Job ID = 6457917 SRX = SRX485219 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:08:40 prefetch.2.10.7: 1) Downloading 'SRR1187977'... 2020-06-21T12:08:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:12:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:12:11 prefetch.2.10.7: 1) 'SRR1187977' was downloaded successfully 2020-06-21T12:12:11 prefetch.2.10.7: 'SRR1187977' has 0 unresolved dependencies Read 28181672 spots for SRR1187977/SRR1187977.sra Written 28181672 spots for SRR1187977/SRR1187977.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: 00:05:47 28181672 reads; of these: 28181672 (100.00%) were unpaired; of these: 2051890 (7.28%) aligned 0 times 23685425 (84.05%) aligned exactly 1 time 2444357 (8.67%) aligned >1 times 92.72% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 11854859 / 26129782 = 0.4537 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 21:25:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.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 21:25:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:25:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:25:08: 1000000 INFO @ Sun, 21 Jun 2020 21:25:13: 2000000 INFO @ Sun, 21 Jun 2020 21:25:18: 3000000 INFO @ Sun, 21 Jun 2020 21:25:23: 4000000 INFO @ Sun, 21 Jun 2020 21:25:28: 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 21:25:33: 6000000 INFO @ Sun, 21 Jun 2020 21:25:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.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 21:25:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:25:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:25:38: 7000000 INFO @ Sun, 21 Jun 2020 21:25:38: 1000000 INFO @ Sun, 21 Jun 2020 21:25:43: 8000000 INFO @ Sun, 21 Jun 2020 21:25:43: 2000000 INFO @ Sun, 21 Jun 2020 21:25:48: 9000000 INFO @ Sun, 21 Jun 2020 21:25:48: 3000000 INFO @ Sun, 21 Jun 2020 21:25:53: 10000000 INFO @ Sun, 21 Jun 2020 21:25:53: 4000000 INFO @ Sun, 21 Jun 2020 21:25:58: 11000000 INFO @ Sun, 21 Jun 2020 21:25:58: 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 21:26:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.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 21:26:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:03: 6000000 INFO @ Sun, 21 Jun 2020 21:26:04: 12000000 INFO @ Sun, 21 Jun 2020 21:26:08: 1000000 INFO @ Sun, 21 Jun 2020 21:26:09: 7000000 INFO @ Sun, 21 Jun 2020 21:26:09: 13000000 INFO @ Sun, 21 Jun 2020 21:26:14: 2000000 INFO @ Sun, 21 Jun 2020 21:26:14: 8000000 INFO @ Sun, 21 Jun 2020 21:26:14: 14000000 INFO @ Sun, 21 Jun 2020 21:26:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:26:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:26:16: #1 total tags in treatment: 14274923 INFO @ Sun, 21 Jun 2020 21:26:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:26:16: #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 21:26:16: #1 tags after filtering in treatment: 14274752 INFO @ Sun, 21 Jun 2020 21:26:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:26:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:26:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:26:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:26:18: #2 number of paired peaks: 8165 INFO @ Sun, 21 Jun 2020 21:26:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:26:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:26:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:26:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:26:18: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 21:26:18: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 21:26:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.05_model.r INFO @ Sun, 21 Jun 2020 21:26:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:26:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:26:19: 3000000 INFO @ Sun, 21 Jun 2020 21:26:19: 9000000 INFO @ Sun, 21 Jun 2020 21:26:24: 4000000 INFO @ Sun, 21 Jun 2020 21:26:24: 10000000 INFO @ Sun, 21 Jun 2020 21:26:29: 5000000 INFO @ Sun, 21 Jun 2020 21:26:30: 11000000 INFO @ Sun, 21 Jun 2020 21:26:34: 6000000 INFO @ Sun, 21 Jun 2020 21:26:35: 12000000 INFO @ Sun, 21 Jun 2020 21:26:39: 7000000 INFO @ Sun, 21 Jun 2020 21:26:40: 13000000 INFO @ Sun, 21 Jun 2020 21:26:45: 8000000 INFO @ Sun, 21 Jun 2020 21:26:46: 14000000 INFO @ Sun, 21 Jun 2020 21:26:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:26:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:26:47: #1 total tags in treatment: 14274923 INFO @ Sun, 21 Jun 2020 21:26:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:26:47: #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 21:26:48: #1 tags after filtering in treatment: 14274752 INFO @ Sun, 21 Jun 2020 21:26:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:26:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:26:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:26:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:26:49: #2 number of paired peaks: 8165 INFO @ Sun, 21 Jun 2020 21:26:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:26:50: start X-correlation... INFO @ Sun, 21 Jun 2020 21:26:50: end of X-cor INFO @ Sun, 21 Jun 2020 21:26:50: #2 finished! INFO @ Sun, 21 Jun 2020 21:26:50: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 21:26:50: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 21:26:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.10_model.r INFO @ Sun, 21 Jun 2020 21:26:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:26:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:26:50: 9000000 INFO @ Sun, 21 Jun 2020 21:26:55: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:27:00: 11000000 INFO @ Sun, 21 Jun 2020 21:27:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:27:06: 12000000 INFO @ Sun, 21 Jun 2020 21:27:11: 13000000 INFO @ Sun, 21 Jun 2020 21:27:16: 14000000 INFO @ Sun, 21 Jun 2020 21:27:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:27:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:27:18: #1 total tags in treatment: 14274923 INFO @ Sun, 21 Jun 2020 21:27:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:27:18: #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 21:27:18: #1 tags after filtering in treatment: 14274752 INFO @ Sun, 21 Jun 2020 21:27:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:27:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:27:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:27:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:27:20: #2 number of paired peaks: 8165 INFO @ Sun, 21 Jun 2020 21:27:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:27:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:27:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:27:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:27:20: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 21:27:20: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 21:27:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.20_model.r INFO @ Sun, 21 Jun 2020 21:27:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:27:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:27:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:27:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:27:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.05_summits.bed INFO @ Sun, 21 Jun 2020 21:27:21: Done! pass1 - making usageList (110 chroms): 2 millis pass2 - checking and writing primary data (8390 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:27:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:27:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:27:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:27:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.10_summits.bed INFO @ Sun, 21 Jun 2020 21:27:55: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (6820 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:28:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:28:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:28:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485219/SRX485219.20_summits.bed INFO @ Sun, 21 Jun 2020 21:28:23: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (5277 records, 4 fields): 8 millis CompletedMACS2peakCalling