Job ID = 6453162 SRX = SRX104977 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:16:03 prefetch.2.10.7: 1) Downloading 'SRR363421'... 2020-06-21T08:16:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:18:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:18:18 prefetch.2.10.7: 'SRR363421' is valid 2020-06-21T08:18:18 prefetch.2.10.7: 1) 'SRR363421' was downloaded successfully Read 22856531 spots for SRR363421/SRR363421.sra Written 22856531 spots for SRR363421/SRR363421.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: 00:04:35 22856531 reads; of these: 22856531 (100.00%) were unpaired; of these: 790586 (3.46%) aligned 0 times 17308343 (75.73%) aligned exactly 1 time 4757602 (20.82%) aligned >1 times 96.54% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:35 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] 6176478 / 22065945 = 0.2799 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 17:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.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 17:28:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:12: 1000000 INFO @ Sun, 21 Jun 2020 17:28:17: 2000000 INFO @ Sun, 21 Jun 2020 17:28:21: 3000000 INFO @ Sun, 21 Jun 2020 17:28:26: 4000000 INFO @ Sun, 21 Jun 2020 17:28:31: 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 17:28:35: 6000000 INFO @ Sun, 21 Jun 2020 17:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.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 17:28:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:40: 7000000 INFO @ Sun, 21 Jun 2020 17:28:42: 1000000 INFO @ Sun, 21 Jun 2020 17:28:46: 8000000 INFO @ Sun, 21 Jun 2020 17:28:47: 2000000 INFO @ Sun, 21 Jun 2020 17:28:51: 9000000 INFO @ Sun, 21 Jun 2020 17:28:53: 3000000 INFO @ Sun, 21 Jun 2020 17:28:56: 10000000 INFO @ Sun, 21 Jun 2020 17:28:58: 4000000 INFO @ Sun, 21 Jun 2020 17:29:01: 11000000 INFO @ Sun, 21 Jun 2020 17:29:03: 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 17:29:06: 12000000 INFO @ Sun, 21 Jun 2020 17:29:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.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 17:29:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:29:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:29:08: 6000000 INFO @ Sun, 21 Jun 2020 17:29:11: 13000000 INFO @ Sun, 21 Jun 2020 17:29:12: 1000000 INFO @ Sun, 21 Jun 2020 17:29:14: 7000000 INFO @ Sun, 21 Jun 2020 17:29:16: 14000000 INFO @ Sun, 21 Jun 2020 17:29:18: 2000000 INFO @ Sun, 21 Jun 2020 17:29:19: 8000000 INFO @ Sun, 21 Jun 2020 17:29:21: 15000000 INFO @ Sun, 21 Jun 2020 17:29:23: 3000000 INFO @ Sun, 21 Jun 2020 17:29:24: 9000000 INFO @ Sun, 21 Jun 2020 17:29:26: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:29:26: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:29:26: #1 total tags in treatment: 15889467 INFO @ Sun, 21 Jun 2020 17:29:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:26: #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 17:29:27: #1 tags after filtering in treatment: 15889458 INFO @ Sun, 21 Jun 2020 17:29:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:29:28: 4000000 INFO @ Sun, 21 Jun 2020 17:29:28: #2 number of paired peaks: 1640 INFO @ Sun, 21 Jun 2020 17:29:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:28: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 17:29:28: #2 alternative fragment length(s) may be 127,595 bps INFO @ Sun, 21 Jun 2020 17:29:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.05_model.r INFO @ Sun, 21 Jun 2020 17:29:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:30: 10000000 INFO @ Sun, 21 Jun 2020 17:29:33: 5000000 INFO @ Sun, 21 Jun 2020 17:29:35: 11000000 INFO @ Sun, 21 Jun 2020 17:29:38: 6000000 INFO @ Sun, 21 Jun 2020 17:29:40: 12000000 INFO @ Sun, 21 Jun 2020 17:29:43: 7000000 INFO @ Sun, 21 Jun 2020 17:29:45: 13000000 INFO @ Sun, 21 Jun 2020 17:29:48: 8000000 INFO @ Sun, 21 Jun 2020 17:29:51: 14000000 INFO @ Sun, 21 Jun 2020 17:29:54: 9000000 INFO @ Sun, 21 Jun 2020 17:29:56: 15000000 INFO @ Sun, 21 Jun 2020 17:29:59: 10000000 INFO @ Sun, 21 Jun 2020 17:30:00: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:30:00: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:30:00: #1 total tags in treatment: 15889467 INFO @ Sun, 21 Jun 2020 17:30:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:30:00: #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 17:30:01: #1 tags after filtering in treatment: 15889458 INFO @ Sun, 21 Jun 2020 17:30:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:30:01: #1 finished! INFO @ Sun, 21 Jun 2020 17:30:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:30:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:30:02: #2 number of paired peaks: 1640 INFO @ Sun, 21 Jun 2020 17:30:02: start model_add_line... INFO @ Sun, 21 Jun 2020 17:30:02: start X-correlation... INFO @ Sun, 21 Jun 2020 17:30:02: end of X-cor INFO @ Sun, 21 Jun 2020 17:30:02: #2 finished! INFO @ Sun, 21 Jun 2020 17:30:02: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 17:30:02: #2 alternative fragment length(s) may be 127,595 bps INFO @ Sun, 21 Jun 2020 17:30:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.10_model.r INFO @ Sun, 21 Jun 2020 17:30:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:30:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:30:04: 11000000 INFO @ Sun, 21 Jun 2020 17:30:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:30:09: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:30:14: 13000000 INFO @ Sun, 21 Jun 2020 17:30:18: 14000000 INFO @ Sun, 21 Jun 2020 17:30:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.05_summits.bed INFO @ Sun, 21 Jun 2020 17:30:21: Done! pass1 - making usageList (388 chroms): 2 millis pass2 - checking and writing primary data (10359 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:30:23: 15000000 INFO @ Sun, 21 Jun 2020 17:30:28: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:30:28: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:30:28: #1 total tags in treatment: 15889467 INFO @ Sun, 21 Jun 2020 17:30:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:30:28: #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 17:30:28: #1 tags after filtering in treatment: 15889458 INFO @ Sun, 21 Jun 2020 17:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:30:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:30:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:30:29: #2 number of paired peaks: 1640 INFO @ Sun, 21 Jun 2020 17:30:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:30:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:30:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:30:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:30:29: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 17:30:29: #2 alternative fragment length(s) may be 127,595 bps INFO @ Sun, 21 Jun 2020 17:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.20_model.r INFO @ Sun, 21 Jun 2020 17:30:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:30:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:30:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.10_summits.bed INFO @ Sun, 21 Jun 2020 17:30:55: Done! pass1 - making usageList (290 chroms): 1 millis pass2 - checking and writing primary data (3211 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:31:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104977/SRX104977.20_summits.bed INFO @ Sun, 21 Jun 2020 17:31:20: Done! pass1 - making usageList (200 chroms): 1 millis pass2 - checking and writing primary data (681 records, 4 fields): 8 millis CompletedMACS2peakCalling