Job ID = 6498730 SRX = SRX749055 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T00:19:12 prefetch.2.10.7: 1) Downloading 'SRR1636783'... 2020-06-26T00:19:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:22:43 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:22:43 prefetch.2.10.7: 1) 'SRR1636783' was downloaded successfully Read 16938638 spots for SRR1636783/SRR1636783.sra Written 16938638 spots for SRR1636783/SRR1636783.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: 00:34:23 16938638 reads; of these: 16938638 (100.00%) were paired; of these: 1329690 (7.85%) aligned concordantly 0 times 12114115 (71.52%) aligned concordantly exactly 1 time 3494833 (20.63%) aligned concordantly >1 times ---- 1329690 pairs aligned concordantly 0 times; of these: 66037 (4.97%) aligned discordantly 1 time ---- 1263653 pairs aligned 0 times concordantly or discordantly; of these: 2527306 mates make up the pairs; of these: 1671817 (66.15%) aligned 0 times 596349 (23.60%) aligned exactly 1 time 259140 (10.25%) aligned >1 times 95.07% overall alignment rate Time searching: 00:34:23 Overall time: 00:34:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 829759 / 15655753 = 0.0530 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 @ Fri, 26 Jun 2020 10:10:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.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 @ Fri, 26 Jun 2020 10:10:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:10:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:10:48: 1000000 INFO @ Fri, 26 Jun 2020 10:10:53: 2000000 INFO @ Fri, 26 Jun 2020 10:10:59: 3000000 INFO @ Fri, 26 Jun 2020 10:11:04: 4000000 INFO @ Fri, 26 Jun 2020 10:11:09: 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 @ Fri, 26 Jun 2020 10:11:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.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 @ Fri, 26 Jun 2020 10:11:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:11:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:11:15: 6000000 INFO @ Fri, 26 Jun 2020 10:11:19: 1000000 INFO @ Fri, 26 Jun 2020 10:11:20: 7000000 INFO @ Fri, 26 Jun 2020 10:11:25: 2000000 INFO @ Fri, 26 Jun 2020 10:11:26: 8000000 INFO @ Fri, 26 Jun 2020 10:11:31: 3000000 INFO @ Fri, 26 Jun 2020 10:11:32: 9000000 INFO @ Fri, 26 Jun 2020 10:11:38: 4000000 INFO @ Fri, 26 Jun 2020 10:11:38: 10000000 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 @ Fri, 26 Jun 2020 10:11:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.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 @ Fri, 26 Jun 2020 10:11:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:11:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:11:44: 11000000 INFO @ Fri, 26 Jun 2020 10:11:44: 5000000 INFO @ Fri, 26 Jun 2020 10:11:50: 1000000 INFO @ Fri, 26 Jun 2020 10:11:50: 12000000 INFO @ Fri, 26 Jun 2020 10:11:52: 6000000 INFO @ Fri, 26 Jun 2020 10:11:56: 13000000 INFO @ Fri, 26 Jun 2020 10:11:57: 2000000 INFO @ Fri, 26 Jun 2020 10:11:59: 7000000 INFO @ Fri, 26 Jun 2020 10:12:02: 14000000 INFO @ Fri, 26 Jun 2020 10:12:04: 3000000 INFO @ Fri, 26 Jun 2020 10:12:07: 8000000 INFO @ Fri, 26 Jun 2020 10:12:08: 15000000 INFO @ Fri, 26 Jun 2020 10:12:12: 4000000 INFO @ Fri, 26 Jun 2020 10:12:14: 16000000 INFO @ Fri, 26 Jun 2020 10:12:15: 9000000 INFO @ Fri, 26 Jun 2020 10:12:19: 5000000 INFO @ Fri, 26 Jun 2020 10:12:19: 17000000 INFO @ Fri, 26 Jun 2020 10:12:22: 10000000 INFO @ Fri, 26 Jun 2020 10:12:27: 6000000 INFO @ Fri, 26 Jun 2020 10:12:28: 18000000 INFO @ Fri, 26 Jun 2020 10:12:30: 11000000 INFO @ Fri, 26 Jun 2020 10:12:34: 7000000 INFO @ Fri, 