Job ID = 5720643 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,054,008 reads read : 17,054,008 reads written : 17,054,008 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289743.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: 00:04:22 17054008 reads; of these: 17054008 (100.00%) were unpaired; of these: 2436954 (14.29%) aligned 0 times 12178337 (71.41%) aligned exactly 1 time 2438717 (14.30%) aligned >1 times 85.71% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 3896318 / 14617054 = 0.2666 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 00:53:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.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 00:53:42: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:53:42: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:53:47: 1000000 INFO @ Thu, 16 Apr 2020 00:53:53: 2000000 INFO @ Thu, 16 Apr 2020 00:53:59: 3000000 INFO @ Thu, 16 Apr 2020 00:54:04: 4000000 INFO @ Thu, 16 Apr 2020 00:54:10: 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 00:54:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.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 00:54:12: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:12: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:16: 6000000 INFO @ Thu, 16 Apr 2020 00:54:19: 1000000 INFO @ Thu, 16 Apr 2020 00:54:23: 7000000 INFO @ Thu, 16 Apr 2020 00:54:27: 2000000 INFO @ Thu, 16 Apr 2020 00:54:30: 8000000 INFO @ Thu, 16 Apr 2020 00:54:34: 3000000 INFO @ Thu, 16 Apr 2020 00:54:36: 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 00:54:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.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 00:54:42: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:42: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:42: 4000000 INFO @ Thu, 16 Apr 2020 00:54:43: 10000000 INFO @ Thu, 16 Apr 2020 00:54:48: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:54:48: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:54:48: #1 total tags in treatment: 10720736 INFO @ Thu, 16 Apr 2020 00:54:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:54:48: #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 00:54:48: #1 tags after filtering in treatment: 10720736 INFO @ Thu, 16 Apr 2020 00:54:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:54:48: #1 finished! INFO @ Thu, 16 Apr 2020 00:54:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:54:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:54:49: #2 number of paired peaks: 7614 INFO @ Thu, 16 Apr 2020 00:54:49: start model_add_line... INFO @ Thu, 16 Apr 2020 00:54:49: 1000000 INFO @ Thu, 16 Apr 2020 00:54:49: start X-correlation... INFO @ Thu, 16 Apr 2020 00:54:49: end of X-cor INFO @ Thu, 16 Apr 2020 00:54:49: #2 finished! INFO @ Thu, 16 Apr 2020 00:54:49: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 00:54:49: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 00:54:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.05_model.r INFO @ Thu, 16 Apr 2020 00:54:49: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:54:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:54:50: 5000000 INFO @ Thu, 16 Apr 2020 00:54:57: 6000000 INFO @ Thu, 16 Apr 2020 00:54:57: 2000000 INFO @ Thu, 16 Apr 2020 00:55:04: 7000000 INFO @ Thu, 16 Apr 2020 00:55:05: 3000000 INFO @ Thu, 16 Apr 2020 00:55:12: 8000000 INFO @ Thu, 16 Apr 2020 00:55:12: 4000000 INFO @ Thu, 16 Apr 2020 00:55:20: 9000000 INFO @ Thu, 16 Apr 2020 00:55:20: 5000000 INFO @ Thu, 16 Apr 2020 00:55:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:55:27: 10000000 INFO @ Thu, 16 Apr 2020 00:55:27: 6000000 INFO @ Thu, 16 Apr 2020 00:55:32: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:55:32: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:55:32: #1 total tags in treatment: 10720736 INFO @ Thu, 16 Apr 2020 00:55:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:55:32: #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 00:55:32: #1 tags after filtering in treatment: 10720736 INFO @ Thu, 16 Apr 2020 00:55:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:55:32: #1 finished! INFO @ Thu, 16 Apr 2020 00:55:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:55:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:55:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:55:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.05_summits.bed INFO @ Thu, 16 Apr 2020 00:55:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10744 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:55:34: #2 number of paired peaks: 7614 INFO @ Thu, 16 Apr 2020 00:55:34: start model_add_line... INFO @ Thu, 16 Apr 2020 00:55:34: start X-correlation... INFO @ Thu, 16 Apr 2020 00:55:34: end of X-cor INFO @ Thu, 16 Apr 2020 00:55:34: #2 finished! INFO @ Thu, 16 Apr 2020 00:55:34: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 00:55:34: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 00:55:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.10_model.r INFO @ Thu, 16 Apr 2020 00:55:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:55:34: 7000000 INFO @ Thu, 16 Apr 2020 00:55:41: 8000000 INFO @ Thu, 16 Apr 2020 00:55:48: 9000000 INFO @ Thu, 16 Apr 2020 00:55:55: 10000000 INFO @ Thu, 16 Apr 2020 00:56:00: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:00: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:00: #1 total tags in treatment: 10720736 INFO @ Thu, 16 Apr 2020 00:56:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:00: #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 00:56:00: #1 tags after filtering in treatment: 10720736 INFO @ Thu, 16 Apr 2020 00:56:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:00: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:01: #2 number of paired peaks: 7614 INFO @ Thu, 16 Apr 2020 00:56:01: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:01: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:01: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:01: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:01: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 00:56:01: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 00:56:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.20_model.r INFO @ Thu, 16 Apr 2020 00:56:01: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:06: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:56:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.10_summits.bed INFO @ Thu, 16 Apr 2020 00:56:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8269 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:56:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 16 Apr 2020 00:56:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592466/SRX2592466.20_summits.bed INFO @ Thu, 16 Apr 2020 00:56:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5710 records, 4 fields): 7 millis CompletedMACS2peakCalling