Job ID = 5720400 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,050,454 reads read : 7,050,454 reads written : 7,050,454 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289669.sra.cache’: No such file or directory 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: 00:01:56 7050454 reads; of these: 7050454 (100.00%) were unpaired; of these: 494243 (7.01%) aligned 0 times 5348955 (75.87%) aligned exactly 1 time 1207256 (17.12%) aligned >1 times 92.99% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 1321440 / 6556211 = 0.2016 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 @ Thu, 16 Apr 2020 00:23:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.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 @ Thu, 16 Apr 2020 00:23:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:23:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:23:57: 1000000 INFO @ Thu, 16 Apr 2020 00:24:02: 2000000 INFO @ Thu, 16 Apr 2020 00:24:07: 3000000 INFO @ Thu, 16 Apr 2020 00:24:12: 4000000 INFO @ Thu, 16 Apr 2020 00:24:18: 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 @ Thu, 16 Apr 2020 00:24:19: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:24:19: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:24:19: #1 total tags in treatment: 5234771 INFO @ Thu, 16 Apr 2020 00:24:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:24:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:24:19: #1 tags after filtering in treatment: 5234771 INFO @ Thu, 16 Apr 2020 00:24:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:24:19: #1 finished! INFO @ Thu, 16 Apr 2020 00:24:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:24:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:24:20: #2 number of paired peaks: 2134 INFO @ Thu, 16 Apr 2020 00:24:20: start model_add_line... INFO @ Thu, 16 Apr 2020 00:24:20: start X-correlation... INFO @ Thu, 16 Apr 2020 00:24:20: end of X-cor INFO @ Thu, 16 Apr 2020 00:24:20: #2 finished! INFO @ Thu, 16 Apr 2020 00:24:20: #2 predicted fragment length is 201 bps INFO @ Thu, 16 Apr 2020 00:24:20: #2 alternative fragment length(s) may be 201 bps INFO @ Thu, 16 Apr 2020 00:24:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.05_model.r INFO @ Thu, 16 Apr 2020 00:24:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:24:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.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 @ Thu, 16 Apr 2020 00:24:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:24:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:24:27: 1000000 INFO @ Thu, 16 Apr 2020 00:24:32: 2000000 INFO @ Thu, 16 Apr 2020 00:24:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:24:37: 3000000 INFO @ Thu, 16 Apr 2020 00:24:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:24:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:24:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.05_summits.bed INFO @ Thu, 16 Apr 2020 00:24:40: Done! INFO @ Thu, 16 Apr 2020 00:24:42: 4000000 pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (9400 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:24:47: 5000000 INFO @ Thu, 16 Apr 2020 00:24:48: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:24:48: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:24:48: #1 total tags in treatment: 5234771 INFO @ Thu, 16 Apr 2020 00:24:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:24:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:24:48: #1 tags after filtering in treatment: 5234771 INFO @ Thu, 16 Apr 2020 00:24:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:24:48: #1 finished! INFO @ Thu, 16 Apr 2020 00:24:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:24:48: #2 looking for paired plus/minus strand peaks... 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 @ Thu, 16 Apr 2020 00:24:49: #2 number of paired peaks: 2134 INFO @ Thu, 16 Apr 2020 00:24:49: start model_add_line... INFO @ Thu, 16 Apr 2020 00:24:49: start X-correlation... INFO @ Thu, 16 Apr 2020 00:24:49: end of X-cor INFO @ Thu, 16 Apr 2020 00:24:49: #2 finished! INFO @ Thu, 16 Apr 2020 00:24:49: #2 predicted fragment length is 201 bps INFO @ Thu, 16 Apr 2020 00:24:49: #2 alternative fragment length(s) may be 201 bps INFO @ Thu, 16 Apr 2020 00:24:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.10_model.r INFO @ Thu, 16 Apr 2020 00:24:49: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:24:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:24:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.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 @ Thu, 16 Apr 2020 00:24:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:24:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:24:57: 1000000 INFO @ Thu, 16 Apr 2020 00:25:02: 2000000 INFO @ Thu, 16 Apr 2020 00:25:02: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:25:07: 3000000 INFO @ Thu, 16 Apr 2020 00:25:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:25:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:25:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.10_summits.bed INFO @ Thu, 16 Apr 2020 00:25:08: Done! INFO @ Thu, 16 Apr 2020 00:25:12: 4000000 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5121 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:25:17: 5000000 INFO @ Thu, 16 Apr 2020 00:25:18: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:25:18: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:25:18: #1 total tags in treatment: 5234771 INFO @ Thu, 16 Apr 2020 00:25:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:25:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:25:18: #1 tags after filtering in treatment: 5234771 INFO @ Thu, 16 Apr 2020 00:25:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:25:18: #1 finished! INFO @ Thu, 16 Apr 2020 00:25:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:25:19: #2 number of paired peaks: 2134 INFO @ Thu, 16 Apr 2020 00:25:19: start model_add_line... INFO @ Thu, 16 Apr 2020 00:25:19: start X-correlation... INFO @ Thu, 16 Apr 2020 00:25:19: end of X-cor INFO @ Thu, 16 Apr 2020 00:25:19: #2 finished! INFO @ Thu, 16 Apr 2020 00:25:19: #2 predicted fragment length is 201 bps INFO @ Thu, 16 Apr 2020 00:25:19: #2 alternative fragment length(s) may be 201 bps INFO @ Thu, 16 Apr 2020 00:25:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.20_model.r INFO @ Thu, 16 Apr 2020 00:25:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:25:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:25:32: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:25:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:25:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:25:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592392/SRX2592392.20_summits.bed INFO @ Thu, 16 Apr 2020 00:25:38: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (2165 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。