Job ID = 6458578 SRX = SRX5343114 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:31:55 prefetch.2.10.7: 1) Downloading 'SRR8540814'... 2020-06-21T12:31:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:34:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:34:35 prefetch.2.10.7: 1) 'SRR8540814' was downloaded successfully 2020-06-21T12:34:35 prefetch.2.10.7: 'SRR8540814' has 0 unresolved dependencies Read 24653565 spots for SRR8540814/SRR8540814.sra Written 24653565 spots for SRR8540814/SRR8540814.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: 00:06:41 24653565 reads; of these: 24653565 (100.00%) were unpaired; of these: 5743100 (23.30%) aligned 0 times 15946166 (64.68%) aligned exactly 1 time 2964299 (12.02%) aligned >1 times 76.70% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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] 10774706 / 18910465 = 0.5698 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 21:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.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 21:46:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:51: 1000000 INFO @ Sun, 21 Jun 2020 21:46:57: 2000000 INFO @ Sun, 21 Jun 2020 21:47:03: 3000000 INFO @ Sun, 21 Jun 2020 21:47:10: 4000000 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 21:47:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.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 21:47:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:47:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:47:16: 5000000 INFO @ Sun, 21 Jun 2020 21:47:21: 1000000 INFO @ Sun, 21 Jun 2020 21:47:22: 6000000 INFO @ Sun, 21 Jun 2020 21:47:26: 2000000 INFO @ Sun, 21 Jun 2020 21:47:29: 7000000 INFO @ Sun, 21 Jun 2020 21:47:32: 3000000 INFO @ Sun, 21 Jun 2020 21:47:35: 8000000 INFO @ Sun, 21 Jun 2020 21:47:36: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:47:36: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:47:36: #1 total tags in treatment: 8135759 INFO @ Sun, 21 Jun 2020 21:47:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:36: #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 21:47:37: #1 tags after filtering in treatment: 8135756 INFO @ Sun, 21 Jun 2020 21:47:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:37: 4000000 INFO @ Sun, 21 Jun 2020 21:47:38: #2 number of paired peaks: 7567 INFO @ Sun, 21 Jun 2020 21:47:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:38: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:38: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:38: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 21:47:38: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 21:47:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.05_model.r INFO @ Sun, 21 Jun 2020 21:47:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Sun, 21 Jun 2020 21:47:43: 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 21:47:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.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 21:47:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:47:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:47:48: 6000000 INFO @ Sun, 21 Jun 2020 21:47:51: 1000000 INFO @ Sun, 21 Jun 2020 21:47:54: 7000000 INFO @ Sun, 21 Jun 2020 21:47:57: 2000000 INFO @ Sun, 21 Jun 2020 21:48:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:00: 8000000 INFO @ Sun, 21 Jun 2020 21:48:01: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:48:01: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:48:01: #1 total tags in treatment: 8135759 INFO @ Sun, 21 Jun 2020 21:48:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:48:01: #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 21:48:02: #1 tags after filtering in treatment: 8135756 INFO @ Sun, 21 Jun 2020 21:48:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:48:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:48:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:48:03: #2 number of paired peaks: 7567 INFO @ Sun, 21 Jun 2020 21:48:03: start model_add_line... INFO @ Sun, 21 Jun 2020 21:48:03: start X-correlation... INFO @ Sun, 21 Jun 2020 21:48:03: end of X-cor INFO @ Sun, 21 Jun 2020 21:48:03: #2 finished! INFO @ Sun, 21 Jun 2020 21:48:03: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 21:48:03: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 21:48:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.10_model.r INFO @ Sun, 21 Jun 2020 21:48:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:48:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:48:04: 3000000 INFO @ Sun, 21 Jun 2020 21:48:10: 4000000 INFO @ Sun, 21 Jun 2020 21:48:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.05_summits.bed INFO @ Sun, 21 Jun 2020 21:48:11: Done! pass1 - making usageList (493 chroms): 2 millis pass2 - checking and writing primary data (7834 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:48:16: 5000000 INFO @ Sun, 21 Jun 2020 21:48:22: 6000000 INFO @ Sun, 21 Jun 2020 21:48:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:29: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:48:35: 8000000 INFO @ Sun, 21 Jun 2020 21:48:36: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:48:36: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:48:36: #1 total tags in treatment: 8135759 INFO @ Sun, 21 Jun 2020 21:48:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:48:36: #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 21:48:36: #1 tags after filtering in treatment: 8135756 INFO @ Sun, 21 Jun 2020 21:48:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:48:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:48:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:48:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:48:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.10_summits.bed INFO @ Sun, 21 Jun 2020 21:48:37: Done! pass1 - making usageList (337 chroms): 1 millis pass2 - checking and writing primary data (6834 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:48:37: #2 number of paired peaks: 7567 INFO @ Sun, 21 Jun 2020 21:48:37: start model_add_line... INFO @ Sun, 21 Jun 2020 21:48:37: start X-correlation... INFO @ Sun, 21 Jun 2020 21:48:37: end of X-cor INFO @ Sun, 21 Jun 2020 21:48:37: #2 finished! INFO @ Sun, 21 Jun 2020 21:48:37: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 21:48:37: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 21:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.20_model.r INFO @ Sun, 21 Jun 2020 21:48:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:48:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:48:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:49:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:49:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:49:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343114/SRX5343114.20_summits.bed INFO @ Sun, 21 Jun 2020 21:49:10: Done! pass1 - making usageList (158 chroms): 2 millis pass2 - checking and writing primary data (5345 records, 4 fields): 11 millis CompletedMACS2peakCalling