Job ID = 6454133 SRX = SRX1837981 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:58:19 prefetch.2.10.7: 1) Downloading 'SRR3658922'... 2020-06-21T08:58:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:01:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:01:45 prefetch.2.10.7: 1) 'SRR3658922' was downloaded successfully 2020-06-21T09:01:45 prefetch.2.10.7: 'SRR3658922' has 0 unresolved dependencies Read 17677079 spots for SRR3658922/SRR3658922.sra Written 17677079 spots for SRR3658922/SRR3658922.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: 00:11:15 17677079 reads; of these: 17677079 (100.00%) were unpaired; of these: 414246 (2.34%) aligned 0 times 14912153 (84.36%) aligned exactly 1 time 2350680 (13.30%) aligned >1 times 97.66% overall alignment rate Time searching: 00:11:15 Overall time: 00:11:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 3571558 / 17262833 = 0.2069 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 @ Sun, 21 Jun 2020 18:21:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:21:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:17: 1000000 INFO @ Sun, 21 Jun 2020 18:21:24: 2000000 INFO @ Sun, 21 Jun 2020 18:21:31: 3000000 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 @ Sun, 21 Jun 2020 18:21:38: 4000000 INFO @ Sun, 21 Jun 2020 18:21:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:21:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:46: 5000000 INFO @ Sun, 21 Jun 2020 18:21:47: 1000000 INFO @ Sun, 21 Jun 2020 18:21:53: 6000000 INFO @ Sun, 21 Jun 2020 18:21:55: 2000000 INFO @ Sun, 21 Jun 2020 18:22:01: 7000000 INFO @ Sun, 21 Jun 2020 18:22:03: 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 @ Sun, 21 Jun 2020 18:22:09: 8000000 INFO @ Sun, 21 Jun 2020 18:22:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:22:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:11: 4000000 INFO @ Sun, 21 Jun 2020 18:22:16: 9000000 INFO @ Sun, 21 Jun 2020 18:22:18: 1000000 INFO @ Sun, 21 Jun 2020 18:22:19: 5000000 INFO @ Sun, 21 Jun 2020 18:22:24: 10000000 INFO @ Sun, 21 Jun 2020 18:22:26: 2000000 INFO @ Sun, 21 Jun 2020 18:22:27: 6000000 INFO @ Sun, 21 Jun 2020 18:22:33: 11000000 INFO @ Sun, 21 Jun 2020 18:22:35: 7000000 INFO @ Sun, 21 Jun 2020 18:22:35: 3000000 INFO @ Sun, 21 Jun 2020 18:22:41: 12000000 INFO @ Sun, 21 Jun 2020 18:22:43: 8000000 INFO @ Sun, 21 Jun 2020 18:22:44: 4000000 INFO @ Sun, 21 Jun 2020 18:22:49: 13000000 INFO @ Sun, 21 Jun 2020 18:22:51: 9000000 INFO @ Sun, 21 Jun 2020 18:22:54: 5000000 INFO @ Sun, 21 Jun 2020 18:22:55: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 18:22:55: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 18:22:55: #1 total tags in treatment: 13691275 INFO @ Sun, 21 Jun 2020 18:22:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:22:55: #1 tags after filtering in treatment: 13691187 INFO @ Sun, 21 Jun 2020 18:22:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:56: #2 number of paired peaks: 2454 INFO @ Sun, 21 Jun 2020 18:22:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:57: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 18:22:57: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 18:22:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.05_model.r WARNING @ Sun, 21 Jun 2020 18:22:57: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:22:57: #2 You may need to consider one of the other alternative d(s): 175 WARNING @ Sun, 21 Jun 2020 18:22:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:22:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:22:59: 10000000 INFO @ Sun, 21 Jun 2020 18:23:03: 6000000 INFO @ Sun, 21 Jun 2020 18:23:07: 11000000 INFO @ Sun, 21 Jun 2020 18:23:12: 7000000 INFO @ Sun, 21 Jun 2020 18:23:16: 12000000 INFO @ Sun, 21 Jun 2020 18:23:21: 8000000 INFO @ Sun, 21 Jun 2020 18:23:23: 13000000 INFO @ Sun, 21 Jun 2020 18:23:29: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 18:23:29: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 18:23:29: #1 total tags in treatment: 13691275 INFO @ Sun, 21 Jun 2020 18:23:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:23:29: 9000000 INFO @ Sun, 21 Jun 2020 18:23:30: #1 tags after filtering in treatment: 13691187 INFO @ Sun, 21 Jun 2020 18:23:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:31: #2 number of paired peaks: 2454 INFO @ Sun, 21 Jun 2020 18:23:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:31: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 18:23:31: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 18:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.10_model.r WARNING @ Sun, 21 Jun 2020 18:23:31: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:23:31: #2 You may need to consider one of the other alternative d(s): 175 WARNING @ Sun, 21 Jun 2020 18:23:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:23:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:38: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:23:46: 11000000 INFO @ Sun, 21 Jun 2020 18:23:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.05_summits.bed INFO @ Sun, 21 Jun 2020 18:23:47: Done! pass1 - making usageList (276 chroms): 2 millis pass2 - checking and writing primary data (6916 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:23:55: 12000000 INFO @ Sun, 21 Jun 2020 18:24:03: 13000000 INFO @ Sun, 21 Jun 2020 18:24:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:09: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 18:24:09: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 18:24:09: #1 total tags in treatment: 13691275 INFO @ Sun, 21 Jun 2020 18:24:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:24:10: #1 tags after filtering in treatment: 13691187 INFO @ Sun, 21 Jun 2020 18:24:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:10: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:24:11: #2 number of paired peaks: 2454 INFO @ Sun, 21 Jun 2020 18:24:11: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:11: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:11: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:11: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:11: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 18:24:11: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 18:24:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.20_model.r WARNING @ Sun, 21 Jun 2020 18:24:11: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:24:11: #2 You may need to consider one of the other alternative d(s): 175 WARNING @ Sun, 21 Jun 2020 18:24:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:24:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:24:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.10_summits.bed INFO @ Sun, 21 Jun 2020 18:24:23: Done! pass1 - making usageList (199 chroms): 1 millis pass2 - checking and writing primary data (3663 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:24:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:25:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:25:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:25:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837981/SRX1837981.20_summits.bed INFO @ Sun, 21 Jun 2020 18:25:00: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (1665 records, 4 fields): 6 millis CompletedMACS2peakCalling