Job ID = 5720668 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,380,208 reads read : 6,380,208 reads written : 6,380,208 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289763.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: 00:01:20 6380208 reads; of these: 6380208 (100.00%) were unpaired; of these: 2484481 (38.94%) aligned 0 times 3123870 (48.96%) aligned exactly 1 time 771857 (12.10%) aligned >1 times 61.06% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 448805 / 3895727 = 0.1152 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 00:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.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 00:52:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:52:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:52:05: 1000000 INFO @ Thu, 16 Apr 2020 00:52:10: 2000000 INFO @ Thu, 16 Apr 2020 00:52:15: 3000000 INFO @ Thu, 16 Apr 2020 00:52:18: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:52:18: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:52:18: #1 total tags in treatment: 3446922 INFO @ Thu, 16 Apr 2020 00:52:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:52:18: #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 00:52:18: #1 tags after filtering in treatment: 3446922 INFO @ Thu, 16 Apr 2020 00:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:52:18: #1 finished! INFO @ Thu, 16 Apr 2020 00:52:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:52:18: #2 number of paired peaks: 2889 INFO @ Thu, 16 Apr 2020 00:52:18: start model_add_line... INFO @ Thu, 16 Apr 2020 00:52:18: start X-correlation... INFO @ Thu, 16 Apr 2020 00:52:18: end of X-cor INFO @ Thu, 16 Apr 2020 00:52:18: #2 finished! INFO @ Thu, 16 Apr 2020 00:52:18: #2 predicted fragment length is 121 bps INFO @ Thu, 16 Apr 2020 00:52:18: #2 alternative fragment length(s) may be 121 bps INFO @ Thu, 16 Apr 2020 00:52:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.05_model.r INFO @ Thu, 16 Apr 2020 00:52:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:52:26: #3 Call peaks for each chromosome... 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 00:52:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:52:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:52:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.05_summits.bed INFO @ Thu, 16 Apr 2020 00:52:30: Done! INFO @ Thu, 16 Apr 2020 00:52:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.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 00:52:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:52:31: #1 read treatment tags... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5226 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:52:39: 1000000 INFO @ Thu, 16 Apr 2020 00:52:44: 2000000 INFO @ Thu, 16 Apr 2020 00:52:49: 3000000 INFO @ Thu, 16 Apr 2020 00:52:51: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:52:51: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:52:51: #1 total tags in treatment: 3446922 INFO @ Thu, 16 Apr 2020 00:52:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:52:51: #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 00:52:51: #1 tags after filtering in treatment: 3446922 INFO @ Thu, 16 Apr 2020 00:52:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:52:51: #1 finished! INFO @ Thu, 16 Apr 2020 00:52:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:52:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:52:52: #2 number of paired peaks: 2889 INFO @ Thu, 16 Apr 2020 00:52:52: start model_add_line... INFO @ Thu, 16 Apr 2020 00:52:52: start X-correlation... INFO @ Thu, 16 Apr 2020 00:52:52: end of X-cor INFO @ Thu, 16 Apr 2020 00:52:52: #2 finished! INFO @ Thu, 16 Apr 2020 00:52:52: #2 predicted fragment length is 121 bps INFO @ Thu, 16 Apr 2020 00:52:52: #2 alternative fragment length(s) may be 121 bps INFO @ Thu, 16 Apr 2020 00:52:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.10_model.r INFO @ Thu, 16 Apr 2020 00:52:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:52:52: #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 @ Thu, 16 Apr 2020 00:53:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.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 00:53:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:53:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.10_summits.bed INFO @ Thu, 16 Apr 2020 00:53:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2692 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:53:07: 1000000 INFO @ Thu, 16 Apr 2020 00:53:12: 2000000 INFO @ Thu, 16 Apr 2020 00:53:17: 3000000 INFO @ Thu, 16 Apr 2020 00:53:19: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:53:19: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:53:19: #1 total tags in treatment: 3446922 INFO @ Thu, 16 Apr 2020 00:53:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:53:19: #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 00:53:19: #1 tags after filtering in treatment: 3446922 INFO @ Thu, 16 Apr 2020 00:53:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:53:19: #1 finished! INFO @ Thu, 16 Apr 2020 00:53:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:53:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:53:19: #2 number of paired peaks: 2889 INFO @ Thu, 16 Apr 2020 00:53:19: start model_add_line... INFO @ Thu, 16 Apr 2020 00:53:19: start X-correlation... INFO @ Thu, 16 Apr 2020 00:53:19: end of X-cor INFO @ Thu, 16 Apr 2020 00:53:19: #2 finished! INFO @ Thu, 16 Apr 2020 00:53:19: #2 predicted fragment length is 121 bps INFO @ Thu, 16 Apr 2020 00:53:19: #2 alternative fragment length(s) may be 121 bps INFO @ Thu, 16 Apr 2020 00:53:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.20_model.r INFO @ Thu, 16 Apr 2020 00:53:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:53:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:53:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:53:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:53:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592486/SRX2592486.20_summits.bed INFO @ Thu, 16 Apr 2020 00:53:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1141 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。