Job ID = 6452983 SRX = SRX085404 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:53:01 prefetch.2.10.7: 1) Downloading 'SRR317182'... 2020-06-21T07:53:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:55:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:55:29 prefetch.2.10.7: 'SRR317182' is valid 2020-06-21T07:55:29 prefetch.2.10.7: 1) 'SRR317182' was downloaded successfully Read 22527747 spots for SRR317182/SRR317182.sra Written 22527747 spots for SRR317182/SRR317182.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: 00:03:26 22527747 reads; of these: 22527747 (100.00%) were unpaired; of these: 7496310 (33.28%) aligned 0 times 12789427 (56.77%) aligned exactly 1 time 2242010 (9.95%) aligned >1 times 66.72% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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_rmdupse_core] 10020431 / 15031437 = 0.6666 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 17:02:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.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 17:02:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:02:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:02:38: 1000000 INFO @ Sun, 21 Jun 2020 17:02:43: 2000000 INFO @ Sun, 21 Jun 2020 17:02:48: 3000000 INFO @ Sun, 21 Jun 2020 17:02:53: 4000000 INFO @ Sun, 21 Jun 2020 17:02:58: 5000000 INFO @ Sun, 21 Jun 2020 17:02:58: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:02:58: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:02:58: #1 total tags in treatment: 5011006 INFO @ Sun, 21 Jun 2020 17:02:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:02:58: #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 17:02:58: #1 tags after filtering in treatment: 5010872 INFO @ Sun, 21 Jun 2020 17:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:02:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:02:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:02:59: #2 number of paired peaks: 2893 INFO @ Sun, 21 Jun 2020 17:02:59: start model_add_line... INFO @ Sun, 21 Jun 2020 17:02:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:02:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:02:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:02:59: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 17:02:59: #2 alternative fragment length(s) may be 113 bps INFO @ Sun, 21 Jun 2020 17:02:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.05_model.r INFO @ Sun, 21 Jun 2020 17:02:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:02:59: #3 Pre-compute pvalue-qvalue table... 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 17:03:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.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 17:03:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:03:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:03:09: 1000000 INFO @ Sun, 21 Jun 2020 17:03:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:03:13: 2000000 INFO @ Sun, 21 Jun 2020 17:03:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:03:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:03:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.05_summits.bed INFO @ Sun, 21 Jun 2020 17:03:17: Done! pass1 - making usageList (377 chroms): 2 millis pass2 - checking and writing primary data (6169 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:03:18: 3000000 INFO @ Sun, 21 Jun 2020 17:03:23: 4000000 INFO @ Sun, 21 Jun 2020 17:03:28: 5000000 INFO @ Sun, 21 Jun 2020 17:03:28: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:03:28: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:03:28: #1 total tags in treatment: 5011006 INFO @ Sun, 21 Jun 2020 17:03:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:03:28: #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 17:03:29: #1 tags after filtering in treatment: 5010872 INFO @ Sun, 21 Jun 2020 17:03:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:03:29: #1 finished! INFO @ Sun, 21 Jun 2020 17:03:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:03:29: #2 number of paired peaks: 2893 INFO @ Sun, 21 Jun 2020 17:03:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:03:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:03:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:03:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:03:29: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 17:03:29: #2 alternative fragment length(s) may be 113 bps INFO @ Sun, 21 Jun 2020 17:03:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.10_model.r INFO @ Sun, 21 Jun 2020 17:03:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:03:29: #3 Pre-compute pvalue-qvalue table... 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 17:03:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.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 17:03:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:03:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:03:39: 1000000 INFO @ Sun, 21 Jun 2020 17:03:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:03:44: 2000000 INFO @ Sun, 21 Jun 2020 17:03:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:03:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:03:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.10_summits.bed INFO @ Sun, 21 Jun 2020 17:03:47: Done! pass1 - making usageList (240 chroms): 2 millis pass2 - checking and writing primary data (4086 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:03:50: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:03:55: 4000000 INFO @ Sun, 21 Jun 2020 17:04:01: 5000000 INFO @ Sun, 21 Jun 2020 17:04:01: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:04:01: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:04:01: #1 total tags in treatment: 5011006 INFO @ Sun, 21 Jun 2020 17:04:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:04:01: #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 17:04:01: #1 tags after filtering in treatment: 5010872 INFO @ Sun, 21 Jun 2020 17:04:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:04:01: #1 finished! INFO @ Sun, 21 Jun 2020 17:04:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:04:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:04:02: #2 number of paired peaks: 2893 INFO @ Sun, 21 Jun 2020 17:04:02: start model_add_line... INFO @ Sun, 21 Jun 2020 17:04:02: start X-correlation... INFO @ Sun, 21 Jun 2020 17:04:02: end of X-cor INFO @ Sun, 21 Jun 2020 17:04:02: #2 finished! INFO @ Sun, 21 Jun 2020 17:04:02: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 17:04:02: #2 alternative fragment length(s) may be 113 bps INFO @ Sun, 21 Jun 2020 17:04:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.20_model.r INFO @ Sun, 21 Jun 2020 17:04:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:04:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:04:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:04:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:04:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:04:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085404/SRX085404.20_summits.bed INFO @ Sun, 21 Jun 2020 17:04:19: Done! pass1 - making usageList (168 chroms): 1 millis pass2 - checking and writing primary data (2809 records, 4 fields): 8 millis CompletedMACS2peakCalling