Job ID = 6454801 SRX = SRX2592400 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:38:55 prefetch.2.10.7: 1) Downloading 'SRR5289677'... 2020-06-21T09:38:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:43:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:43:56 prefetch.2.10.7: 1) 'SRR5289677' was downloaded successfully Read 27822632 spots for SRR5289677/SRR5289677.sra Written 27822632 spots for SRR5289677/SRR5289677.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: 00:08:38 27822632 reads; of these: 27822632 (100.00%) were unpaired; of these: 1996388 (7.18%) aligned 0 times 20696200 (74.39%) aligned exactly 1 time 5130044 (18.44%) aligned >1 times 92.82% overall alignment rate Time searching: 00:08:38 Overall time: 00:08:38 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] 7376667 / 25826244 = 0.2856 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 19:00:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.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 19:00:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:56: 1000000 INFO @ Sun, 21 Jun 2020 19:01:02: 2000000 INFO @ Sun, 21 Jun 2020 19:01:08: 3000000 INFO @ Sun, 21 Jun 2020 19:01:14: 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 19:01:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.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 19:01:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:20: 5000000 INFO @ Sun, 21 Jun 2020 19:01:27: 1000000 INFO @ Sun, 21 Jun 2020 19:01:27: 6000000 INFO @ Sun, 21 Jun 2020 19:01:35: 7000000 INFO @ Sun, 21 Jun 2020 19:01:35: 2000000 INFO @ Sun, 21 Jun 2020 19:01:42: 8000000 INFO @ Sun, 21 Jun 2020 19:01:43: 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 19:01:49: 9000000 INFO @ Sun, 21 Jun 2020 19:01:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.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 19:01:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:51: 4000000 INFO @ Sun, 21 Jun 2020 19:01:57: 10000000 INFO @ Sun, 21 Jun 2020 19:01:57: 1000000 INFO @ Sun, 21 Jun 2020 19:01:59: 5000000 INFO @ Sun, 21 Jun 2020 19:02:04: 11000000 INFO @ Sun, 21 Jun 2020 19:02:05: 2000000 INFO @ Sun, 21 Jun 2020 19:02:07: 6000000 INFO @ Sun, 21 Jun 2020 19:02:12: 12000000 INFO @ Sun, 21 Jun 2020 19:02:13: 3000000 INFO @ Sun, 21 Jun 2020 19:02:15: 7000000 INFO @ Sun, 21 Jun 2020 19:02:20: 13000000 INFO @ Sun, 21 Jun 2020 19:02:20: 4000000 INFO @ Sun, 21 Jun 2020 19:02:23: 8000000 INFO @ Sun, 21 Jun 2020 19:02:27: 14000000 INFO @ Sun, 21 Jun 2020 19:02:28: 5000000 INFO @ Sun, 21 Jun 2020 19:02:31: 9000000 INFO @ Sun, 21 Jun 2020 19:02:35: 6000000 INFO @ Sun, 21 Jun 2020 19:02:36: 15000000 INFO @ Sun, 21 Jun 2020 19:02:39: 10000000 INFO @ Sun, 21 Jun 2020 19:02:43: 7000000 INFO @ Sun, 21 Jun 2020 19:02:43: 16000000 INFO @ Sun, 21 Jun 2020 19:02:48: 11000000 INFO @ Sun, 21 Jun 2020 19:02:51: 8000000 INFO @ Sun, 21 Jun 2020 19:02:51: 17000000 INFO @ Sun, 21 Jun 2020 19:02:56: 12000000 INFO @ Sun, 21 Jun 2020 19:02:58: 9000000 INFO @ Sun, 21 Jun 2020 19:02:58: 18000000 INFO @ Sun, 21 Jun 2020 19:03:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:03:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:03:02: #1 total tags in treatment: 18449577 INFO @ Sun, 21 Jun 2020 19:03:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:02: #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 19:03:03: #1 tags after filtering in treatment: 18449507 INFO @ Sun, 21 Jun 2020 19:03:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:04: 13000000 INFO @ Sun, 21 Jun 2020 19:03:04: #2 number of paired peaks: 3206 INFO @ Sun, 21 Jun 2020 19:03:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:05: #2 predicted fragment length is 181 bps INFO @ Sun, 21 Jun 2020 19:03:05: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 21 Jun 2020 19:03:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.05_model.r INFO @ Sun, 21 Jun 2020 19:03:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:06: 10000000 INFO @ Sun, 21 Jun 2020 19:03:12: 14000000 INFO @ Sun, 21 Jun 2020 19:03:13: 11000000 INFO @ Sun, 21 Jun 2020 19:03:20: 12000000 INFO @ Sun, 21 Jun 2020 19:03:21: 15000000 INFO @ Sun, 21 Jun 2020 19:03:28: 13000000 INFO @ Sun, 21 Jun 2020 19:03:30: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:03:35: 14000000 INFO @ Sun, 21 Jun 2020 19:03:38: 17000000 INFO @ Sun, 21 Jun 2020 19:03:43: 15000000 INFO @ Sun, 21 Jun 2020 19:03:46: 18000000 INFO @ Sun, 21 Jun 2020 19:03:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:03:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:03:50: #1 total tags in treatment: 18449577 INFO @ Sun, 21 Jun 2020 19:03:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:50: #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 19:03:51: 16000000 INFO @ Sun, 21 Jun 2020 19:03:51: #1 tags after filtering in treatment: 18449507 INFO @ Sun, 21 Jun 2020 19:03:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:53: #2 number of paired peaks: 3206 INFO @ Sun, 21 Jun 2020 19:03:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:53: #2 predicted fragment length is 181 bps INFO @ Sun, 21 Jun 2020 19:03:53: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 21 Jun 2020 19:03:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.10_model.r INFO @ Sun, 21 Jun 2020 19:03:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:57: 17000000 INFO @ Sun, 21 Jun 2020 19:04:05: 18000000 INFO @ Sun, 21 Jun 2020 19:04:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:08: #1 total tags in treatment: 18449577 INFO @ Sun, 21 Jun 2020 19:04:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:08: #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 19:04:08: #1 tags after filtering in treatment: 18449507 INFO @ Sun, 21 Jun 2020 19:04:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:08: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:04:10: #2 number of paired peaks: 3206 INFO @ Sun, 21 Jun 2020 19:04:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:11: #2 predicted fragment length is 181 bps INFO @ Sun, 21 Jun 2020 19:04:11: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 21 Jun 2020 19:04:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.20_model.r INFO @ Sun, 21 Jun 2020 19:04:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.05_summits.bed INFO @ Sun, 21 Jun 2020 19:04:17: Done! pass1 - making usageList (430 chroms): 3 millis pass2 - checking and writing primary data (16595 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:04:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.10_summits.bed INFO @ Sun, 21 Jun 2020 19:05:02: Done! pass1 - making usageList (299 chroms): 3 millis pass2 - checking and writing primary data (12847 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592400/SRX2592400.20_summits.bed INFO @ Sun, 21 Jun 2020 19:05:22: Done! pass1 - making usageList (186 chroms): 2 millis pass2 - checking and writing primary data (8157 records, 4 fields): 15 millis CompletedMACS2peakCalling