Job ID = 5720646 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,926,342 reads read : 17,926,342 reads written : 17,926,342 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289745.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: 00:04:08 17926342 reads; of these: 17926342 (100.00%) were unpaired; of these: 3120329 (17.41%) aligned 0 times 12030022 (67.11%) aligned exactly 1 time 2775991 (15.49%) aligned >1 times 82.59% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 3934229 / 14806013 = 0.2657 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 00:54:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.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 00:54:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:46: 1000000 INFO @ Thu, 16 Apr 2020 00:54:50: 2000000 INFO @ Thu, 16 Apr 2020 00:54:55: 3000000 INFO @ Thu, 16 Apr 2020 00:55:00: 4000000 INFO @ Thu, 16 Apr 2020 00:55:05: 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 00:55:10: 6000000 INFO @ Thu, 16 Apr 2020 00:55:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.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 00:55:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:15: 7000000 INFO @ Thu, 16 Apr 2020 00:55:16: 1000000 INFO @ Thu, 16 Apr 2020 00:55:20: 8000000 INFO @ Thu, 16 Apr 2020 00:55:21: 2000000 INFO @ Thu, 16 Apr 2020 00:55:25: 9000000 INFO @ Thu, 16 Apr 2020 00:55:26: 3000000 INFO @ Thu, 16 Apr 2020 00:55:30: 10000000 INFO @ Thu, 16 Apr 2020 00:55:31: 4000000 INFO @ Thu, 16 Apr 2020 00:55:34: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:55:34: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:55:34: #1 total tags in treatment: 10871784 INFO @ Thu, 16 Apr 2020 00:55:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:55:34: #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 00:55:34: #1 tags after filtering in treatment: 10871784 INFO @ Thu, 16 Apr 2020 00:55:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:55:34: #1 finished! INFO @ Thu, 16 Apr 2020 00:55:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:55:36: #2 number of paired peaks: 7477 INFO @ Thu, 16 Apr 2020 00:55:36: start model_add_line... INFO @ Thu, 16 Apr 2020 00:55:36: start X-correlation... INFO @ Thu, 16 Apr 2020 00:55:36: end of X-cor INFO @ Thu, 16 Apr 2020 00:55:36: #2 finished! INFO @ Thu, 16 Apr 2020 00:55:36: #2 predicted fragment length is 179 bps INFO @ Thu, 16 Apr 2020 00:55:36: #2 alternative fragment length(s) may be 179 bps INFO @ Thu, 16 Apr 2020 00:55:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.05_model.r INFO @ Thu, 16 Apr 2020 00:55:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:55:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:55:37: 5000000 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 00:55:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.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 00:55:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:42: 6000000 INFO @ Thu, 16 Apr 2020 00:55:47: 7000000 INFO @ Thu, 16 Apr 2020 00:55:47: 1000000 INFO @ Thu, 16 Apr 2020 00:55:52: 8000000 INFO @ Thu, 16 Apr 2020 00:55:54: 2000000 INFO @ Thu, 16 Apr 2020 00:55:57: 9000000 INFO @ Thu, 16 Apr 2020 00:56:00: 3000000 INFO @ Thu, 16 Apr 2020 00:56:02: 10000000 INFO @ Thu, 16 Apr 2020 00:56:06: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:06: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:06: #1 total tags in treatment: 10871784 INFO @ Thu, 16 Apr 2020 00:56:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:06: #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 00:56:06: 4000000 INFO @ Thu, 16 Apr 2020 00:56:06: #1 tags after filtering in treatment: 10871784 INFO @ Thu, 16 Apr 2020 00:56:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:06: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:56:07: #2 number of paired peaks: 7477 INFO @ Thu, 16 Apr 2020 00:56:07: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:07: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:07: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:07: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:07: #2 predicted fragment length is 179 bps INFO @ Thu, 16 Apr 2020 00:56:07: #2 alternative fragment length(s) may be 179 bps INFO @ Thu, 16 Apr 2020 00:56:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.10_model.r INFO @ Thu, 16 Apr 2020 00:56:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:12: 5000000 INFO @ Thu, 16 Apr 2020 00:56:18: 6000000 INFO @ Thu, 16 Apr 2020 00:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.05_summits.bed INFO @ Thu, 16 Apr 2020 00:56:20: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11480 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:56:24: 7000000 INFO @ Thu, 16 Apr 2020 00:56:30: 8000000 INFO @ Thu, 16 Apr 2020 00:56:36: 9000000 INFO @ Thu, 16 Apr 2020 00:56:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:56:42: 10000000 INFO @ Thu, 16 Apr 2020 00:56:47: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:47: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:47: #1 total tags in treatment: 10871784 INFO @ Thu, 16 Apr 2020 00:56:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:47: #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 00:56:47: #1 tags after filtering in treatment: 10871784 INFO @ Thu, 16 Apr 2020 00:56:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:47: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:49: #2 number of paired peaks: 7477 INFO @ Thu, 16 Apr 2020 00:56:49: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:49: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:49: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:49: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:49: #2 predicted fragment length is 179 bps INFO @ Thu, 16 Apr 2020 00:56:49: #2 alternative fragment length(s) may be 179 bps INFO @ Thu, 16 Apr 2020 00:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.20_model.r INFO @ Thu, 16 Apr 2020 00:56:49: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.10_summits.bed INFO @ Thu, 16 Apr 2020 00:56:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8586 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:57:21: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592468/SRX2592468.20_summits.bed INFO @ Thu, 16 Apr 2020 00:57:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5825 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。