Job ID = 6454087 SRX = SRX181432 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:00:04 prefetch.2.10.7: 1) Downloading 'SRR548169'... 2020-06-21T09:00:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:05:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:05:14 prefetch.2.10.7: 1) 'SRR548169' was downloaded successfully Read 32989589 spots for SRR548169/SRR548169.sra Written 32989589 spots for SRR548169/SRR548169.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: 00:06:48 32989589 reads; of these: 32989589 (100.00%) were unpaired; of these: 2260060 (6.85%) aligned 0 times 27383012 (83.01%) aligned exactly 1 time 3346517 (10.14%) aligned >1 times 93.15% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 14412783 / 30729529 = 0.4690 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 18:18:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.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 18:18:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:52: 1000000 INFO @ Sun, 21 Jun 2020 18:18:57: 2000000 INFO @ Sun, 21 Jun 2020 18:19:01: 3000000 INFO @ Sun, 21 Jun 2020 18:19:06: 4000000 INFO @ Sun, 21 Jun 2020 18:19:11: 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 18:19:16: 6000000 INFO @ Sun, 21 Jun 2020 18:19:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.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 18:19:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:21: 7000000 INFO @ Sun, 21 Jun 2020 18:19:23: 1000000 INFO @ Sun, 21 Jun 2020 18:19:26: 8000000 INFO @ Sun, 21 Jun 2020 18:19:29: 2000000 INFO @ Sun, 21 Jun 2020 18:19:32: 9000000 INFO @ Sun, 21 Jun 2020 18:19:36: 3000000 INFO @ Sun, 21 Jun 2020 18:19:37: 10000000 INFO @ Sun, 21 Jun 2020 18:19:42: 4000000 INFO @ Sun, 21 Jun 2020 18:19:43: 11000000 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 18:19:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.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 18:19:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:47: 5000000 INFO @ Sun, 21 Jun 2020 18:19:49: 12000000 INFO @ Sun, 21 Jun 2020 18:19:53: 6000000 INFO @ Sun, 21 Jun 2020 18:19:53: 1000000 INFO @ Sun, 21 Jun 2020 18:19:55: 13000000 INFO @ Sun, 21 Jun 2020 18:19:58: 7000000 INFO @ Sun, 21 Jun 2020 18:19:58: 2000000 INFO @ Sun, 21 Jun 2020 18:20:01: 14000000 INFO @ Sun, 21 Jun 2020 18:20:03: 8000000 INFO @ Sun, 21 Jun 2020 18:20:04: 3000000 INFO @ Sun, 21 Jun 2020 18:20:06: 15000000 INFO @ Sun, 21 Jun 2020 18:20:09: 9000000 INFO @ Sun, 21 Jun 2020 18:20:09: 4000000 INFO @ Sun, 21 Jun 2020 18:20:12: 16000000 INFO @ Sun, 21 Jun 2020 18:20:14: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:20:14: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:20:14: #1 total tags in treatment: 16316746 INFO @ Sun, 21 Jun 2020 18:20:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:14: #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 18:20:14: #1 tags after filtering in treatment: 16316737 INFO @ Sun, 21 Jun 2020 18:20:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:15: 5000000 INFO @ Sun, 21 Jun 2020 18:20:15: 10000000 INFO @ Sun, 21 Jun 2020 18:20:15: #2 number of paired peaks: 1632 INFO @ Sun, 21 Jun 2020 18:20:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:16: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 18:20:16: #2 alternative fragment length(s) may be 127 bps INFO @ Sun, 21 Jun 2020 18:20:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.05_model.r INFO @ Sun, 21 Jun 2020 18:20:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:20: 6000000 INFO @ Sun, 21 Jun 2020 18:20:21: 11000000 INFO @ Sun, 21 Jun 2020 18:20:26: 7000000 INFO @ Sun, 21 Jun 2020 18:20:27: 12000000 INFO @ Sun, 21 Jun 2020 18:20:33: 8000000 INFO @ Sun, 21 Jun 2020 18:20:33: 13000000 INFO @ Sun, 21 Jun 2020 18:20:39: 9000000 INFO @ Sun, 21 Jun 2020 18:20:39: 14000000 INFO @ Sun, 21 Jun 2020 18:20:45: 10000000 INFO @ Sun, 21 Jun 2020 18:20:45: 15000000 INFO @ Sun, 21 Jun 2020 18:20:50: 11000000 INFO @ Sun, 21 Jun 2020 18:20:50: 16000000 INFO @ Sun, 21 Jun 2020 18:20:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:52: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:20:52: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:20:52: #1 total tags in treatment: 16316746 INFO @ Sun, 21 Jun 2020 18:20:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:20:53: #1 tags after filtering in treatment: 16316737 INFO @ Sun, 21 Jun 2020 18:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:54: #2 number of paired peaks: 1632 INFO @ Sun, 21 Jun 2020 18:20:54: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:55: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 18:20:55: #2 alternative fragment length(s) may be 127 bps INFO @ Sun, 21 Jun 2020 18:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.10_model.r INFO @ Sun, 21 Jun 2020 18:20:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:56: 12000000 INFO @ Sun, 21 Jun 2020 18:21:02: 13000000 INFO @ Sun, 21 Jun 2020 18:21:07: 14000000 INFO @ Sun, 21 Jun 2020 18:21:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.05_summits.bed INFO @ Sun, 21 Jun 2020 18:21:09: Done! pass1 - making usageList (445 chroms): 2 millis pass2 - checking and writing primary data (10612 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:12: 15000000 INFO @ Sun, 21 Jun 2020 18:21:17: 16000000 INFO @ Sun, 21 Jun 2020 18:21:19: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:21:19: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:21:19: #1 total tags in treatment: 16316746 INFO @ Sun, 21 Jun 2020 18:21:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:19: #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 18:21:20: #1 tags after filtering in treatment: 16316737 INFO @ Sun, 21 Jun 2020 18:21:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:21: #2 number of paired peaks: 1632 INFO @ Sun, 21 Jun 2020 18:21:21: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:21: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:21: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:21: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:21: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 18:21:21: #2 alternative fragment length(s) may be 127 bps INFO @ Sun, 21 Jun 2020 18:21:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.20_model.r INFO @ Sun, 21 Jun 2020 18:21:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:21:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:50: Done! pass1 - making usageList (407 chroms): 2 millis pass2 - checking and writing primary data (7852 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181432/SRX181432.20_summits.bed INFO @ Sun, 21 Jun 2020 18:22:17: Done! pass1 - making usageList (341 chroms): 1 millis pass2 - checking and writing primary data (4246 records, 4 fields): 13 millis CompletedMACS2peakCalling