Job ID = 6368718 SRX = SRX5402742 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:34:43 prefetch.2.10.7: 1) Downloading 'SRR8602976'... 2020-06-16T00:34:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:37:37 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:37:37 prefetch.2.10.7: 1) 'SRR8602976' was downloaded successfully Read 18678904 spots for SRR8602976/SRR8602976.sra Written 18678904 spots for SRR8602976/SRR8602976.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: 00:04:25 18678904 reads; of these: 18678904 (100.00%) were unpaired; of these: 3136636 (16.79%) aligned 0 times 9736127 (52.12%) aligned exactly 1 time 5806141 (31.08%) aligned >1 times 83.21% overall alignment rate Time searching: 00:04:25 Overall time: 00:04:25 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 8 files... [bam_rmdupse_core] 4027190 / 15542268 = 0.2591 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 09:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.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 09:48:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:13: 1000000 INFO @ Tue, 16 Jun 2020 09:48:19: 2000000 INFO @ Tue, 16 Jun 2020 09:48:25: 3000000 INFO @ Tue, 16 Jun 2020 09:48:31: 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 09:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.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 09:48:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:37: 5000000 INFO @ Tue, 16 Jun 2020 09:48:42: 1000000 INFO @ Tue, 16 Jun 2020 09:48:43: 6000000 INFO @ Tue, 16 Jun 2020 09:48:48: 2000000 INFO @ Tue, 16 Jun 2020 09:48:50: 7000000 INFO @ Tue, 16 Jun 2020 09:48:54: 3000000 INFO @ Tue, 16 Jun 2020 09:48:56: 8000000 INFO @ Tue, 16 Jun 2020 09:49:00: 4000000 INFO @ Tue, 16 Jun 2020 09:49:02: 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 09:49:06: 5000000 INFO @ Tue, 16 Jun 2020 09:49:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.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 09:49:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:09: 10000000 INFO @ Tue, 16 Jun 2020 09:49:11: 6000000 INFO @ Tue, 16 Jun 2020 09:49:13: 1000000 INFO @ Tue, 16 Jun 2020 09:49:15: 11000000 INFO @ Tue, 16 Jun 2020 09:49:17: 7000000 INFO @ Tue, 16 Jun 2020 09:49:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:19: #1 total tags in treatment: 11515078 INFO @ Tue, 16 Jun 2020 09:49:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:19: #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 09:49:19: #1 tags after filtering in treatment: 11515078 INFO @ Tue, 16 Jun 2020 09:49:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:20: 2000000 INFO @ Tue, 16 Jun 2020 09:49:20: #2 number of paired peaks: 1604 INFO @ Tue, 16 Jun 2020 09:49:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:20: #2 predicted fragment length is 73 bps INFO @ Tue, 16 Jun 2020 09:49:20: #2 alternative fragment length(s) may be 4,73 bps INFO @ Tue, 16 Jun 2020 09:49:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.05_model.r WARNING @ Tue, 16 Jun 2020 09:49:20: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:20: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Tue, 16 Jun 2020 09:49:20: #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 09:49:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:23: 8000000 INFO @ Tue, 16 Jun 2020 09:49:26: 3000000 INFO @ Tue, 16 Jun 2020 09:49:29: 9000000 INFO @ Tue, 16 Jun 2020 09:49:32: 4000000 INFO @ Tue, 16 Jun 2020 09:49:35: 10000000 INFO @ Tue, 16 Jun 2020 09:49:39: 5000000 INFO @ Tue, 16 Jun 2020 09:49:41: 11000000 INFO @ Tue, 16 Jun 2020 09:49:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:44: #1 total tags in treatment: 11515078 INFO @ Tue, 16 Jun 2020 09:49:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:44: #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 09:49:44: #1 tags after filtering in treatment: 11515078 INFO @ Tue, 16 Jun 2020 09:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:45: 6000000 INFO @ Tue, 16 Jun 2020 09:49:45: #2 number of paired peaks: 1604 INFO @ Tue, 16 Jun 2020 09:49:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:45: #2 predicted fragment length is 73 bps INFO @ Tue, 16 Jun 2020 09:49:45: #2 alternative fragment length(s) may be 4,73 bps INFO @ Tue, 16 Jun 2020 09:49:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.10_model.r WARNING @ Tue, 16 Jun 2020 09:49:45: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:45: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Tue, 16 Jun 2020 09:49:45: #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 09:49:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:51: 7000000 INFO @ Tue, 16 Jun 2020 09:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:56: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (9782 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:57: 8000000 INFO @ Tue, 16 Jun 2020 09:50:03: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:50:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:09: 10000000 INFO @ Tue, 16 Jun 2020 09:50:15: 11000000 INFO @ Tue, 16 Jun 2020 09:50:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:19: #1 total tags in treatment: 11515078 INFO @ Tue, 16 Jun 2020 09:50:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:19: #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 09:50:19: #1 tags after filtering in treatment: 11515078 INFO @ Tue, 16 Jun 2020 09:50:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.10_summits.bed INFO @ Tue, 16 Jun 2020 09:50:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5300 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:50:20: #2 number of paired peaks: 1604 INFO @ Tue, 16 Jun 2020 09:50:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:20: #2 predicted fragment length is 73 bps INFO @ Tue, 16 Jun 2020 09:50:20: #2 alternative fragment length(s) may be 4,73 bps INFO @ Tue, 16 Jun 2020 09:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.20_model.r WARNING @ Tue, 16 Jun 2020 09:50:20: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:20: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Tue, 16 Jun 2020 09:50:20: #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 09:50:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:50:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402742/SRX5402742.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2046 records, 4 fields): 3 millis CompletedMACS2peakCalling