Job ID = 6455709 SRX = SRX288009 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:21:06 prefetch.2.10.7: 1) Downloading 'SRR870198'... 2020-06-21T10:21:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:17 prefetch.2.10.7: 1) 'SRR870198' was downloaded successfully Read 16267419 spots for SRR870198/SRR870198.sra Written 16267419 spots for SRR870198/SRR870198.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: 00:03:55 16267419 reads; of these: 16267419 (100.00%) were unpaired; of these: 1530141 (9.41%) aligned 0 times 12212499 (75.07%) aligned exactly 1 time 2524779 (15.52%) aligned >1 times 90.59% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 3066458 / 14737278 = 0.2081 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 19:32:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.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 19:32:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:18: 1000000 INFO @ Sun, 21 Jun 2020 19:32:23: 2000000 INFO @ Sun, 21 Jun 2020 19:32:28: 3000000 INFO @ Sun, 21 Jun 2020 19:32:33: 4000000 INFO @ Sun, 21 Jun 2020 19:32:38: 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 19:32:42: 6000000 INFO @ Sun, 21 Jun 2020 19:32:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.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 19:32:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:47: 7000000 INFO @ Sun, 21 Jun 2020 19:32:48: 1000000 INFO @ Sun, 21 Jun 2020 19:32:53: 8000000 INFO @ Sun, 21 Jun 2020 19:32:54: 2000000 INFO @ Sun, 21 Jun 2020 19:32:58: 9000000 INFO @ Sun, 21 Jun 2020 19:32:59: 3000000 INFO @ Sun, 21 Jun 2020 19:33:03: 10000000 INFO @ Sun, 21 Jun 2020 19:33:04: 4000000 INFO @ Sun, 21 Jun 2020 19:33:08: 11000000 INFO @ Sun, 21 Jun 2020 19:33:09: 5000000 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 19:33:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:33:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:33:12: #1 total tags in treatment: 11670820 INFO @ Sun, 21 Jun 2020 19:33:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:12: #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 19:33:13: #1 tags after filtering in treatment: 11670813 INFO @ Sun, 21 Jun 2020 19:33:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:13: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.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 19:33:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:14: #2 number of paired peaks: 3643 INFO @ Sun, 21 Jun 2020 19:33:14: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:14: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:14: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:14: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:14: #2 predicted fragment length is 245 bps INFO @ Sun, 21 Jun 2020 19:33:14: #2 alternative fragment length(s) may be 245 bps INFO @ Sun, 21 Jun 2020 19:33:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.05_model.r INFO @ Sun, 21 Jun 2020 19:33:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:33:14: 6000000 INFO @ Sun, 21 Jun 2020 19:33:18: 1000000 INFO @ Sun, 21 Jun 2020 19:33:19: 7000000 INFO @ Sun, 21 Jun 2020 19:33:23: 2000000 INFO @ Sun, 21 Jun 2020 19:33:25: 8000000 INFO @ Sun, 21 Jun 2020 19:33:28: 3000000 INFO @ Sun, 21 Jun 2020 19:33:30: 9000000 INFO @ Sun, 21 Jun 2020 19:33:33: 4000000 INFO @ Sun, 21 Jun 2020 19:33:36: 10000000 INFO @ Sun, 21 Jun 2020 19:33:39: 5000000 INFO @ Sun, 21 Jun 2020 19:33:42: 11000000 INFO @ Sun, 21 Jun 2020 19:33:44: 6000000 INFO @ Sun, 21 Jun 2020 19:33:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:33:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:33:46: #1 total tags in treatment: 11670820 INFO @ Sun, 21 Jun 2020 19:33:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:46: #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 19:33:47: #1 tags after filtering in treatment: 11670813 INFO @ Sun, 21 Jun 2020 19:33:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:33:48: #2 number of paired peaks: 3643 INFO @ Sun, 21 Jun 2020 19:33:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:48: #2 predicted fragment length is 245 bps INFO @ Sun, 21 Jun 2020 19:33:48: #2 alternative fragment length(s) may be 245 bps INFO @ Sun, 21 Jun 2020 19:33:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.10_model.r INFO @ Sun, 21 Jun 2020 19:33:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:33:49: 7000000 INFO @ Sun, 21 Jun 2020 19:33:54: 8000000 INFO @ Sun, 21 Jun 2020 19:33:59: 9000000 INFO @ Sun, 21 Jun 2020 19:34:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.05_summits.bed INFO @ Sun, 21 Jun 2020 19:34:04: Done! INFO @ Sun, 21 Jun 2020 19:34:04: 10000000 pass1 - making usageList (467 chroms): 2 millis pass2 - checking and writing primary data (8385 records, 4 fields): 35 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:34:10: 11000000 INFO @ Sun, 21 Jun 2020 19:34:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:13: #1 total tags in treatment: 11670820 INFO @ Sun, 21 Jun 2020 19:34:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:13: #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 19:34:14: #1 tags after filtering in treatment: 11670813 INFO @ Sun, 21 Jun 2020 19:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:15: #2 number of paired peaks: 3643 INFO @ Sun, 21 Jun 2020 19:34:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:15: #2 predicted fragment length is 245 bps INFO @ Sun, 21 Jun 2020 19:34:15: #2 alternative fragment length(s) may be 245 bps INFO @ Sun, 21 Jun 2020 19:34:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.20_model.r INFO @ Sun, 21 Jun 2020 19:34:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:34:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.10_summits.bed INFO @ Sun, 21 Jun 2020 19:34:35: Done! pass1 - making usageList (294 chroms): 1 millis pass2 - checking and writing primary data (6411 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:34:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288009/SRX288009.20_summits.bed INFO @ Sun, 21 Jun 2020 19:35:03: Done! pass1 - making usageList (148 chroms): 1 millis pass2 - checking and writing primary data (4565 records, 4 fields): 11 millis CompletedMACS2peakCalling