09:52:31: 13000000 INFO @ Tue, 16 Jun 2020 09:52:31: 8000000 INFO @ Tue, 16 Jun 2020 09:52:34: 3000000 INFO @ Tue, 16 Jun 2020 09:52:37: 14000000 INFO @ Tue, 16 Jun 2020 09:52:37: 9000000 INFO @ Tue, 16 Jun 2020 09:52:39: 4000000 INFO @ Tue, 16 Jun 2020 09:52:42: 15000000 INFO @ Tue, 16 Jun 2020 09:52:43: 10000000 INFO @ Tue, 16 Jun 2020 09:52:45: 5000000 INFO @ Tue, 16 Jun 2020 09:52:48: 16000000 INFO @ Tue, 16 Jun 2020 09:52:48: 11000000 INFO @ Tue, 16 Jun 2020 09:52:50: 6000000 INFO @ Tue, 16 Jun 2020 09:52:50: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:50: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:50: #1 total tags in treatment: 16458799 INFO @ Tue, 16 Jun 2020 09:52:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:50: #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 09:52:51: #1 tags after filtering in treatment: 16458799 INFO @ Tue, 16 Jun 2020 09:52:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:52: #2 number of paired peaks: 1873 INFO @ Tue, 16 Jun 2020 09:52:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:52: #2 predicted fragment length is 77 bps INFO @ Tue, 16 Jun 2020 09:52:52: #2 alternative fragment length(s) may be 4,77 bps INFO @ Tue, 16 Jun 2020 09:52:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.05_model.r WARNING @ Tue, 16 Jun 2020 09:52:52: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:52:52: #2 You may need to consider one of the other alternative d(s): 4,77 WARNING @ Tue, 16 Jun 2020 09:52:52: #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 09:52:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:54: 12000000 INFO @ Tue, 16 Jun 2020 09:52:56: 7000000 INFO @ Tue, 16 Jun 2020 09:53:00: 13000000 INFO @ Tue, 16 Jun 2020 09:53:01: 8000000 INFO @ Tue, 16 Jun 2020 09:53:05: 14000000 INFO @ Tue, 16 Jun 2020 09:53:07: 9000000 INFO @ Tue, 16 Jun 2020 09:53:11: 15000000 INFO @ Tue, 16 Jun 2020 09:53:12: 10000000 INFO @ Tue, 16 Jun 2020 09:53:17: 16000000 INFO @ Tue, 16 Jun 2020 09:53:17: 11000000 INFO @ Tue, 16 Jun 2020 09:53:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:19: #1 total tags in treatment: 16458799 INFO @ Tue, 16 Jun 2020 09:53:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:19: #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 09:53:19: #1 tags after filtering in treatment: 16458799 INFO @ Tue, 16 Jun 2020 09:53:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:21: #2 number of paired peaks: 1873 INFO @ Tue, 16 Jun 2020 09:53:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:21: #2 predicted fragment length is 77 bps INFO @ Tue, 16 Jun 2020 09:53:21: #2 alternative fragment length(s) may be 4,77 bps INFO @ Tue, 16 Jun 2020 09:53:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.10_model.r WARNING @ Tue, 16 Jun 2020 09:53:21: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:21: #2 You may need to consider one of the other alternative d(s): 4,77 WARNING @ Tue, 16 Jun 2020 09:53:21: #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 09:53:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:23: 12000000 INFO @ Tue, 16 Jun 2020 09:53:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:28: 13000000 INFO @ Tue, 16 Jun 2020 09:53:33: 14000000 INFO @ Tue, 16 Jun 2020 09:53:38: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:53:44: 16000000 INFO @ Tue, 16 Jun 2020 09:53:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.05_summits.bed INFO @ Tue, 16 Jun 2020 09:53:44: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10378 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:46: #1 total tags in treatment: 16458799 INFO @ Tue, 16 Jun 2020 09:53:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:46: #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 09:53:46: #1 tags after filtering in treatment: 16458799 INFO @ Tue, 16 Jun 2020 09:53:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:48: #2 number of paired peaks: 1873 INFO @ Tue, 16 Jun 2020 09:53:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:48: #2 predicted fragment length is 77 bps INFO @ Tue, 16 Jun 2020 09:53:48: #2 alternative fragment length(s) may be 4,77 bps INFO @ Tue, 16 Jun 2020 09:53:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.20_model.r WARNING @ Tue, 16 Jun 2020 09:53:48: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:48: #2 You may need to consider one of the other alternative d(s): 4,77 WARNING @ Tue, 16 Jun 2020 09:53:48: #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 09:53:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.10_summits.bed INFO @ Tue, 16 Jun 2020 09:54:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6570 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:54:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402748/SRX5402748.20_summits.bed INFO @ Tue, 16 Jun 2020 09:54:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2954 records, 4 fields): 4 millis CompletedMACS2peakCalling