Job ID = 6452994 SRX = SRX089333 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:57:15 prefetch.2.10.7: 1) Downloading 'SRR327604'... 2020-06-21T07:57:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:59:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:59:31 prefetch.2.10.7: 1) 'SRR327604' was downloaded successfully Read 33442200 spots for SRR327604/SRR327604.sra Written 33442200 spots for SRR327604/SRR327604.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: 00:05:31 33442200 reads; of these: 33442200 (100.00%) were unpaired; of these: 11031258 (32.99%) aligned 0 times 17733914 (53.03%) aligned exactly 1 time 4677028 (13.99%) aligned >1 times 67.01% overall alignment rate Time searching: 00:05:31 Overall time: 00:05:31 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] 6356626 / 22410942 = 0.2836 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 17:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.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 17:11:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:11:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:11:10: 1000000 INFO @ Sun, 21 Jun 2020 17:11:15: 2000000 INFO @ Sun, 21 Jun 2020 17:11:21: 3000000 INFO @ Sun, 21 Jun 2020 17:11:26: 4000000 INFO @ Sun, 21 Jun 2020 17:11:32: 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 17:11:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.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 17:11:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:11:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:11:38: 6000000 INFO @ Sun, 21 Jun 2020 17:11:41: 1000000 INFO @ Sun, 21 Jun 2020 17:11:44: 7000000 INFO @ Sun, 21 Jun 2020 17:11:47: 2000000 INFO @ Sun, 21 Jun 2020 17:11:50: 8000000 INFO @ Sun, 21 Jun 2020 17:11:53: 3000000 INFO @ Sun, 21 Jun 2020 17:11:57: 9000000 INFO @ Sun, 21 Jun 2020 17:12:00: 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 17:12:03: 10000000 INFO @ Sun, 21 Jun 2020 17:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.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 17:12:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:12:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:12:06: 5000000 INFO @ Sun, 21 Jun 2020 17:12:09: 11000000 INFO @ Sun, 21 Jun 2020 17:12:11: 1000000 INFO @ Sun, 21 Jun 2020 17:12:12: 6000000 INFO @ Sun, 21 Jun 2020 17:12:16: 12000000 INFO @ Sun, 21 Jun 2020 17:12:17: 2000000 INFO @ Sun, 21 Jun 2020 17:12:19: 7000000 INFO @ Sun, 21 Jun 2020 17:12:22: 13000000 INFO @ Sun, 21 Jun 2020 17:12:23: 3000000 INFO @ Sun, 21 Jun 2020 17:12:25: 8000000 INFO @ Sun, 21 Jun 2020 17:12:29: 14000000 INFO @ Sun, 21 Jun 2020 17:12:30: 4000000 INFO @ Sun, 21 Jun 2020 17:12:31: 9000000 INFO @ Sun, 21 Jun 2020 17:12:35: 15000000 INFO @ Sun, 21 Jun 2020 17:12:36: 5000000 INFO @ Sun, 21 Jun 2020 17:12:38: 10000000 INFO @ Sun, 21 Jun 2020 17:12:42: 16000000 INFO @ Sun, 21 Jun 2020 17:12:42: #1 tag size is determined as 38 bps INFO @ Sun, 21 Jun 2020 17:12:42: #1 tag size = 38 INFO @ Sun, 21 Jun 2020 17:12:42: #1 total tags in treatment: 16054316 INFO @ Sun, 21 Jun 2020 17:12:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:12:42: #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 17:12:43: 6000000 INFO @ Sun, 21 Jun 2020 17:12:43: #1 tags after filtering in treatment: 16054213 INFO @ Sun, 21 Jun 2020 17:12:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:12:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:12:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:12:44: #2 number of paired peaks: 1969 INFO @ Sun, 21 Jun 2020 17:12:44: start model_add_line... INFO @ Sun, 21 Jun 2020 17:12:44: start X-correlation... INFO @ Sun, 21 Jun 2020 17:12:44: end of X-cor INFO @ Sun, 21 Jun 2020 17:12:44: #2 finished! INFO @ Sun, 21 Jun 2020 17:12:44: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 17:12:44: #2 alternative fragment length(s) may be 88 bps INFO @ Sun, 21 Jun 2020 17:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.05_model.r INFO @ Sun, 21 Jun 2020 17:12:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:12:44: 11000000 INFO @ Sun, 21 Jun 2020 17:12:49: 7000000 INFO @ Sun, 21 Jun 2020 17:12:50: 12000000 INFO @ Sun, 21 Jun 2020 