Job ID = 6459416 SRX = SRX6747982 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:14:19 prefetch.2.10.7: 1) Downloading 'SRR10009757'... 2020-06-21T13:14:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:16:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:16:49 prefetch.2.10.7: 'SRR10009757' is valid 2020-06-21T13:16:49 prefetch.2.10.7: 1) 'SRR10009757' was downloaded successfully 2020-06-21T13:16:49 prefetch.2.10.7: 'SRR10009757' has 0 unresolved dependencies Read 15479041 spots for SRR10009757/SRR10009757.sra Written 15479041 spots for SRR10009757/SRR10009757.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:50 15479041 reads; of these: 15479041 (100.00%) were unpaired; of these: 7529593 (48.64%) aligned 0 times 5474098 (35.36%) aligned exactly 1 time 2475350 (15.99%) aligned >1 times 51.36% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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_rmdupse_core] 914670 / 7949448 = 0.1151 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 22:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.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 22:24:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:24:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:24:27: 1000000 INFO @ Sun, 21 Jun 2020 22:24:34: 2000000 INFO @ Sun, 21 Jun 2020 22:24:41: 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 22:24:48: 4000000 INFO @ Sun, 21 Jun 2020 22:24:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.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 22:24:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:24:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:24:55: 5000000 INFO @ Sun, 21 Jun 2020 22:24:57: 1000000 INFO @ Sun, 21 Jun 2020 22:25:03: 6000000 INFO @ Sun, 21 Jun 2020 22:25:05: 2000000 INFO @ Sun, 21 Jun 2020 22:25:11: 7000000 INFO @ Sun, 21 Jun 2020 22:25:11: #1 tag size is determined as 73 bps INFO @ Sun, 21 Jun 2020 22:25:11: #1 tag size = 73 INFO @ Sun, 21 Jun 2020 22:25:11: #1 total tags in treatment: 7034778 INFO @ Sun, 21 Jun 2020 22:25:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:25:11: #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 22:25:11: #1 tags after filtering in treatment: 7034628 INFO @ Sun, 21 Jun 2020 22:25:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:25:11: #1 finished! INFO @ Sun, 21 Jun 2020 22:25:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:25:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:25:12: #2 number of paired peaks: 1801 INFO @ Sun, 21 Jun 2020 22:25:12: start model_add_line... INFO @ Sun, 21 Jun 2020 22:25:12: start X-correlation... INFO @ Sun, 21 Jun 2020 22:25:12: end of X-cor INFO @ Sun, 21 Jun 2020 22:25:12: #2 finished! INFO @ Sun, 21 Jun 2020 22:25:12: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 22:25:12: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 21 Jun 2020 22:25:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.05_model.r WARNING @ Sun, 21 Jun 2020 22:25:12: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:25:12: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 21 Jun 2020 22:25:12: #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 22:25:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:25:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:25:13: 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 22:25:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.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 22:25:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:25:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:25:20: 4000000 INFO @ Sun, 21 Jun 2020 22:25:27: 1000000 INFO @ Sun, 21 Jun 2020 22:25:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:25:28: 5000000 INFO @ Sun, 21 Jun 2020 22:25:34: 2000000 INFO @ Sun, 21 Jun 2020 22:25:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:25:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:25:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.05_summits.bed INFO @ Sun, 21 Jun 2020 22:25:35: Done! pass1 - making usageList (540 chroms): 1 millis pass2 - checking and writing primary data (2032 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:25:35: 6000000 INFO @ Sun, 21 Jun 2020 22:25:41: 3000000 INFO @ Sun, 21 Jun 2020 22:25:43: 7000000 INFO @ Sun, 21 Jun 2020 22:25:43: #1 tag size is determined as 73 bps INFO @ Sun, 21 Jun 2020 22:25:43: #1 tag size = 73 INFO @ Sun, 21 Jun 2020 22:25:43: #1 total tags in treatment: 7034778 INFO @ Sun, 21 Jun 2020 22:25:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:25:43: #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 22:25:44: #1 tags after filtering in treatment: 7034628 INFO @ Sun, 21 Jun 2020 22:25:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:25:44: #1 finished! INFO @ Sun, 21 Jun 2020 22:25:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:25:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:25:44: #2 number of paired peaks: 1801 INFO @ Sun, 21 Jun 2020 22:25:44: start model_add_line... INFO @ Sun, 21 Jun 2020 22:25:44: start X-correlation... INFO @ Sun, 21 Jun 2020 22:25:44: end of X-cor INFO @ Sun, 21 Jun 2020 22:25:44: #2 finished! INFO @ Sun, 21 Jun 2020 22:25:44: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 22:25:44: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 21 Jun 2020 22:25:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.10_model.r WARNING @ Sun, 21 Jun 2020 22:25:44: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:25:44: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 21 Jun 2020 22:25:44: #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 22:25:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:25:48: 4000000 INFO @ Sun, 21 Jun 2020 22:25:54: 5000000 INFO @ Sun, 21 Jun 2020 22:25:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:26:01: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.10_summits.bed INFO @ Sun, 21 Jun 2020 22:26:06: Done! pass1 - making usageList (442 chroms): 1 millis pass2 - checking and writing primary data (1209 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:26:07: 7000000 INFO @ Sun, 21 Jun 2020 22:26:07: #1 tag size is determined as 73 bps INFO @ Sun, 21 Jun 2020 22:26:07: #1 tag size = 73 INFO @ Sun, 21 Jun 2020 22:26:07: #1 total tags in treatment: 7034778 INFO @ Sun, 21 Jun 2020 22:26:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:26:07: #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 22:26:07: #1 tags after filtering in treatment: 7034628 INFO @ Sun, 21 Jun 2020 22:26:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:26:07: #1 finished! INFO @ Sun, 21 Jun 2020 22:26:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:26:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:26:08: #2 number of paired peaks: 1801 INFO @ Sun, 21 Jun 2020 22:26:08: start model_add_line... INFO @ Sun, 21 Jun 2020 22:26:08: start X-correlation... INFO @ Sun, 21 Jun 2020 22:26:08: end of X-cor INFO @ Sun, 21 Jun 2020 22:26:08: #2 finished! INFO @ Sun, 21 Jun 2020 22:26:08: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 22:26:08: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 21 Jun 2020 22:26:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.20_model.r WARNING @ Sun, 21 Jun 2020 22:26:08: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:26:08: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 21 Jun 2020 22:26:08: #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 22:26:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:26:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:26:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:26:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:26:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:26:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747982/SRX6747982.20_summits.bed INFO @ Sun, 21 Jun 2020 22:26:31: Done! pass1 - making usageList (256 chroms): 1 millis pass2 - checking and writing primary data (488 records, 4 fields): 9 millis CompletedMACS2peakCalling