Job ID = 6454669 SRX = SRX2458930 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:27:14 prefetch.2.10.7: 1) Downloading 'SRR5140279'... 2020-06-21T09:27:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:30:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:30:06 prefetch.2.10.7: 1) 'SRR5140279' was downloaded successfully Read 18711155 spots for SRR5140279/SRR5140279.sra Written 18711155 spots for SRR5140279/SRR5140279.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: 00:04:22 18711155 reads; of these: 18711155 (100.00%) were unpaired; of these: 588456 (3.14%) aligned 0 times 14455829 (77.26%) aligned exactly 1 time 3666870 (19.60%) aligned >1 times 96.86% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 2454077 / 18122699 = 0.1354 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 18:40:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.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 18:40:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:07: 1000000 INFO @ Sun, 21 Jun 2020 18:40:12: 2000000 INFO @ Sun, 21 Jun 2020 18:40:16: 3000000 INFO @ Sun, 21 Jun 2020 18:40:21: 4000000 INFO @ Sun, 21 Jun 2020 18:40:26: 5000000 INFO @ Sun, 21 Jun 2020 18:40:30: 6000000 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 18:40:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.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 18:40:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:35: 7000000 INFO @ Sun, 21 Jun 2020 18:40:38: 1000000 INFO @ Sun, 21 Jun 2020 18:40:40: 8000000 INFO @ Sun, 21 Jun 2020 18:40:42: 2000000 INFO @ Sun, 21 Jun 2020 18:40:45: 9000000 INFO @ Sun, 21 Jun 2020 18:40:47: 3000000 INFO @ Sun, 21 Jun 2020 18:40:49: 10000000 INFO @ Sun, 21 Jun 2020 18:40:52: 4000000 INFO @ Sun, 21 Jun 2020 18:40:54: 11000000 INFO @ Sun, 21 Jun 2020 18:40:56: 5000000 INFO @ Sun, 21 Jun 2020 18:40:59: 12000000 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 18:41:01: 6000000 INFO @ Sun, 21 Jun 2020 18:41:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.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 18:41:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:41:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:41:04: 13000000 INFO @ Sun, 21 Jun 2020 18:41:06: 7000000 INFO @ Sun, 21 Jun 2020 18:41:08: 1000000 INFO @ Sun, 21 Jun 2020 18:41:08: 14000000 INFO @ Sun, 21 Jun 2020 18:41:10: 8000000 INFO @ Sun, 21 Jun 2020 18:41:13: 15000000 INFO @ Sun, 21 Jun 2020 18:41:13: 2000000 INFO @ Sun, 21 Jun 2020 18:41:15: 9000000 INFO @ Sun, 21 Jun 2020 18:41:16: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:41:16: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:41:16: #1 total tags in treatment: 15668622 INFO @ Sun, 21 Jun 2020 18:41:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:16: #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 18:41:17: #1 tags after filtering in treatment: 15668522 INFO @ Sun, 21 Jun 2020 18:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:18: #2 number of paired peaks: 2251 INFO @ Sun, 21 Jun 2020 18:41:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:18: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:18: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:18: #2 predicted fragment length is 162 bps INFO @ Sun, 21 Jun 2020 18:41:18: #2 alternative fragment length(s) may be 4,162 bps INFO @ Sun, 21 Jun 2020 18:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.05_model.r INFO @ Sun, 21 Jun 2020 18:41:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:41:19: 3000000 INFO @ Sun, 21 Jun 2020 18:41:19: 10000000 INFO @ Sun, 21 Jun 2020 18:41:24: 4000000 INFO @ Sun, 21 Jun 2020 18:41:24: 11000000 INFO @ Sun, 21 Jun 2020 18:41:29: 12000000 INFO @ Sun, 21 Jun 2020 18:41:29: 5000000 INFO @ Sun, 21 Jun 2020 18:41:34: 13000000 INFO @ Sun, 21 Jun 2020 18:41:35: 6000000 INFO @ Sun, 21 Jun 2020 18:41:39: 14000000 INFO @ Sun, 21 Jun 2020 18:41:40: 7000000 INFO @ Sun, 21 Jun 2020 18:41:43: 15000000 INFO @ Sun, 21 Jun 2020 18:41:45: 8000000 INFO @ Sun, 21 Jun 2020 18:41:47: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:41:47: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:41:47: #1 total tags in treatment: 15668622 INFO @ Sun, 21 Jun 2020 18:41:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:47: #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 18:41:47: #1 tags after filtering in treatment: 15668522 INFO @ Sun, 21 Jun 2020 18:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:48: #2 number of paired peaks: 2251 INFO @ Sun, 21 Jun 2020 18:41:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:49: #2 predicted fragment length is 162 bps INFO @ Sun, 21 Jun 2020 18:41:49: #2 alternative fragment length(s) may be 4,162 bps INFO @ Sun, 21 Jun 2020 18:41:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.10_model.r INFO @ Sun, 21 Jun 2020 18:41:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:41:51: 9000000 INFO @ Sun, 21 Jun 2020 18:41:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:56: 10000000 INFO @ Sun, 21 Jun 2020 18:42:01: 11000000 INFO @ Sun, 21 Jun 2020 18:42:07: 12000000 INFO @ Sun, 21 Jun 2020 18:42:12: 13000000 INFO @ Sun, 21 Jun 2020 18:42:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:42:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:42:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.05_summits.bed INFO @ Sun, 21 Jun 2020 18:42:13: Done! pass1 - making usageList (489 chroms): 2 millis pass2 - checking and writing primary data (6211 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:42:18: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:42:23: 15000000 INFO @ Sun, 21 Jun 2020 18:42:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:42:26: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:42:26: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:42:26: #1 total tags in treatment: 15668622 INFO @ Sun, 21 Jun 2020 18:42:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:42:26: #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 18:42:27: #1 tags after filtering in treatment: 15668522 INFO @ Sun, 21 Jun 2020 18:42:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:42:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:42:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:42:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:42:28: #2 number of paired peaks: 2251 INFO @ Sun, 21 Jun 2020 18:42:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:42:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:42:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:42:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:42:28: #2 predicted fragment length is 162 bps INFO @ Sun, 21 Jun 2020 18:42:28: #2 alternative fragment length(s) may be 4,162 bps INFO @ Sun, 21 Jun 2020 18:42:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.20_model.r INFO @ Sun, 21 Jun 2020 18:42:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:42:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:42:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:42:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:42:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.10_summits.bed INFO @ Sun, 21 Jun 2020 18:42:43: Done! pass1 - making usageList (381 chroms): 2 millis pass2 - checking and writing primary data (3530 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:43:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:43:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:43:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:43:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458930/SRX2458930.20_summits.bed INFO @ Sun, 21 Jun 2020 18:43:22: Done! pass1 - making usageList (200 chroms): 1 millis pass2 - checking and writing primary data (1130 records, 4 fields): 7 millis CompletedMACS2peakCalling