Job ID = 6452980 SRX = SRX085401 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:56:45 prefetch.2.10.7: 1) Downloading 'SRR317179'... 2020-06-21T07:56:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:04:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:04:41 prefetch.2.10.7: 1) 'SRR317179' was downloaded successfully Read 33553611 spots for SRR317179/SRR317179.sra Written 33553611 spots for SRR317179/SRR317179.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: 00:06:28 33553611 reads; of these: 33553611 (100.00%) were unpaired; of these: 3330394 (9.93%) aligned 0 times 24259840 (72.30%) aligned exactly 1 time 5963377 (17.77%) aligned >1 times 90.07% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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] 16523382 / 30223217 = 0.5467 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 17:20:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.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 17:20:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:20:58: 1000000 INFO @ Sun, 21 Jun 2020 17:21:03: 2000000 INFO @ Sun, 21 Jun 2020 17:21:08: 3000000 INFO @ Sun, 21 Jun 2020 17:21:14: 4000000 INFO @ Sun, 21 Jun 2020 17:21:19: 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 17:21:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.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 17:21:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:21:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:21:25: 6000000 INFO @ Sun, 21 Jun 2020 17:21:28: 1000000 INFO @ Sun, 21 Jun 2020 17:21:31: 7000000 INFO @ Sun, 21 Jun 2020 17:21:34: 2000000 INFO @ Sun, 21 Jun 2020 17:21:37: 8000000 INFO @ Sun, 21 Jun 2020 17:21:40: 3000000 INFO @ Sun, 21 Jun 2020 17:21:43: 9000000 INFO @ Sun, 21 Jun 2020 17:21:46: 4000000 INFO @ Sun, 21 Jun 2020 17:21:49: 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 @ Sun, 21 Jun 2020 17:21:52: 5000000 INFO @ Sun, 21 Jun 2020 17:21:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.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 17:21:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:21:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:21:56: 11000000 INFO @ Sun, 21 Jun 2020 17:21:58: 6000000 INFO @ Sun, 21 Jun 2020 17:21:59: 1000000 INFO @ Sun, 21 Jun 2020 17:22:03: 12000000 INFO @ Sun, 21 Jun 2020 17:22:04: 7000000 INFO @ Sun, 21 Jun 2020 17:22:05: 2000000 INFO @ Sun, 21 Jun 2020 17:22:09: 13000000 INFO @ Sun, 21 Jun 2020 17:22:11: 8000000 INFO @ Sun, 21 Jun 2020 17:22:11: 3000000 INFO @ Sun, 21 Jun 2020 17:22:14: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:22:14: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:22:14: #1 total tags in treatment: 13699835 INFO @ Sun, 21 Jun 2020 17:22:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:14: #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 17:22:15: #1 tags after filtering in treatment: 13699768 INFO @ Sun, 21 Jun 2020 17:22:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:15: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:16: #2 number of paired peaks: 2648 INFO @ Sun, 21 Jun 2020 17:22:16: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:16: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:17: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:17: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:17: #2 predicted fragment length is 132 bps INFO @ Sun, 21 Jun 2020 17:22:17: #2 alternative fragment length(s) may be 132 bps INFO @ Sun, 21 Jun 2020 17:22:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.05_model.r INFO @ Sun, 21 Jun 2020 17:22:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:22:17: 9000000 INFO @ Sun, 21 Jun 2020 17:22:17: 4000000 INFO @ Sun, 21 Jun 2020 17:22:23: 10000000 INFO @ Sun, 21 Jun 2020 17:22:23: 5000000 INFO @ Sun, 21 Jun 2020 17:22:29: 6000000 INFO @ Sun, 21 Jun 2020 17:22:30: 11000000 INFO @ Sun, 21 Jun 2020 17:22:35: 7000000 INFO @ Sun, 21 Jun 2020 17:22:36: 12000000 INFO @ Sun, 21 Jun 2020 17:22:41: 8000000 INFO @ Sun, 21 Jun 2020 17:22:42: 13000000 INFO @ Sun, 21 Jun 2020 17:22:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:22:46: 9000000 INFO @ Sun, 21 Jun 2020 17:22:47: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:22:47: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:22:47: #1 total tags in treatment: 13699835 INFO @ Sun, 21 Jun 2020 17:22:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:47: #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 17:22:47: #1 tags after filtering in treatment: 13699768 INFO @ Sun, 21 Jun 2020 17:22:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:47: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:49: #2 number of paired peaks: 2648 INFO @ Sun, 21 Jun 2020 17:22:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:49: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:49: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:49: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:49: #2 predicted fragment length is 132 bps INFO @ Sun, 21 Jun 2020 17:22:49: #2 alternative fragment length(s) may be 132 bps INFO @ Sun, 21 Jun 2020 17:22:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.10_model.r INFO @ Sun, 21 Jun 2020 17:22:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:22:52: 10000000 INFO @ Sun, 21 Jun 2020 17:22:58: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:23:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.05_summits.bed INFO @ Sun, 21 Jun 2020 17:23:01: Done! pass1 - making usageList (704 chroms): 3 millis pass2 - checking and writing primary data (11013 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:23:04: 12000000 INFO @ Sun, 21 Jun 2020 17:23:09: 13000000 INFO @ Sun, 21 Jun 2020 17:23:14: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:23:14: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:23:14: #1 total tags in treatment: 13699835 INFO @ Sun, 21 Jun 2020 17:23:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:14: #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 17:23:15: #1 tags after filtering in treatment: 13699768 INFO @ Sun, 21 Jun 2020 17:23:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:15: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:16: #2 number of paired peaks: 2648 INFO @ Sun, 21 Jun 2020 17:23:16: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:16: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:16: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:16: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:16: #2 predicted fragment length is 132 bps INFO @ Sun, 21 Jun 2020 17:23:16: #2 alternative fragment length(s) may be 132 bps INFO @ Sun, 21 Jun 2020 17:23:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.20_model.r INFO @ Sun, 21 Jun 2020 17:23:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:23:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.10_summits.bed INFO @ Sun, 21 Jun 2020 17:23:32: Done! pass1 - making usageList (535 chroms): 2 millis pass2 - checking and writing primary data (7930 records, 4 fields): 38 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:23:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085401/SRX085401.20_summits.bed INFO @ Sun, 21 Jun 2020 17:23:59: Done! pass1 - making usageList (283 chroms): 2 millis pass2 - checking and writing primary data (5539 records, 4 fields): 23 millis CompletedMACS2peakCalling