Job ID = 6457848 SRX = SRX4801812 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:11:19 prefetch.2.10.7: 1) Downloading 'SRR7968397'... 2020-06-21T12:11:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:12:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:12:45 prefetch.2.10.7: 'SRR7968397' is valid 2020-06-21T12:12:45 prefetch.2.10.7: 1) 'SRR7968397' was downloaded successfully Read 12987980 spots for SRR7968397/SRR7968397.sra Written 12987980 spots for SRR7968397/SRR7968397.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: 00:04:41 12987980 reads; of these: 12987980 (100.00%) were unpaired; of these: 373305 (2.87%) aligned 0 times 8605993 (66.26%) aligned exactly 1 time 4008682 (30.86%) aligned >1 times 97.13% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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 8 files... [bam_rmdupse_core] 1477962 / 12614675 = 0.1172 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 21:22:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.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 21:22:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:22:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:22:08: 1000000 INFO @ Sun, 21 Jun 2020 21:22:14: 2000000 INFO @ Sun, 21 Jun 2020 21:22:20: 3000000 INFO @ Sun, 21 Jun 2020 21:22:27: 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 @ Sun, 21 Jun 2020 21:22:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.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 21:22:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:22:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:22:33: 5000000 INFO @ Sun, 21 Jun 2020 21:22:38: 1000000 INFO @ Sun, 21 Jun 2020 21:22:40: 6000000 INFO @ Sun, 21 Jun 2020 21:22:44: 2000000 INFO @ Sun, 21 Jun 2020 21:22:46: 7000000 INFO @ Sun, 21 Jun 2020 21:22:51: 3000000 INFO @ Sun, 21 Jun 2020 21:22:53: 8000000 INFO @ Sun, 21 Jun 2020 21:22:57: 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 @ Sun, 21 Jun 2020 21:23:00: 9000000 INFO @ Sun, 21 Jun 2020 21:23:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.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 21:23:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:23:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:23:04: 5000000 INFO @ Sun, 21 Jun 2020 21:23:08: 10000000 INFO @ Sun, 21 Jun 2020 21:23:08: 1000000 INFO @ Sun, 21 Jun 2020 21:23:11: 6000000 INFO @ Sun, 21 Jun 2020 21:23:15: 11000000 INFO @ Sun, 21 Jun 2020 21:23:15: 2000000 INFO @ Sun, 21 Jun 2020 21:23:16: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:23:16: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:23:16: #1 total tags in treatment: 11136713 INFO @ Sun, 21 Jun 2020 21:23:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:23:16: #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 21:23:16: #1 tags after filtering in treatment: 11136579 INFO @ Sun, 21 Jun 2020 21:23:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:23:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:23:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:23:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:23:17: #2 number of paired peaks: 1793 INFO @ Sun, 21 Jun 2020 21:23:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:23:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:23:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:23:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:23:17: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 21:23:17: #2 alternative fragment length(s) may be 3,74,590 bps INFO @ Sun, 21 Jun 2020 21:23:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.05_model.r WARNING @ Sun, 21 Jun 2020 21:23:17: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:23:17: #2 You may need to consider one of the other alternative d(s): 3,74,590 WARNING @ Sun, 21 Jun 2020 21:23:17: #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 21:23:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:23:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:23:17: 7000000 INFO @ Sun, 21 Jun 2020 21:23:21: 3000000 INFO @ Sun, 21 Jun 2020 21:23:24: 8000000 INFO @ Sun, 21 Jun 2020 21:23:28: 4000000 INFO @ Sun, 21 Jun 2020 21:23:30: 9000000 INFO @ Sun, 21 Jun 2020 21:23:34: 5000000 INFO @ Sun, 21 Jun 2020 21:23:37: 10000000 INFO @ Sun, 21 Jun 2020 21:23:41: 6000000 INFO @ Sun, 21 Jun 2020 21:23:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:44: 11000000 INFO @ Sun, 21 Jun 2020 21:23:45: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:23:45: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:23:45: #1 total tags in treatment: 11136713 INFO @ Sun, 21 Jun 2020 21:23:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:23:45: #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 21:23:46: #1 tags after filtering in treatment: 11136579 INFO @ Sun, 21 Jun 2020 21:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:23:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:23:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:23:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:23:47: #2 number of paired peaks: 1793 INFO @ Sun, 21 Jun 2020 21:23:47: start model_add_line... INFO @ Sun, 21 Jun 2020 21:23:47: start X-correlation... INFO @ Sun, 21 Jun 2020 21:23:47: end of X-cor INFO @ Sun, 21 Jun 2020 21:23:47: #2 finished! INFO @ Sun, 21 Jun 2020 21:23:47: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 21:23:47: #2 alternative fragment length(s) may be 3,74,590 bps INFO @ Sun, 21 Jun 2020 21:23:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.10_model.r WARNING @ Sun, 21 Jun 2020 21:23:47: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:23:47: #2 You may need to consider one of the other alternative d(s): 3,74,590 WARNING @ Sun, 21 Jun 2020 21:23:47: #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 21:23:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:23:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:23:47: 7000000 INFO @ Sun, 21 Jun 2020 21:23:54: 8000000 INFO @ Sun, 21 Jun 2020 21:23:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.05_summits.bed INFO @ Sun, 21 Jun 2020 21:23:55: Done! pass1 - making usageList (582 chroms): 1 millis pass2 - checking and writing primary data (2766 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:24:00: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:24:06: 10000000 INFO @ Sun, 21 Jun 2020 21:24:13: 11000000 INFO @ Sun, 21 Jun 2020 21:24:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:24:14: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:24:14: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:24:14: #1 total tags in treatment: 11136713 INFO @ Sun, 21 Jun 2020 21:24:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:24:14: #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 21:24:14: #1 tags after filtering in treatment: 11136579 INFO @ Sun, 21 Jun 2020 21:24:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:24:14: #1 finished! INFO @ Sun, 21 Jun 2020 21:24:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:24:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:24:15: #2 number of paired peaks: 1793 INFO @ Sun, 21 Jun 2020 21:24:15: start model_add_line... INFO @ Sun, 21 Jun 2020 21:24:15: start X-correlation... INFO @ Sun, 21 Jun 2020 21:24:15: end of X-cor INFO @ Sun, 21 Jun 2020 21:24:15: #2 finished! INFO @ Sun, 21 Jun 2020 21:24:15: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 21:24:15: #2 alternative fragment length(s) may be 3,74,590 bps INFO @ Sun, 21 Jun 2020 21:24:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.20_model.r WARNING @ Sun, 21 Jun 2020 21:24:15: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:24:15: #2 You may need to consider one of the other alternative d(s): 3,74,590 WARNING @ Sun, 21 Jun 2020 21:24:15: #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 21:24:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:24:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:24:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:24:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:24:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.10_summits.bed INFO @ Sun, 21 Jun 2020 21:24:26: Done! pass1 - making usageList (493 chroms): 1 millis pass2 - checking and writing primary data (1646 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:24:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:24:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:24:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:24:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801812/SRX4801812.20_summits.bed INFO @ Sun, 21 Jun 2020 21:24:55: Done! pass1 - making usageList (315 chroms): 1 millis pass2 - checking and writing primary data (692 records, 4 fields): 10 millis CompletedMACS2peakCalling