Job ID = 6454522 SRX = SRX220295 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:36:25 prefetch.2.10.7: 1) Downloading 'SRR653340'... 2020-06-21T09:36:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:41:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:41:54 prefetch.2.10.7: 1) 'SRR653340' was downloaded successfully Read 17006469 spots for SRR653340/SRR653340.sra Written 17006469 spots for SRR653340/SRR653340.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: 00:03:54 17006469 reads; of these: 17006469 (100.00%) were unpaired; of these: 1089607 (6.41%) aligned 0 times 10283272 (60.47%) aligned exactly 1 time 5633590 (33.13%) aligned >1 times 93.59% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 9576128 / 15916862 = 0.6016 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 18:50:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.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 18:50:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:31: 1000000 INFO @ Sun, 21 Jun 2020 18:50:37: 2000000 INFO @ Sun, 21 Jun 2020 18:50:43: 3000000 INFO @ Sun, 21 Jun 2020 18:50:49: 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 18:50:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.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 18:50:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:56: 5000000 INFO @ Sun, 21 Jun 2020 18:51:02: 1000000 INFO @ Sun, 21 Jun 2020 18:51:03: 6000000 INFO @ Sun, 21 Jun 2020 18:51:05: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:51:05: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:51:05: #1 total tags in treatment: 6340734 INFO @ Sun, 21 Jun 2020 18:51:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:05: #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 18:51:06: #1 tags after filtering in treatment: 6340692 INFO @ Sun, 21 Jun 2020 18:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:06: #2 number of paired peaks: 3151 INFO @ Sun, 21 Jun 2020 18:51:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:06: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 18:51:06: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sun, 21 Jun 2020 18:51:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.05_model.r INFO @ Sun, 21 Jun 2020 18:51:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:08: 2000000 INFO @ Sun, 21 Jun 2020 18:51:14: 3000000 INFO @ Sun, 21 Jun 2020 18:51:20: 4000000 INFO @ Sun, 21 Jun 2020 18:51:21: #3 Call peaks for each chromosome... 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 18:51:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.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 18:51:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:28: 5000000 INFO @ Sun, 21 Jun 2020 18:51:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.05_summits.bed INFO @ Sun, 21 Jun 2020 18:51:29: Done! pass1 - making usageList (949 chroms): 2 millis pass2 - checking and writing primary data (3930 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:33: 1000000 INFO @ Sun, 21 Jun 2020 18:51:34: 6000000 INFO @ Sun, 21 Jun 2020 18:51:36: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:51:36: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:51:36: #1 total tags in treatment: 6340734 INFO @ Sun, 21 Jun 2020 18:51:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:36: #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 18:51:37: #1 tags after filtering in treatment: 6340692 INFO @ Sun, 21 Jun 2020 18:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:38: #2 number of paired peaks: 3151 INFO @ Sun, 21 Jun 2020 18:51:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:38: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 18:51:38: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sun, 21 Jun 2020 18:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.10_model.r INFO @ Sun, 21 Jun 2020 18:51:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:40: 2000000 INFO @ Sun, 21 Jun 2020 18:51:48: 3000000 INFO @ Sun, 21 Jun 2020 18:51:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:55: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:52:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.10_summits.bed INFO @ Sun, 21 Jun 2020 18:52:01: Done! pass1 - making usageList (684 chroms): 2 millis pass2 - checking and writing primary data (1753 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:52:03: 5000000 INFO @ Sun, 21 Jun 2020 18:52:11: 6000000 INFO @ Sun, 21 Jun 2020 18:52:14: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:52:14: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:52:14: #1 total tags in treatment: 6340734 INFO @ Sun, 21 Jun 2020 18:52:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:14: #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 18:52:14: #1 tags after filtering in treatment: 6340692 INFO @ Sun, 21 Jun 2020 18:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:15: #2 number of paired peaks: 3151 INFO @ Sun, 21 Jun 2020 18:52:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:15: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 18:52:15: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sun, 21 Jun 2020 18:52:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.20_model.r INFO @ Sun, 21 Jun 2020 18:52:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:52:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220295/SRX220295.20_summits.bed INFO @ Sun, 21 Jun 2020 18:52:38: Done! pass1 - making usageList (227 chroms): 1 millis pass2 - checking and writing primary data (401 records, 4 fields): 14 millis CompletedMACS2peakCalling