Job ID = 6456169 SRX = SRX3279758 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:33:19 prefetch.2.10.7: 1) Downloading 'SRR6168908'... 2020-06-21T10:33:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:37:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:37:54 prefetch.2.10.7: 1) 'SRR6168908' was downloaded successfully 2020-06-21T10:37:54 prefetch.2.10.7: 'SRR6168908' has 0 unresolved dependencies Read 28004200 spots for SRR6168908/SRR6168908.sra Written 28004200 spots for SRR6168908/SRR6168908.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: 00:08:47 28004200 reads; of these: 28004200 (100.00%) were unpaired; of these: 432996 (1.55%) aligned 0 times 25556181 (91.26%) aligned exactly 1 time 2015023 (7.20%) aligned >1 times 98.45% overall alignment rate Time searching: 00:08:47 Overall time: 00:08:47 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] 9961588 / 27571204 = 0.3613 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 19:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.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 19:56:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:44: 1000000 INFO @ Sun, 21 Jun 2020 19:56:50: 2000000 INFO @ Sun, 21 Jun 2020 19:56:56: 3000000 INFO @ Sun, 21 Jun 2020 19:57:02: 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 19:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.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 19:57:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:08: 5000000 INFO @ Sun, 21 Jun 2020 19:57:15: 1000000 INFO @ Sun, 21 Jun 2020 19:57:15: 6000000 INFO @ Sun, 21 Jun 2020 19:57:21: 7000000 INFO @ Sun, 21 Jun 2020 19:57:21: 2000000 INFO @ Sun, 21 Jun 2020 19:57:28: 8000000 INFO @ Sun, 21 Jun 2020 19:57:28: 3000000 INFO @ Sun, 21 Jun 2020 19:57:35: 9000000 INFO @ Sun, 21 Jun 2020 19:57:35: 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 19:57:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.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 19:57:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:42: 10000000 INFO @ Sun, 21 Jun 2020 19:57:42: 5000000 INFO @ Sun, 21 Jun 2020 19:57:47: 1000000 INFO @ Sun, 21 Jun 2020 19:57:49: 11000000 INFO @ Sun, 21 Jun 2020 19:57:49: 6000000 INFO @ Sun, 21 Jun 2020 19:57:55: 2000000 INFO @ Sun, 21 Jun 2020 19:57:56: 12000000 INFO @ Sun, 21 Jun 2020 19:57:56: 7000000 INFO @ Sun, 21 Jun 2020 19:58:03: 3000000 INFO @ Sun, 21 Jun 2020 19:58:03: 13000000 INFO @ Sun, 21 Jun 2020 19:58:04: 8000000 INFO @ Sun, 21 Jun 2020 19:58:11: 14000000 INFO @ Sun, 21 Jun 2020 19:58:11: 9000000 INFO @ Sun, 21 Jun 2020 19:58:12: 4000000 INFO @ Sun, 21 Jun 2020 19:58:18: 10000000 INFO @ Sun, 21 Jun 2020 19:58:18: 15000000 INFO @ Sun, 21 Jun 2020 19:58:20: 5000000 INFO @ Sun, 21 Jun 2020 19:58:25: 11000000 INFO @ Sun, 21 Jun 2020 19:58:25: 16000000 INFO @ Sun, 21 Jun 2020 19:58:29: 6000000 INFO @ Sun, 21 Jun 2020 19:58:32: 12000000 INFO @ Sun, 21 Jun 2020 19:58:33: 17000000 INFO @ Sun, 21 Jun 2020 19:58:37: 7000000 INFO @ Sun, 21 Jun 2020 19:58:37: #1 tag size is determined as 79 bps INFO @ Sun, 21 Jun 2020 19:58:37: #1 tag size = 79 INFO @ Sun, 21 Jun 2020 19:58:37: #1 total tags in treatment: 17609616 INFO @ Sun, 21 Jun 2020 19:58:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:37: #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 19:58:38: #1 tags after filtering in treatment: 17609385 INFO @ Sun, 21 Jun 2020 19:58:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:40: 13000000 INFO @ Sun, 21 Jun 2020 19:58:40: #2 number of paired peaks: 14586 INFO @ Sun, 21 Jun 2020 19:58:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:40: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 19:58:40: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 19:58:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.05_model.r INFO @ Sun, 21 Jun 2020 19:58:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:58:45: 8000000 INFO @ Sun, 21 Jun 2020 19:58:47: 14000000 INFO @ Sun, 21 Jun 2020 19:58:53: 9000000 INFO @ Sun, 21 Jun 2020 19:58:54: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:59:01: 16000000 INFO @ Sun, 21 Jun 2020 19:59:02: 10000000 INFO @ Sun, 21 Jun 2020 19:59:09: 17000000 INFO @ Sun, 21 Jun 2020 19:59:09: 11000000 INFO @ Sun, 21 Jun 2020 19:59:13: #1 tag size is determined as 79 bps INFO @ Sun, 21 Jun 2020 19:59:13: #1 tag size = 79 INFO @ Sun, 21 Jun 2020 19:59:13: #1 total tags in treatment: 17609616 INFO @ Sun, 21 Jun 2020 19:59:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:59:13: #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 19:59:14: #1 tags after filtering in treatment: 17609385 INFO @ Sun, 21 Jun 2020 19:59:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:59:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:59:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:59:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:59:16: #2 number of paired peaks: 14586 INFO @ Sun, 21 Jun 2020 19:59:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:59:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:59:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:59:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:59:16: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 19:59:16: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 19:59:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.10_model.r INFO @ Sun, 21 Jun 2020 19:59:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:59:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:59:17: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:59:25: 13000000 INFO @ Sun, 21 Jun 2020 19:59:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:59:33: 14000000 INFO @ Sun, 21 Jun 2020 19:59:41: 15000000 INFO @ Sun, 21 Jun 2020 19:59:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:59:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:59:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.05_summits.bed INFO @ Sun, 21 Jun 2020 19:59:43: Done! pass1 - making usageList (163 chroms): 2 millis pass2 - checking and writing primary data (8611 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:59:48: 16000000 INFO @ Sun, 21 Jun 2020 19:59:56: 17000000 INFO @ Sun, 21 Jun 2020 20:00:00: #1 tag size is determined as 79 bps INFO @ Sun, 21 Jun 2020 20:00:00: #1 tag size = 79 INFO @ Sun, 21 Jun 2020 20:00:00: #1 total tags in treatment: 17609616 INFO @ Sun, 21 Jun 2020 20:00:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:00: #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 20:00:01: #1 tags after filtering in treatment: 17609385 INFO @ Sun, 21 Jun 2020 20:00:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:01: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:00:03: #2 number of paired peaks: 14586 INFO @ Sun, 21 Jun 2020 20:00:03: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:04: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:04: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:04: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:04: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 20:00:04: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 20:00:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.20_model.r INFO @ Sun, 21 Jun 2020 20:00:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:00:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:00:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.10_summits.bed INFO @ Sun, 21 Jun 2020 20:00:20: Done! pass1 - making usageList (116 chroms): 2 millis pass2 - checking and writing primary data (8093 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:00:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:01:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:01:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:01:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3279758/SRX3279758.20_summits.bed INFO @ Sun, 21 Jun 2020 20:01:11: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (7499 records, 4 fields): 13 millis CompletedMACS2peakCalling