Job ID = 6455152 SRX = SRX2804214 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:38:10 prefetch.2.10.7: 1) Downloading 'SRR5534642'... 2020-06-21T09:38:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:40:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:40:44 prefetch.2.10.7: 'SRR5534642' is valid 2020-06-21T09:40:44 prefetch.2.10.7: 1) 'SRR5534642' was downloaded successfully 2020-06-21T09:40:44 prefetch.2.10.7: 'SRR5534642' has 0 unresolved dependencies Read 26750825 spots for SRR5534642/SRR5534642.sra Written 26750825 spots for SRR5534642/SRR5534642.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: 00:05:42 26750825 reads; of these: 26750825 (100.00%) were unpaired; of these: 9998330 (37.38%) aligned 0 times 12410365 (46.39%) aligned exactly 1 time 4342130 (16.23%) aligned >1 times 62.62% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 3972891 / 16752495 = 0.2372 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 18:51:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.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 18:51:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:29: 1000000 INFO @ Sun, 21 Jun 2020 18:51:35: 2000000 INFO @ Sun, 21 Jun 2020 18:51:40: 3000000 INFO @ Sun, 21 Jun 2020 18:51:45: 4000000 INFO @ Sun, 21 Jun 2020 18:51:51: 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 18:51:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.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 18:51:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:56: 6000000 INFO @ Sun, 21 Jun 2020 18:52:00: 1000000 INFO @ Sun, 21 Jun 2020 18:52:02: 7000000 INFO @ Sun, 21 Jun 2020 18:52:07: 2000000 INFO @ Sun, 21 Jun 2020 18:52:08: 8000000 INFO @ Sun, 21 Jun 2020 18:52:14: 3000000 INFO @ Sun, 21 Jun 2020 18:52:14: 9000000 INFO @ Sun, 21 Jun 2020 18:52:20: 10000000 INFO @ Sun, 21 Jun 2020 18:52:21: 4000000 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 18:52:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.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 18:52:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:27: 11000000 INFO @ Sun, 21 Jun 2020 18:52:28: 5000000 INFO @ Sun, 21 Jun 2020 18:52:30: 1000000 INFO @ Sun, 21 Jun 2020 18:52:33: 12000000 INFO @ Sun, 21 Jun 2020 18:52:35: 6000000 INFO @ Sun, 21 Jun 2020 18:52:37: 2000000 INFO @ Sun, 21 Jun 2020 18:52:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:52:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:52:38: #1 total tags in treatment: 12779604 INFO @ Sun, 21 Jun 2020 18:52:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:38: #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 18:52:38: #1 tags after filtering in treatment: 12779603 INFO @ Sun, 21 Jun 2020 18:52:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:39: #2 number of paired peaks: 2427 INFO @ Sun, 21 Jun 2020 18:52:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:40: #2 predicted fragment length is 282 bps INFO @ Sun, 21 Jun 2020 18:52:40: #2 alternative fragment length(s) may be 282 bps INFO @ Sun, 21 Jun 2020 18:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.05_model.r INFO @ Sun, 21 Jun 2020 18:52:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:42: 7000000 INFO @ Sun, 21 Jun 2020 18:52:44: 3000000 INFO @ Sun, 21 Jun 2020 18:52:48: 8000000 INFO @ Sun, 21 Jun 2020 18:52:51: 4000000 INFO @ Sun, 21 Jun 2020 18:52:55: 9000000 INFO @ Sun, 21 Jun 2020 18:52:57: 5000000 INFO @ Sun, 21 Jun 2020 18:53:02: 10000000 INFO @ Sun, 21 Jun 2020 18:53:04: 6000000 INFO @ Sun, 21 Jun 2020 18:53:09: 11000000 INFO @ Sun, 21 Jun 2020 18:53:11: 7000000 INFO @ Sun, 21 Jun 2020 18:53:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:16: 12000000 INFO @ Sun, 21 Jun 2020 18:53:17: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:53:22: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:53:22: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:53:22: #1 total tags in treatment: 12779604 INFO @ Sun, 21 Jun 2020 18:53:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:22: #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 18:53:22: #1 tags after filtering in treatment: 12779603 INFO @ Sun, 21 Jun 2020 18:53:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:22: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:23: #2 number of paired peaks: 2427 INFO @ Sun, 21 Jun 2020 18:53:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:23: #2 predicted fragment length is 282 bps INFO @ Sun, 21 Jun 2020 18:53:23: #2 alternative fragment length(s) may be 282 bps INFO @ Sun, 21 Jun 2020 18:53:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.10_model.r INFO @ Sun, 21 Jun 2020 18:53:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:24: 9000000 INFO @ Sun, 21 Jun 2020 18:53:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.05_summits.bed INFO @ Sun, 21 Jun 2020 18:53:28: Done! pass1 - making usageList (707 chroms): 2 millis pass2 - checking and writing primary data (6078 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:53:30: 10000000 INFO @ Sun, 21 Jun 2020 18:53:37: 11000000 INFO @ Sun, 21 Jun 2020 18:53:44: 12000000 INFO @ Sun, 21 Jun 2020 18:53:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:53:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:53:49: #1 total tags in treatment: 12779604 INFO @ Sun, 21 Jun 2020 18:53:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:53:49: #1 tags after filtering in treatment: 12779603 INFO @ Sun, 21 Jun 2020 18:53:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:50: #2 number of paired peaks: 2427 INFO @ Sun, 21 Jun 2020 18:53:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:50: #2 predicted fragment length is 282 bps INFO @ Sun, 21 Jun 2020 18:53:50: #2 alternative fragment length(s) may be 282 bps INFO @ Sun, 21 Jun 2020 18:53:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.20_model.r INFO @ Sun, 21 Jun 2020 18:53:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.10_summits.bed INFO @ Sun, 21 Jun 2020 18:54:12: Done! pass1 - making usageList (625 chroms): 1 millis pass2 - checking and writing primary data (4983 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:54:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804214/SRX2804214.20_summits.bed INFO @ Sun, 21 Jun 2020 18:54:38: Done! pass1 - making usageList (508 chroms): 1 millis pass2 - checking and writing primary data (3875 records, 4 fields): 17 millis CompletedMACS2peakCalling