Job ID = 6458290 SRX = SRX5011047 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:27:19 prefetch.2.10.7: 1) Downloading 'SRR8191496'... 2020-06-21T12:27:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:28:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:28:54 prefetch.2.10.7: 'SRR8191496' is valid 2020-06-21T12:28:54 prefetch.2.10.7: 1) 'SRR8191496' was downloaded successfully 2020-06-21T12:28:54 prefetch.2.10.7: 'SRR8191496' has 0 unresolved dependencies Read 21993989 spots for SRR8191496/SRR8191496.sra Written 21993989 spots for SRR8191496/SRR8191496.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: 00:06:11 21993989 reads; of these: 21993989 (100.00%) were unpaired; of these: 2450222 (11.14%) aligned 0 times 14163982 (64.40%) aligned exactly 1 time 5379785 (24.46%) aligned >1 times 88.86% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 8537645 / 19543767 = 0.4368 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 21:40:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.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 21:40:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:14: 1000000 INFO @ Sun, 21 Jun 2020 21:40:18: 2000000 INFO @ Sun, 21 Jun 2020 21:40:23: 3000000 INFO @ Sun, 21 Jun 2020 21:40:28: 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 21:40:33: 5000000 INFO @ Sun, 21 Jun 2020 21:40:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.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 21:40:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:38: 6000000 INFO @ Sun, 21 Jun 2020 21:40:40: 1000000 INFO @ Sun, 21 Jun 2020 21:40:43: 7000000 INFO @ Sun, 21 Jun 2020 21:40:45: 2000000 INFO @ Sun, 21 Jun 2020 21:40:48: 8000000 INFO @ Sun, 21 Jun 2020 21:40:51: 3000000 INFO @ Sun, 21 Jun 2020 21:40:54: 9000000 INFO @ Sun, 21 Jun 2020 21:40:57: 4000000 INFO @ Sun, 21 Jun 2020 21:40:59: 10000000 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 21:41:02: 5000000 INFO @ Sun, 21 Jun 2020 21:41:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.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 21:41:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:05: 11000000 INFO @ Sun, 21 Jun 2020 21:41:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:41:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:41:05: #1 total tags in treatment: 11006122 INFO @ Sun, 21 Jun 2020 21:41:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:05: #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 21:41:05: #1 tags after filtering in treatment: 11006041 INFO @ Sun, 21 Jun 2020 21:41:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:05: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:06: #2 number of paired peaks: 1473 INFO @ Sun, 21 Jun 2020 21:41:06: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:06: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:06: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:06: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:06: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 21:41:06: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sun, 21 Jun 2020 21:41:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.05_model.r WARNING @ Sun, 21 Jun 2020 21:41:06: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:41:06: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sun, 21 Jun 2020 21:41:06: #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 21:41:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:08: 6000000 INFO @ Sun, 21 Jun 2020 21:41:10: 1000000 INFO @ Sun, 21 Jun 2020 21:41:13: 7000000 INFO @ Sun, 21 Jun 2020 21:41:15: 2000000 INFO @ Sun, 21 Jun 2020 21:41:19: 8000000 INFO @ Sun, 21 Jun 2020 21:41:21: 3000000 INFO @ Sun, 21 Jun 2020 21:41:25: 9000000 INFO @ Sun, 21 Jun 2020 21:41:27: 4000000 INFO @ Sun, 21 Jun 2020 21:41:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:30: 10000000 INFO @ Sun, 21 Jun 2020 21:41:32: 5000000 INFO @ Sun, 21 Jun 2020 21:41:36: 11000000 INFO @ Sun, 21 Jun 2020 21:41:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:41:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:41:36: #1 total tags in treatment: 11006122 INFO @ Sun, 21 Jun 2020 21:41:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:36: #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 21:41:37: #1 tags after filtering in treatment: 11006041 INFO @ Sun, 21 Jun 2020 21:41:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:38: #2 number of paired peaks: 1473 INFO @ Sun, 21 Jun 2020 21:41:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:38: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:38: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:38: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 21:41:38: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sun, 21 Jun 2020 21:41:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.10_model.r WARNING @ Sun, 21 Jun 2020 21:41:38: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:41:38: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sun, 21 Jun 2020 21:41:38: #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 21:41:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:38: 6000000 INFO @ Sun, 21 Jun 2020 21:41:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.05_summits.bed INFO @ Sun, 21 Jun 2020 21:41:42: Done! pass1 - making usageList (730 chroms): 1 millis pass2 - checking and writing primary data (3582 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:41:43: 7000000 INFO @ Sun, 21 Jun 2020 21:41:49: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:41:55: 9000000 INFO @ Sun, 21 Jun 2020 21:42:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:00: 10000000 INFO @ Sun, 21 Jun 2020 21:42:06: 11000000 INFO @ Sun, 21 Jun 2020 21:42:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:42:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:42:06: #1 total tags in treatment: 11006122 INFO @ Sun, 21 Jun 2020 21:42:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:06: #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 21:42:07: #1 tags after filtering in treatment: 11006041 INFO @ Sun, 21 Jun 2020 21:42:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:07: #2 number of paired peaks: 1473 INFO @ Sun, 21 Jun 2020 21:42:07: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:08: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:08: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:08: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:08: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 21:42:08: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sun, 21 Jun 2020 21:42:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.20_model.r WARNING @ Sun, 21 Jun 2020 21:42:08: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:42:08: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sun, 21 Jun 2020 21:42:08: #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 21:42:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.10_summits.bed INFO @ Sun, 21 Jun 2020 21:42:11: Done! pass1 - making usageList (602 chroms): 2 millis pass2 - checking and writing primary data (2048 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:42:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011047/SRX5011047.20_summits.bed INFO @ Sun, 21 Jun 2020 21:42:41: Done! pass1 - making usageList (280 chroms): 1 millis pass2 - checking and writing primary data (622 records, 4 fields): 10 millis CompletedMACS2peakCalling