Job ID = 6456354 SRX = SRX3380800 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:35:29 prefetch.2.10.7: 1) Downloading 'SRR6278163'... 2020-06-21T10:35:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:39:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:39:05 prefetch.2.10.7: 'SRR6278163' is valid 2020-06-21T10:39:05 prefetch.2.10.7: 1) 'SRR6278163' was downloaded successfully Read 12668505 spots for SRR6278163/SRR6278163.sra Written 12668505 spots for SRR6278163/SRR6278163.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: 00:03:05 12668505 reads; of these: 12668505 (100.00%) were unpaired; of these: 393497 (3.11%) aligned 0 times 9205447 (72.66%) aligned exactly 1 time 3069561 (24.23%) aligned >1 times 96.89% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 2101498 / 12275008 = 0.1712 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 19:46:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.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 19:46:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:46:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:46:16: 1000000 INFO @ Sun, 21 Jun 2020 19:46:20: 2000000 INFO @ Sun, 21 Jun 2020 19:46:25: 3000000 INFO @ Sun, 21 Jun 2020 19:46:30: 4000000 INFO @ Sun, 21 Jun 2020 19:46:35: 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 19:46:39: 6000000 INFO @ Sun, 21 Jun 2020 19:46:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.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 19:46:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:46:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:46:44: 7000000 INFO @ Sun, 21 Jun 2020 19:46:46: 1000000 INFO @ Sun, 21 Jun 2020 19:46:49: 8000000 INFO @ Sun, 21 Jun 2020 19:46:51: 2000000 INFO @ Sun, 21 Jun 2020 19:46:55: 9000000 INFO @ Sun, 21 Jun 2020 19:46:56: 3000000 INFO @ Sun, 21 Jun 2020 19:47:00: 10000000 INFO @ Sun, 21 Jun 2020 19:47:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:47:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:47:01: #1 total tags in treatment: 10173510 INFO @ Sun, 21 Jun 2020 19:47:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:01: #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 19:47:01: #1 tags after filtering in treatment: 10173306 INFO @ Sun, 21 Jun 2020 19:47:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:01: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:01: 4000000 INFO @ Sun, 21 Jun 2020 19:47:02: #2 number of paired peaks: 1461 INFO @ Sun, 21 Jun 2020 19:47:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:02: #2 predicted fragment length is 170 bps INFO @ Sun, 21 Jun 2020 19:47:02: #2 alternative fragment length(s) may be 170 bps INFO @ Sun, 21 Jun 2020 19:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.05_model.r INFO @ Sun, 21 Jun 2020 19:47:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:06: 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 19:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.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 19:47:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:11: 6000000 INFO @ Sun, 21 Jun 2020 19:47:16: 1000000 INFO @ Sun, 21 Jun 2020 19:47:16: 7000000 INFO @ Sun, 21 Jun 2020 19:47:21: 2000000 INFO @ Sun, 21 Jun 2020 19:47:21: 8000000 INFO @ Sun, 21 Jun 2020 19:47:26: 3000000 INFO @ Sun, 21 Jun 2020 19:47:27: 9000000 INFO @ Sun, 21 Jun 2020 19:47:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:47:31: 4000000 INFO @ Sun, 21 Jun 2020 19:47:32: 10000000 INFO @ Sun, 21 Jun 2020 19:47:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:47:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:47:33: #1 total tags in treatment: 10173510 INFO @ Sun, 21 Jun 2020 19:47:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:33: #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 19:47:33: #1 tags after filtering in treatment: 10173306 INFO @ Sun, 21 Jun 2020 19:47:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:33: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:34: #2 number of paired peaks: 1461 INFO @ Sun, 21 Jun 2020 19:47:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:34: #2 predicted fragment length is 170 bps INFO @ Sun, 21 Jun 2020 19:47:34: #2 alternative fragment length(s) may be 170 bps INFO @ Sun, 21 Jun 2020 19:47:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.10_model.r INFO @ Sun, 21 Jun 2020 19:47:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:35: 5000000 INFO @ Sun, 21 Jun 2020 19:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.05_summits.bed INFO @ Sun, 21 Jun 2020 19:47:39: Done! pass1 - making usageList (420 chroms): 2 millis pass2 - checking and writing primary data (12614 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:47:40: 6000000 INFO @ Sun, 21 Jun 2020 19:47:45: 7000000 INFO @ Sun, 21 Jun 2020 19:47:50: 8000000 INFO @ Sun, 21 Jun 2020 19:47:55: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:47:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:00: 10000000 INFO @ Sun, 21 Jun 2020 19:48:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:48:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:48:01: #1 total tags in treatment: 10173510 INFO @ Sun, 21 Jun 2020 19:48:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:48:01: #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 19:48:01: #1 tags after filtering in treatment: 10173306 INFO @ Sun, 21 Jun 2020 19:48:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:48:01: #1 finished! INFO @ Sun, 21 Jun 2020 19:48:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:48:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:48:02: #2 number of paired peaks: 1461 INFO @ Sun, 21 Jun 2020 19:48:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:48:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:48:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:48:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:48:02: #2 predicted fragment length is 170 bps INFO @ Sun, 21 Jun 2020 19:48:02: #2 alternative fragment length(s) may be 170 bps INFO @ Sun, 21 Jun 2020 19:48:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.20_model.r INFO @ Sun, 21 Jun 2020 19:48:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:48:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:48:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.10_summits.bed INFO @ Sun, 21 Jun 2020 19:48:11: Done! pass1 - making usageList (277 chroms): 1 millis pass2 - checking and writing primary data (5507 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:48:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380800/SRX3380800.20_summits.bed INFO @ Sun, 21 Jun 2020 19:48:38: Done! pass1 - making usageList (184 chroms): 1 millis pass2 - checking and writing primary data (1980 records, 4 fields): 11 millis CompletedMACS2peakCalling