Job ID = 6455337 SRX = SRX287706 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:58:10 prefetch.2.10.7: 1) Downloading 'SRR869894'... 2020-06-21T09:58:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:01:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:01:16 prefetch.2.10.7: 1) 'SRR869894' was downloaded successfully Read 18953572 spots for SRR869894/SRR869894.sra Written 18953572 spots for SRR869894/SRR869894.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: 00:06:10 18953572 reads; of these: 18953572 (100.00%) were unpaired; of these: 1311815 (6.92%) aligned 0 times 11692974 (61.69%) aligned exactly 1 time 5948783 (31.39%) aligned >1 times 93.08% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 3506837 / 17641757 = 0.1988 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 19:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.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 19:13:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:11: 1000000 INFO @ Sun, 21 Jun 2020 19:13:16: 2000000 INFO @ Sun, 21 Jun 2020 19:13:21: 3000000 INFO @ Sun, 21 Jun 2020 19:13:26: 4000000 INFO @ Sun, 21 Jun 2020 19:13:31: 5000000 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 19:13:36: 6000000 INFO @ Sun, 21 Jun 2020 19:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.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 19:13:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:41: 7000000 INFO @ Sun, 21 Jun 2020 19:13:41: 1000000 INFO @ Sun, 21 Jun 2020 19:13:46: 8000000 INFO @ Sun, 21 Jun 2020 19:13:46: 2000000 INFO @ Sun, 21 Jun 2020 19:13:51: 9000000 INFO @ Sun, 21 Jun 2020 19:13:51: 3000000 INFO @ Sun, 21 Jun 2020 19:13:56: 10000000 INFO @ Sun, 21 Jun 2020 19:13:56: 4000000 INFO @ Sun, 21 Jun 2020 19:14:01: 11000000 INFO @ Sun, 21 Jun 2020 19:14:01: 5000000 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 19:14:06: 6000000 INFO @ Sun, 21 Jun 2020 19:14:06: 12000000 INFO @ Sun, 21 Jun 2020 19:14:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.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 19:14:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:10: 7000000 INFO @ Sun, 21 Jun 2020 19:14:11: 13000000 INFO @ Sun, 21 Jun 2020 19:14:11: 1000000 INFO @ Sun, 21 Jun 2020 19:14:15: 8000000 INFO @ Sun, 21 Jun 2020 19:14:16: 14000000 INFO @ Sun, 21 Jun 2020 19:14:16: 2000000 INFO @ Sun, 21 Jun 2020 19:14:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:17: #1 total tags in treatment: 14134920 INFO @ Sun, 21 Jun 2020 19:14:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:17: #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 19:14:18: #1 tags after filtering in treatment: 14134920 INFO @ Sun, 21 Jun 2020 19:14:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:19: #2 number of paired peaks: 685 WARNING @ Sun, 21 Jun 2020 19:14:19: Fewer paired peaks (685) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 685 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:19: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 19:14:19: #2 alternative fragment length(s) may be 3,37 bps INFO @ Sun, 21 Jun 2020 19:14:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.05_model.r WARNING @ Sun, 21 Jun 2020 19:14:19: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:14:19: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Sun, 21 Jun 2020 19:14:19: #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 19:14:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:20: 9000000 INFO @ Sun, 21 Jun 2020 19:14:22: 3000000 INFO @ Sun, 21 Jun 2020 19:14:25: 10000000 INFO @ Sun, 21 Jun 2020 19:14:27: 4000000 INFO @ Sun, 21 Jun 2020 19:14:30: 11000000 INFO @ Sun, 21 Jun 2020 19:14:32: 5000000 INFO @ Sun, 21 Jun 2020 19:14:36: 12000000 INFO @ Sun, 21 Jun 2020 19:14:37: 6000000 INFO @ Sun, 21 Jun 2020 19:14:41: 13000000 INFO @ Sun, 21 Jun 2020 19:14:42: 7000000 INFO @ Sun, 21 Jun 2020 19:14:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:46: 14000000 INFO @ Sun, 21 Jun 2020 19:14:47: 8000000 INFO @ Sun, 21 Jun 2020 19:14:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:47: #1 total tags in treatment: 14134920 INFO @ Sun, 21 Jun 2020 19:14:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:47: #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 19:14:47: #1 tags after filtering in treatment: 14134920 INFO @ Sun, 21 Jun 2020 19:14:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:48: #2 number of paired peaks: 685 WARNING @ Sun, 21 Jun 2020 19:14:48: Fewer paired peaks (685) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 685 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:48: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 19:14:48: #2 alternative fragment length(s) may be 3,37 bps INFO @ Sun, 21 Jun 2020 19:14:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.10_model.r WARNING @ Sun, 21 Jun 2020 19:14:48: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:14:48: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Sun, 21 Jun 2020 19:14:48: #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 19:14:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:52: 9000000 INFO @ Sun, 21 Jun 2020 19:14:57: 10000000 INFO @ Sun, 21 Jun 2020 19:14:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.05_summits.bed INFO @ Sun, 21 Jun 2020 19:14:59: Done! pass1 - making usageList (620 chroms): 1 millis pass2 - checking and writing primary data (2420 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:02: 11000000 INFO @ Sun, 21 Jun 2020 19:15:07: 12000000 INFO @ Sun, 21 Jun 2020 19:15:12: 13000000 INFO @ Sun, 21 Jun 2020 19:15:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:17: 14000000 INFO @ Sun, 21 Jun 2020 19:15:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:18: #1 total tags in treatment: 14134920 INFO @ Sun, 21 Jun 2020 19:15:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:18: #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 19:15:18: #1 tags after filtering in treatment: 14134920 INFO @ Sun, 21 Jun 2020 19:15:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:19: #2 number of paired peaks: 685 WARNING @ Sun, 21 Jun 2020 19:15:19: Fewer paired peaks (685) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 685 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:19: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 19:15:19: #2 alternative fragment length(s) may be 3,37 bps INFO @ Sun, 21 Jun 2020 19:15:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.20_model.r WARNING @ Sun, 21 Jun 2020 19:15:19: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:19: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Sun, 21 Jun 2020 19:15:19: #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 19:15:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:15:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.10_summits.bed INFO @ Sun, 21 Jun 2020 19:15:29: Done! pass1 - making usageList (514 chroms): 1 millis pass2 - checking and writing primary data (1984 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:15:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287706/SRX287706.20_summits.bed INFO @ Sun, 21 Jun 2020 19:15:59: Done! pass1 - making usageList (343 chroms): 1 millis pass2 - checking and writing primary data (761 records, 4 fields): 11 millis CompletedMACS2peakCalling