Job ID = 5721283 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,900,168 reads read : 35,800,336 reads written : 17,900,168 reads 0-length : 17,900,168 rm: cannot remove ‘[DSE]RR*’: 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: 00:04:38 17900168 reads; of these: 17900168 (100.00%) were unpaired; of these: 530666 (2.96%) aligned 0 times 14920532 (83.35%) aligned exactly 1 time 2448970 (13.68%) aligned >1 times 97.04% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3789011 / 17369502 = 0.2181 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 06:24:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.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 06:24:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:24:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:24:07: 1000000 INFO @ Thu, 16 Apr 2020 06:24:13: 2000000 INFO @ Thu, 16 Apr 2020 06:24:19: 3000000 INFO @ Thu, 16 Apr 2020 06:24:24: 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 @ Thu, 16 Apr 2020 06:24:30: 5000000 INFO @ Thu, 16 Apr 2020 06:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.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 06:24:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:24:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:24:37: 6000000 INFO @ Thu, 16 Apr 2020 06:24:39: 1000000 INFO @ Thu, 16 Apr 2020 06:24:44: 7000000 INFO @ Thu, 16 Apr 2020 06:24:47: 2000000 INFO @ Thu, 16 Apr 2020 06:24:51: 8000000 INFO @ Thu, 16 Apr 2020 06:24:55: 3000000 INFO @ Thu, 16 Apr 2020 06:24:58: 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 @ Thu, 16 Apr 2020 06:25:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.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 06:25:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:25:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:25:03: 4000000 INFO @ Thu, 16 Apr 2020 06:25:06: 10000000 INFO @ Thu, 16 Apr 2020 06:25:10: 1000000 INFO @ Thu, 16 Apr 2020 06:25:11: 5000000 INFO @ Thu, 16 Apr 2020 06:25:13: 11000000 INFO @ Thu, 16 Apr 2020 06:25:18: 2000000 INFO @ Thu, 16 Apr 2020 06:25:18: 6000000 INFO @ Thu, 16 Apr 2020 06:25:20: 12000000 INFO @ Thu, 16 Apr 2020 06:25:26: 3000000 INFO @ Thu, 16 Apr 2020 06:25:26: 7000000 INFO @ Thu, 16 Apr 2020 06:25:27: 13000000 INFO @ Thu, 16 Apr 2020 06:25:31: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:25:31: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:25:31: #1 total tags in treatment: 13580491 INFO @ Thu, 16 Apr 2020 06:25:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:25:31: #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 06:25:32: #1 tags after filtering in treatment: 13580491 INFO @ Thu, 16 Apr 2020 06:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:25:32: #1 finished! INFO @ Thu, 16 Apr 2020 06:25:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:25:33: #2 number of paired peaks: 2958 INFO @ Thu, 16 Apr 2020 06:25:33: start model_add_line... INFO @ Thu, 16 Apr 2020 06:25:33: start X-correlation... INFO @ Thu, 16 Apr 2020 06:25:33: end of X-cor INFO @ Thu, 16 Apr 2020 06:25:33: #2 finished! INFO @ Thu, 16 Apr 2020 06:25:33: #2 predicted fragment length is 150 bps INFO @ Thu, 16 Apr 2020 06:25:33: #2 alternative fragment length(s) may be 150 bps INFO @ Thu, 16 Apr 2020 06:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.05_model.r INFO @ Thu, 16 Apr 2020 06:25:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:25:34: 8000000 INFO @ Thu, 16 Apr 2020 06:25:34: 4000000 INFO @ Thu, 16 Apr 2020 06:25:41: 9000000 INFO @ Thu, 16 Apr 2020 06:25:42: 5000000 INFO @ Thu, 16 Apr 2020 06:25:49: 10000000 INFO @ Thu, 16 Apr 2020 06:25:49: 6000000 INFO @ Thu, 16 Apr 2020 06:25:57: 11000000 INFO @ Thu, 16 Apr 2020 06:25:57: 7000000 INFO @ Thu, 16 Apr 2020 06:26:05: 12000000 INFO @ Thu, 16 Apr 2020 06:26:05: 8000000 INFO @ Thu, 16 Apr 2020 06:26:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:26:12: 13000000 INFO @ Thu, 16 Apr 2020 06:26:13: 9000000 INFO @ Thu, 16 Apr 2020 06:26:17: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:26:17: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:26:17: #1 total tags in treatment: 13580491 INFO @ Thu, 16 Apr 2020 06:26:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:26:17: #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 06:26:17: #1 tags after filtering in treatment: 13580491 INFO @ Thu, 16 Apr 2020 06:26:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:26:17: #1 finished! INFO @ Thu, 16 Apr 2020 06:26:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:26:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:26:18: #2 number of paired peaks: 2958 INFO @ Thu, 16 Apr 2020 06:26:18: start model_add_line... INFO @ Thu, 16 Apr 2020 06:26:18: start X-correlation... INFO @ Thu, 16 Apr 2020 06:26:18: end of X-cor INFO @ Thu, 16 Apr 2020 06:26:18: #2 finished! INFO @ Thu, 16 Apr 2020 06:26:18: #2 predicted fragment length is 150 bps INFO @ Thu, 16 Apr 2020 06:26:18: #2 alternative fragment length(s) may be 150 bps INFO @ Thu, 16 Apr 2020 06:26:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.10_model.r INFO @ Thu, 16 Apr 2020 06:26:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:26:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:26:20: 10000000 INFO @ Thu, 16 Apr 2020 06:26:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:26:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:26:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.05_summits.bed INFO @ Thu, 16 Apr 2020 06:26:24: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (14469 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:26:28: 11000000 INFO @ Thu, 16 Apr 2020 06:26:34: 12000000 INFO @ Thu, 16 Apr 2020 06:26:41: 13000000 INFO @ Thu, 16 Apr 2020 06:26:45: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:26:45: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:26:45: #1 total tags in treatment: 13580491 INFO @ Thu, 16 Apr 2020 06:26:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:26:45: #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 06:26:45: #1 tags after filtering in treatment: 13580491 INFO @ Thu, 16 Apr 2020 06:26:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:26:45: #1 finished! INFO @ Thu, 16 Apr 2020 06:26:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:26:46: #2 number of paired peaks: 2958 INFO @ Thu, 16 Apr 2020 06:26:46: start model_add_line... INFO @ Thu, 16 Apr 2020 06:26:46: start X-correlation... INFO @ Thu, 16 Apr 2020 06:26:46: end of X-cor INFO @ Thu, 16 Apr 2020 06:26:46: #2 finished! INFO @ Thu, 16 Apr 2020 06:26:46: #2 predicted fragment length is 150 bps INFO @ Thu, 16 Apr 2020 06:26:46: #2 alternative fragment length(s) may be 150 bps INFO @ Thu, 16 Apr 2020 06:26:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.20_model.r INFO @ Thu, 16 Apr 2020 06:26:46: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:26:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:26:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:27:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:27:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:27:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.10_summits.bed INFO @ Thu, 16 Apr 2020 06:27:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9704 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:27:18: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 06:27:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:27:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:27:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7299240/SRX7299240.20_summits.bed INFO @ Thu, 16 Apr 2020 06:27:33: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (5758 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。