Job ID = 6368687 SRX = SRX5402713 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:31:31 prefetch.2.10.7: 1) Downloading 'SRR8602947'... 2020-06-16T00:31:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:41 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:41 prefetch.2.10.7: 1) 'SRR8602947' was downloaded successfully Read 30087212 spots for SRR8602947/SRR8602947.sra Written 30087212 spots for SRR8602947/SRR8602947.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: 00:05:20 30087212 reads; of these: 30087212 (100.00%) were unpaired; of these: 7322898 (24.34%) aligned 0 times 19927465 (66.23%) aligned exactly 1 time 2836849 (9.43%) aligned >1 times 75.66% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 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] 4246838 / 22764314 = 0.1866 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 09:47:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.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 09:47:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:03: 1000000 INFO @ Tue, 16 Jun 2020 09:48:09: 2000000 INFO @ Tue, 16 Jun 2020 09:48:14: 3000000 INFO @ Tue, 16 Jun 2020 09:48:20: 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 09:48:26: 5000000 INFO @ Tue, 16 Jun 2020 09:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.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 09:48:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:34: 6000000 INFO @ Tue, 16 Jun 2020 09:48:34: 1000000 INFO @ Tue, 16 Jun 2020 09:48:41: 7000000 INFO @ Tue, 16 Jun 2020 09:48:42: 2000000 INFO @ Tue, 16 Jun 2020 09:48:48: 8000000 INFO @ Tue, 16 Jun 2020 09:48:49: 3000000 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 09:48:56: 9000000 INFO @ Tue, 16 Jun 2020 09:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.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 09:48:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:57: 4000000 INFO @ Tue, 16 Jun 2020 09:49:03: 10000000 INFO @ Tue, 16 Jun 2020 09:49:04: 1000000 INFO @ Tue, 16 Jun 2020 09:49:05: 5000000 INFO @ Tue, 16 Jun 2020 09:49:10: 11000000 INFO @ Tue, 16 Jun 2020 09:49:10: 2000000 INFO @ Tue, 16 Jun 2020 09:49:13: 6000000 INFO @ Tue, 16 Jun 2020 09:49:17: 12000000 INFO @ Tue, 16 Jun 2020 09:49:17: 3000000 INFO @ Tue, 16 Jun 2020 09:49:20: 7000000 INFO @ Tue, 16 Jun 2020 09:49:24: 13000000 INFO @ Tue, 16 Jun 2020 09:49:24: 4000000 INFO @ Tue, 16 Jun 2020 09:49:28: 8000000 INFO @ Tue, 16 Jun 2020 09:49:31: 14000000 INFO @ Tue, 16 Jun 2020 09:49:31: 5000000 INFO @ Tue, 16 Jun 2020 09:49:35: 9000000 INFO @ Tue, 16 Jun 2020 09:49:38: 15000000 INFO @ Tue, 16 Jun 2020 09:49:38: 6000000 INFO @ Tue, 16 Jun 2020 09:49:43: 10000000 INFO @ Tue, 16 Jun 2020 09:49:45: 16000000 INFO @ Tue, 16 Jun 2020 09:49:45: 7000000 INFO @ Tue, 16 Jun 2020 09:49:51: 11000000 INFO @ Tue, 16 Jun 2020 09:49:52: 8000000 INFO @ Tue, 16 Jun 2020 09:49:52: 17000000 INFO @ Tue, 16 Jun 2020 09:49:58: 12000000 INFO @ Tue, 16 Jun 2020 09:49:59: 9000000 INFO @ Tue, 16 Jun 2020 09:49:59: 18000000 INFO @ Tue, 16 Jun 2020 09:50:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:03: #1 total tags in treatment: 18517476 INFO @ Tue, 16 Jun 2020 09:50:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:03: #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 09:50:03: #1 tags after filtering in treatment: 18517476 INFO @ Tue, 16 Jun 2020 09:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:05: #2 number of paired peaks: 1456 INFO @ Tue, 16 Jun 2020 09:50:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:05: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:50:05: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 09:50:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.05_model.r WARNING @ Tue, 16 Jun 2020 09:50:05: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:05: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 09:50:05: #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 09:50:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:06: 13000000 INFO @ Tue, 16 Jun 2020 09:50:06: 10000000 INFO @ Tue, 16 Jun 2020 09:50:13: 11000000 INFO @ Tue, 16 Jun 2020 09:50:13: 14000000 INFO @ Tue, 16 Jun 2020 09:50:20: 12000000 INFO @ Tue, 16 Jun 2020 09:50:21: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:50:26: 13000000 INFO @ Tue, 16 Jun 2020 09:50:29: 16000000 INFO @ Tue, 16 Jun 2020 09:50:33: 14000000 INFO @ Tue, 16 Jun 2020 09:50:37: 17000000 INFO @ Tue, 16 Jun 2020 09:50:40: 15000000 INFO @ Tue, 16 Jun 2020 09:50:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:44: 18000000 INFO @ Tue, 16 Jun 2020 09:50:47: 16000000 INFO @ Tue, 16 Jun 2020 09:50:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:48: #1 total tags in treatment: 18517476 INFO @ Tue, 16 Jun 2020 09:50:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:48: #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 09:50:49: #1 tags after filtering in treatment: 18517476 INFO @ Tue, 16 Jun 2020 09:50:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:50: #2 number of paired peaks: 1456 INFO @ Tue, 16 Jun 2020 09:50:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:50: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:50:50: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 09:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.10_model.r WARNING @ Tue, 16 Jun 2020 09:50:50: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:50: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 09:50:50: #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 09:50:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:53: 17000000 INFO @ Tue, 16 Jun 2020 09:50:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.05_peaks.xls BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:50:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.05_summits.bed INFO @ Tue, 16 Jun 2020 09:50:59: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (14450 records, 4 fields): 14 millis INFO @ Tue, 16 Jun 2020 09:50:59: 18000000 CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:02: #1 total tags in treatment: 18517476 INFO @ Tue, 16 Jun 2020 09:51:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:02: #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 09:51:03: #1 tags after filtering in treatment: 18517476 INFO @ Tue, 16 Jun 2020 09:51:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:04: #2 number of paired peaks: 1456 INFO @ Tue, 16 Jun 2020 09:51:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:04: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:51:04: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 09:51:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.20_model.r WARNING @ Tue, 16 Jun 2020 09:51:04: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:51:04: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 09:51:04: #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 09:51:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.10_summits.bed INFO @ Tue, 16 Jun 2020 09:51:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5476 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402713/SRX5402713.20_summits.bed INFO @ Tue, 16 Jun 2020 09:51:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (515 records, 4 fields): 1 millis CompletedMACS2peakCalling