17:12:55: 8000000 INFO @ Sun, 21 Jun 2020 17:12:57: 13000000 INFO @ Sun, 21 Jun 2020 17:13:01: 9000000 INFO @ Sun, 21 Jun 2020 17:13:03: 14000000 INFO @ Sun, 21 Jun 2020 17:13:08: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:13:10: 15000000 INFO @ Sun, 21 Jun 2020 17:13:14: 11000000 INFO @ Sun, 21 Jun 2020 17:13:16: 16000000 INFO @ Sun, 21 Jun 2020 17:13:17: #1 tag size is determined as 38 bps INFO @ Sun, 21 Jun 2020 17:13:17: #1 tag size = 38 INFO @ Sun, 21 Jun 2020 17:13:17: #1 total tags in treatment: 16054316 INFO @ Sun, 21 Jun 2020 17:13:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:13:17: #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 17:13:17: #1 tags after filtering in treatment: 16054213 INFO @ Sun, 21 Jun 2020 17:13:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:13:17: #1 finished! INFO @ Sun, 21 Jun 2020 17:13:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:13:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:13:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:13:18: #2 number of paired peaks: 1969 INFO @ Sun, 21 Jun 2020 17:13:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:13:19: start X-correlation... INFO @ Sun, 21 Jun 2020 17:13:19: end of X-cor INFO @ Sun, 21 Jun 2020 17:13:19: #2 finished! INFO @ Sun, 21 Jun 2020 17:13:19: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 17:13:19: #2 alternative fragment length(s) may be 88 bps INFO @ Sun, 21 Jun 2020 17:13:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.10_model.r INFO @ Sun, 21 Jun 2020 17:13:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:13:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:13:20: 12000000 INFO @ Sun, 21 Jun 2020 17:13:26: 13000000 INFO @ Sun, 21 Jun 2020 17:13:32: 14000000 INFO @ Sun, 21 Jun 2020 17:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.05_summits.bed INFO @ Sun, 21 Jun 2020 17:13:35: Done! pass1 - making usageList (248 chroms): 2 millis pass2 - checking and writing primary data (13081 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:13:38: 15000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:13:43: 16000000 INFO @ Sun, 21 Jun 2020 17:13:44: #1 tag size is determined as 38 bps INFO @ Sun, 21 Jun 2020 17:13:44: #1 tag size = 38 INFO @ Sun, 21 Jun 2020 17:13:44: #1 total tags in treatment: 16054316 INFO @ Sun, 21 Jun 2020 17:13:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:13:44: #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 17:13:44: #1 tags after filtering in treatment: 16054213 INFO @ Sun, 21 Jun 2020 17:13:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:13:44: #1 finished! INFO @ Sun, 21 Jun 2020 17:13:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:13:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:13:45: #2 number of paired peaks: 1969 INFO @ Sun, 21 Jun 2020 17:13:45: start model_add_line... INFO @ Sun, 21 Jun 2020 17:13:46: start X-correlation... INFO @ Sun, 21 Jun 2020 17:13:46: end of X-cor INFO @ Sun, 21 Jun 2020 17:13:46: #2 finished! INFO @ Sun, 21 Jun 2020 17:13:46: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 17:13:46: #2 alternative fragment length(s) may be 88 bps INFO @ Sun, 21 Jun 2020 17:13:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.20_model.r INFO @ Sun, 21 Jun 2020 17:13:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:13:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:14:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:14:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:14:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.10_summits.bed INFO @ Sun, 21 Jun 2020 17:14:10: Done! pass1 - making usageList (211 chroms): 1 millis pass2 - checking and writing primary data (8468 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:14:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:14:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:14:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:14:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX089333/SRX089333.20_summits.bed INFO @ Sun, 21 Jun 2020 17:14:37: Done! pass1 - making usageList (160 chroms): 2 millis pass2 - checking and writing primary data (4044 records, 4 fields): 8 millis CompletedMACS2peakCalling