Job ID = 6456224 SRX = SRX331380 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:35:44 prefetch.2.10.7: 1) Downloading 'SRR947617'... 2020-06-21T10:35:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:38:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:38:10 prefetch.2.10.7: 'SRR947617' is valid 2020-06-21T10:38:10 prefetch.2.10.7: 1) 'SRR947617' was downloaded successfully Read 12734840 spots for SRR947617/SRR947617.sra Written 12734840 spots for SRR947617/SRR947617.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: 00:02:59 12734840 reads; of these: 12734840 (100.00%) were unpaired; of these: 949265 (7.45%) aligned 0 times 9931400 (77.99%) aligned exactly 1 time 1854175 (14.56%) aligned >1 times 92.55% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 1818930 / 11785575 = 0.1543 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 19:45:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.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 19:45:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:26: 1000000 INFO @ Sun, 21 Jun 2020 19:45:32: 2000000 INFO @ Sun, 21 Jun 2020 19:45:38: 3000000 INFO @ Sun, 21 Jun 2020 19:45:44: 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 19:45:49: 5000000 INFO @ Sun, 21 Jun 2020 19:45:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.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 19:45:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:56: 6000000 INFO @ Sun, 21 Jun 2020 19:45:56: 1000000 INFO @ Sun, 21 Jun 2020 19:46:01: 7000000 INFO @ Sun, 21 Jun 2020 19:46:02: 2000000 INFO @ Sun, 21 Jun 2020 19:46:07: 8000000 INFO @ Sun, 21 Jun 2020 19:46:08: 3000000 INFO @ Sun, 21 Jun 2020 19:46:14: 4000000 INFO @ Sun, 21 Jun 2020 19:46:14: 9000000 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 19:46:19: 5000000 INFO @ Sun, 21 Jun 2020 19:46:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.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 19:46:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:46:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:46:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:46:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:46:20: #1 total tags in treatment: 9966645 INFO @ Sun, 21 Jun 2020 19:46:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:46:20: #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 19:46:20: #1 tags after filtering in treatment: 9966634 INFO @ Sun, 21 Jun 2020 19:46:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:46:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:46:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:46:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:46:21: #2 number of paired peaks: 3134 INFO @ Sun, 21 Jun 2020 19:46:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:46:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:46:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:46:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:46:21: #2 predicted fragment length is 233 bps INFO @ Sun, 21 Jun 2020 19:46:21: #2 alternative fragment length(s) may be 4,233 bps INFO @ Sun, 21 Jun 2020 19:46:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.05_model.r INFO @ Sun, 21 Jun 2020 19:46:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:46:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:46:25: 6000000 INFO @ Sun, 21 Jun 2020 19:46:25: 1000000 INFO @ Sun, 21 Jun 2020 19:46:31: 7000000 INFO @ Sun, 21 Jun 2020 19:46:31: 2000000 INFO @ Sun, 21 Jun 2020 19:46:37: 8000000 INFO @ Sun, 21 Jun 2020 19:46:37: 3000000 INFO @ Sun, 21 Jun 2020 19:46:43: 9000000 INFO @ Sun, 21 Jun 2020 19:46:43: 4000000 INFO @ Sun, 21 Jun 2020 19:46:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:46:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:46:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:46:49: #1 total tags in treatment: 9966645 INFO @ Sun, 21 Jun 2020 19:46:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:46:49: #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 19:46:49: 5000000 INFO @ Sun, 21 Jun 2020 19:46:50: #1 tags after filtering in treatment: 9966634 INFO @ Sun, 21 Jun 2020 19:46:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:46:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:46:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:46:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:46:51: #2 number of paired peaks: 3134 INFO @ Sun, 21 Jun 2020 19:46:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:46:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:46:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:46:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:46:51: #2 predicted fragment length is 233 bps INFO @ Sun, 21 Jun 2020 19:46:51: #2 alternative fragment length(s) may be 4,233 bps INFO @ Sun, 21 Jun 2020 19:46:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.10_model.r INFO @ Sun, 21 Jun 2020 19:46:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:46:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:46:55: 6000000 INFO @ Sun, 21 Jun 2020 19:47:00: 7000000 INFO @ Sun, 21 Jun 2020 19:47:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.05_summits.bed INFO @ Sun, 21 Jun 2020 19:47:01: Done! pass1 - making usageList (395 chroms): 1 millis pass2 - checking and writing primary data (1129 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:47:06: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:47:12: 9000000 INFO @ Sun, 21 Jun 2020 19:47:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:47:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:47:17: #1 total tags in treatment: 9966645 INFO @ Sun, 21 Jun 2020 19:47:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:17: #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 19:47:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:47:18: #1 tags after filtering in treatment: 9966634 INFO @ Sun, 21 Jun 2020 19:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:19: #2 number of paired peaks: 3134 INFO @ Sun, 21 Jun 2020 19:47:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:19: #2 predicted fragment length is 233 bps INFO @ Sun, 21 Jun 2020 19:47:19: #2 alternative fragment length(s) may be 4,233 bps INFO @ Sun, 21 Jun 2020 19:47:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.20_model.r INFO @ Sun, 21 Jun 2020 19:47:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.10_summits.bed INFO @ Sun, 21 Jun 2020 19:47:29: Done! pass1 - making usageList (238 chroms): 1 millis pass2 - checking and writing primary data (517 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:47:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:47:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331380/SRX331380.20_summits.bed INFO @ Sun, 21 Jun 2020 19:47:57: Done! pass1 - making usageList (132 chroms): 1 millis pass2 - checking and writing primary data (223 records, 4 fields): 5 millis CompletedMACS2peakCalling