Job ID = 6455113 SRX = SRX2734365 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:43:40 prefetch.2.10.7: 1) Downloading 'SRR5445342'... 2020-06-21T09:43:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:46:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:46:13 prefetch.2.10.7: 1) 'SRR5445342' was downloaded successfully 2020-06-21T09:46:13 prefetch.2.10.7: 'SRR5445342' has 0 unresolved dependencies Read 31529433 spots for SRR5445342/SRR5445342.sra Written 31529433 spots for SRR5445342/SRR5445342.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: 00:06:13 31529433 reads; of these: 31529433 (100.00%) were unpaired; of these: 4778258 (15.15%) aligned 0 times 23130134 (73.36%) aligned exactly 1 time 3621041 (11.48%) aligned >1 times 84.85% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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 12 files... [bam_rmdupse_core] 9899631 / 26751175 = 0.3701 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 18:58:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.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 18:58:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:41: 1000000 INFO @ Sun, 21 Jun 2020 18:58:46: 2000000 INFO @ Sun, 21 Jun 2020 18:58:52: 3000000 INFO @ Sun, 21 Jun 2020 18:58:57: 4000000 INFO @ Sun, 21 Jun 2020 18:59:02: 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 18:59:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.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 18:59:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:08: 6000000 INFO @ Sun, 21 Jun 2020 18:59:12: 1000000 INFO @ Sun, 21 Jun 2020 18:59:13: 7000000 INFO @ Sun, 21 Jun 2020 18:59:18: 2000000 INFO @ Sun, 21 Jun 2020 18:59:19: 8000000 INFO @ Sun, 21 Jun 2020 18:59:23: 3000000 INFO @ Sun, 21 Jun 2020 18:59:25: 9000000 INFO @ Sun, 21 Jun 2020 18:59:29: 4000000 INFO @ Sun, 21 Jun 2020 18:59:31: 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 18:59:35: 5000000 INFO @ Sun, 21 Jun 2020 18:59:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.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 18:59:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:37: 11000000 INFO @ Sun, 21 Jun 2020 18:59:41: 6000000 INFO @ Sun, 21 Jun 2020 18:59:42: 1000000 INFO @ Sun, 21 Jun 2020 18:59:43: 12000000 INFO @ Sun, 21 Jun 2020 18:59:47: 7000000 INFO @ Sun, 21 Jun 2020 18:59:48: 2000000 INFO @ Sun, 21 Jun 2020 18:59:49: 13000000 INFO @ Sun, 21 Jun 2020 18:59:53: 8000000 INFO @ Sun, 21 Jun 2020 18:59:54: 3000000 INFO @ Sun, 21 Jun 2020 18:59:55: 14000000 INFO @ Sun, 21 Jun 2020 18:59:59: 9000000 INFO @ Sun, 21 Jun 2020 19:00:00: 4000000 INFO @ Sun, 21 Jun 2020 19:00:01: 15000000 INFO @ Sun, 21 Jun 2020 19:00:05: 10000000 INFO @ Sun, 21 Jun 2020 19:00:06: 5000000 INFO @ Sun, 21 Jun 2020 19:00:07: 16000000 INFO @ Sun, 21 Jun 2020 19:00:11: 11000000 INFO @ Sun, 21 Jun 2020 19:00:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:00:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:00:12: #1 total tags in treatment: 16851544 INFO @ Sun, 21 Jun 2020 19:00:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:12: #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 19:00:12: 6000000 INFO @ Sun, 21 Jun 2020 19:00:12: #1 tags after filtering in treatment: 16851450 INFO @ Sun, 21 Jun 2020 19:00:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:14: #2 number of paired peaks: 3115 INFO @ Sun, 21 Jun 2020 19:00:14: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:14: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:14: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:14: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:14: #2 predicted fragment length is 206 bps INFO @ Sun, 21 Jun 2020 19:00:14: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 21 Jun 2020 19:00:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.05_model.r INFO @ Sun, 21 Jun 2020 19:00:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:17: 12000000 INFO @ Sun, 21 Jun 2020 19:00:18: 7000000 INFO @ Sun, 21 Jun 2020 19:00:23: 13000000 INFO @ Sun, 21 Jun 2020 19:00:24: 8000000 INFO @ Sun, 21 Jun 2020 19:00:30: 14000000 INFO @ Sun, 21 Jun 2020 19:00:30: 9000000 INFO @ Sun, 21 Jun 2020 19:00:36: 10000000 INFO @ Sun, 21 Jun 2020 19:00:36: 15000000 INFO @ Sun, 21 Jun 2020 19:00:42: 11000000 INFO @ Sun, 21 Jun 2020 19:00:42: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:00:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:00:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:00:47: #1 total tags in treatment: 16851544 INFO @ Sun, 21 Jun 2020 19:00:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:47: #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 19:00:48: 12000000 INFO @ Sun, 21 Jun 2020 19:00:48: #1 tags after filtering in treatment: 16851450 INFO @ Sun, 21 Jun 2020 19:00:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:49: #2 number of paired peaks: 3115 INFO @ Sun, 21 Jun 2020 19:00:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:49: #2 predicted fragment length is 206 bps INFO @ Sun, 21 Jun 2020 19:00:49: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 21 Jun 2020 19:00:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.10_model.r INFO @ Sun, 21 Jun 2020 19:00:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:53: 13000000 INFO @ Sun, 21 Jun 2020 19:00:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:00:59: 14000000 INFO @ Sun, 21 Jun 2020 19:01:04: 15000000 INFO @ Sun, 21 Jun 2020 19:01:10: 16000000 INFO @ Sun, 21 Jun 2020 19:01:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:01:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:01:14: #1 total tags in treatment: 16851544 INFO @ Sun, 21 Jun 2020 19:01:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:14: #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 19:01:15: #1 tags after filtering in treatment: 16851450 INFO @ Sun, 21 Jun 2020 19:01:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:01:16: #2 number of paired peaks: 3115 INFO @ Sun, 21 Jun 2020 19:01:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:16: #2 predicted fragment length is 206 bps INFO @ Sun, 21 Jun 2020 19:01:16: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 21 Jun 2020 19:01:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.20_model.r INFO @ Sun, 21 Jun 2020 19:01:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:01:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.05_summits.bed INFO @ Sun, 21 Jun 2020 19:01:19: Done! pass1 - making usageList (200 chroms): 2 millis pass2 - checking and writing primary data (6540 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:01:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.10_summits.bed INFO @ Sun, 21 Jun 2020 19:01:54: Done! pass1 - making usageList (128 chroms): 2 millis pass2 - checking and writing primary data (5420 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:02:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2734365/SRX2734365.20_summits.bed INFO @ Sun, 21 Jun 2020 19:02:20: Done! pass1 - making usageList (102 chroms): 1 millis pass2 - checking and writing primary data (4140 records, 4 fields): 8 millis CompletedMACS2peakCalling