26 Jun 2020 10:12:34: 19000000 INFO @ Fri, 26 Jun 2020 10:12:37: 12000000 INFO @ Fri, 26 Jun 2020 10:12:40: 20000000 INFO @ Fri, 26 Jun 2020 10:12:41: 8000000 INFO @ Fri, 26 Jun 2020 10:12:45: 13000000 INFO @ Fri, 26 Jun 2020 10:12:46: 21000000 INFO @ Fri, 26 Jun 2020 10:12:49: 9000000 INFO @ Fri, 26 Jun 2020 10:12:53: 22000000 INFO @ Fri, 26 Jun 2020 10:12:53: 14000000 INFO @ Fri, 26 Jun 2020 10:12:56: 10000000 INFO @ Fri, 26 Jun 2020 10:12:59: 23000000 INFO @ Fri, 26 Jun 2020 10:13:01: 15000000 INFO @ Fri, 26 Jun 2020 10:13:04: 11000000 INFO @ Fri, 26 Jun 2020 10:13:05: 24000000 INFO @ Fri, 26 Jun 2020 10:13:08: 16000000 INFO @ Fri, 26 Jun 2020 10:13:11: 12000000 INFO @ Fri, 26 Jun 2020 10:13:12: 25000000 INFO @ Fri, 26 Jun 2020 10:13:16: 17000000 INFO @ Fri, 26 Jun 2020 10:13:18: 26000000 INFO @ Fri, 26 Jun 2020 10:13:19: 13000000 INFO @ Fri, 26 Jun 2020 10:13:24: 18000000 INFO @ Fri, 26 Jun 2020 10:13:24: 27000000 INFO @ Fri, 26 Jun 2020 10:13:27: 14000000 INFO @ Fri, 26 Jun 2020 10:13:31: 28000000 INFO @ Fri, 26 Jun 2020 10:13:31: 19000000 INFO @ Fri, 26 Jun 2020 10:13:34: 15000000 INFO @ Fri, 26 Jun 2020 10:13:37: 29000000 INFO @ Fri, 26 Jun 2020 10:13:39: 20000000 INFO @ Fri, 26 Jun 2020 10:13:42: 16000000 INFO @ Fri, 26 Jun 2020 10:13:43: 30000000 INFO @ Fri, 26 Jun 2020 10:13:46: 21000000 INFO @ Fri, 26 Jun 2020 10:13:47: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:13:47: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:13:47: #1 total tags in treatment: 14780030 INFO @ Fri, 26 Jun 2020 10:13:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:13:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 10:13:47: #1 tags after filtering in treatment: 13048147 INFO @ Fri, 26 Jun 2020 10:13:47: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 10:13:47: #1 finished! INFO @ Fri, 26 Jun 2020 10:13:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:13:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:13:48: #2 number of paired peaks: 4090 INFO @ Fri, 26 Jun 2020 10:13:48: start model_add_line... INFO @ Fri, 26 Jun 2020 10:13:48: start X-correlation... INFO @ Fri, 26 Jun 2020 10:13:48: end of X-cor INFO @ Fri, 26 Jun 2020 10:13:48: #2 finished! INFO @ Fri, 26 Jun 2020 10:13:48: #2 predicted fragment length is 170 bps INFO @ Fri, 26 Jun 2020 10:13:48: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 26 Jun 2020 10:13:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.05_model.r INFO @ Fri, 26 Jun 2020 10:13:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:13:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:13:49: 17000000 INFO @ Fri, 26 Jun 2020 10:13:54: 22000000 INFO @ Fri, 26 Jun 2020 10:13:56: 18000000 INFO @ Fri, 26 Jun 2020 10:14:01: 23000000 INFO @ Fri, 26 Jun 2020 10:14:04: 19000000 INFO @ Fri, 26 Jun 2020 10:14:09: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:14:11: 20000000 INFO @ Fri, 26 Jun 2020 10:14:16: 25000000 INFO @ Fri, 26 Jun 2020 10:14:18: 21000000 INFO @ Fri, 26 Jun 2020 10:14:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:14:23: 26000000 INFO @ Fri, 26 Jun 2020 10:14:26: 22000000 INFO @ Fri, 26 Jun 2020 10:14:31: 27000000 INFO @ Fri, 26 Jun 2020 10:14:33: 23000000 INFO @ Fri, 26 Jun 2020 10:14:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:14:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:14:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.05_summits.bed INFO @ Fri, 26 Jun 2020 10:14:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10885 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:14:38: 28000000 INFO @ Fri, 26 Jun 2020 10:14:40: 24000000 INFO @ Fri, 26 Jun 2020 10:14:45: 29000000 INFO @ Fri, 26 Jun 2020 10:14:47: 25000000 INFO @ Fri, 26 Jun 2020 10:14:53: 30000000 INFO @ Fri, 26 Jun 2020 10:14:54: 26000000 INFO @ Fri, 26 Jun 2020 10:14:57: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:14:57: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:14:57: #1 total tags in treatment: 14780030 INFO @ Fri, 26 Jun 2020 10:14:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:14:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 10:14:57: #1 tags after filtering in treatment: 13048147 INFO @ Fri, 26 Jun 2020 10:14:57: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 10:14:57: #1 finished! INFO @ Fri, 26 Jun 2020 10:14:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:14:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:14:58: #2 number of paired peaks: 4090 INFO @ Fri, 26 Jun 2020 10:14:58: start model_add_line... INFO @ Fri, 26 Jun 2020 10:14:59: start X-correlation... INFO @ Fri, 26 Jun 2020 10:14:59: end of X-cor INFO @ Fri, 26 Jun 2020 10:14:59: #2 finished! INFO @ Fri, 26 Jun 2020 10:14:59: #2 predicted fragment length is 170 bps INFO @ Fri, 26 Jun 2020 10:14:59: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 26 Jun 2020 10:14:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.10_model.r INFO @ Fri, 26 Jun 2020 10:14:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:14:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:15:01: 27000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:15:08: 28000000 INFO @ Fri, 26 Jun 2020 10:15:16: 29000000 INFO @ Fri, 26 Jun 2020 10:15:23: 30000000 INFO @ Fri, 26 Jun 2020 10:15:27: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:15:27: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:15:27: #1 total tags in treatment: 14780030 INFO @ Fri, 26 Jun 2020 10:15:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:15:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 10:15:27: #1 tags after filtering in treatment: 13048147 INFO @ Fri, 26 Jun 2020 10:15:27: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 10:15:27: #1 finished! INFO @ Fri, 26 Jun 2020 10:15:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:15:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:15:28: #2 number of paired peaks: 4090 INFO @ Fri, 26 Jun 2020 10:15:28: start model_add_line... INFO @ Fri, 26 Jun 2020 10:15:28: start X-correlation... INFO @ Fri, 26 Jun 2020 10:15:28: end of X-cor INFO @ Fri, 26 Jun 2020 10:15:28: #2 finished! INFO @ Fri, 26 Jun 2020 10:15:28: #2 predicted fragment length is 170 bps INFO @ Fri, 26 Jun 2020 10:15:28: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 26 Jun 2020 10:15:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.20_model.r INFO @ Fri, 26 Jun 2020 10:15:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:15:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:15:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:15:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:15:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.10_summits.bed INFO @ Fri, 26 Jun 2020 10:15:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7443 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:16:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:16:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:16:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:16:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749055/SRX749055.20_summits.bed INFO @ Fri, 26 Jun 2020 10:16:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3549 records, 4 fields): 6 millis CompletedMACS2peakCalling