Job ID = 5720684 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,055,976 reads read : 19,055,976 reads written : 19,055,976 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289776.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:45 19055976 reads; of these: 19055976 (100.00%) were unpaired; of these: 4718264 (24.76%) aligned 0 times 12684027 (66.56%) aligned exactly 1 time 1653685 (8.68%) aligned >1 times 75.24% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 3468672 / 14337712 = 0.2419 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 01:01:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.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 01:01:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:01:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:01:18: 1000000 INFO @ Thu, 16 Apr 2020 01:01:23: 2000000 INFO @ Thu, 16 Apr 2020 01:01:28: 3000000 INFO @ Thu, 16 Apr 2020 01:01:33: 4000000 INFO @ Thu, 16 Apr 2020 01:01:37: 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 01:01:42: 6000000 INFO @ Thu, 16 Apr 2020 01:01:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.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 01:01:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:01:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:01:47: 7000000 INFO @ Thu, 16 Apr 2020 01:01:49: 1000000 INFO @ Thu, 16 Apr 2020 01:01:52: 8000000 INFO @ Thu, 16 Apr 2020 01:01:55: 2000000 INFO @ Thu, 16 Apr 2020 01:01:57: 9000000 INFO @ Thu, 16 Apr 2020 01:02:01: 3000000 INFO @ Thu, 16 Apr 2020 01:02:02: 10000000 INFO @ Thu, 16 Apr 2020 01:02:07: 4000000 INFO @ Thu, 16 Apr 2020 01:02:07: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:02:07: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:02:07: #1 total tags in treatment: 10869040 INFO @ Thu, 16 Apr 2020 01:02:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:02:07: #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 01:02:07: #1 tags after filtering in treatment: 10869040 INFO @ Thu, 16 Apr 2020 01:02:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:02:07: #1 finished! INFO @ Thu, 16 Apr 2020 01:02:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:02:08: #2 number of paired peaks: 9019 INFO @ Thu, 16 Apr 2020 01:02:08: start model_add_line... INFO @ Thu, 16 Apr 2020 01:02:08: start X-correlation... INFO @ Thu, 16 Apr 2020 01:02:08: end of X-cor INFO @ Thu, 16 Apr 2020 01:02:08: #2 finished! INFO @ Thu, 16 Apr 2020 01:02:08: #2 predicted fragment length is 210 bps INFO @ Thu, 16 Apr 2020 01:02:08: #2 alternative fragment length(s) may be 210 bps INFO @ Thu, 16 Apr 2020 01:02:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.05_model.r INFO @ Thu, 16 Apr 2020 01:02:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:02:08: #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 01:02:12: 5000000 INFO @ Thu, 16 Apr 2020 01:02:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.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 01:02:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:02:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:02:18: 6000000 INFO @ Thu, 16 Apr 2020 01:02:21: 1000000 INFO @ Thu, 16 Apr 2020 01:02:24: 7000000 INFO @ Thu, 16 Apr 2020 01:02:28: 2000000 INFO @ Thu, 16 Apr 2020 01:02:29: 8000000 INFO @ Thu, 16 Apr 2020 01:02:34: 3000000 INFO @ Thu, 16 Apr 2020 01:02:35: 9000000 INFO @ Thu, 16 Apr 2020 01:02:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:02:40: 4000000 INFO @ Thu, 16 Apr 2020 01:02:41: 10000000 INFO @ Thu, 16 Apr 2020 01:02:46: 5000000 INFO @ Thu, 16 Apr 2020 01:02:46: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:02:46: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:02:46: #1 total tags in treatment: 10869040 INFO @ Thu, 16 Apr 2020 01:02:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:02:46: #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 01:02:46: #1 tags after filtering in treatment: 10869040 INFO @ Thu, 16 Apr 2020 01:02:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:02:46: #1 finished! INFO @ Thu, 16 Apr 2020 01:02:46: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:02:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:02:47: #2 number of paired peaks: 9019 INFO @ Thu, 16 Apr 2020 01:02:47: start model_add_line... INFO @ Thu, 16 Apr 2020 01:02:47: start X-correlation... INFO @ Thu, 16 Apr 2020 01:02:47: end of X-cor INFO @ Thu, 16 Apr 2020 01:02:47: #2 finished! INFO @ Thu, 16 Apr 2020 01:02:47: #2 predicted fragment length is 210 bps INFO @ Thu, 16 Apr 2020 01:02:47: #2 alternative fragment length(s) may be 210 bps INFO @ Thu, 16 Apr 2020 01:02:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.10_model.r INFO @ Thu, 16 Apr 2020 01:02:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:02:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:02:51: 6000000 INFO @ Thu, 16 Apr 2020 01:02:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.05_summits.bed INFO @ Thu, 16 Apr 2020 01:02:54: Done! INFO @ Thu, 16 Apr 2020 01:02:57: 7000000 pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11786 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:03:03: 8000000 INFO @ Thu, 16 Apr 2020 01:03:09: 9000000 INFO @ Thu, 16 Apr 2020 01:03:14: 10000000 INFO @ Thu, 16 Apr 2020 01:03:19: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:03:19: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:03:19: #1 total tags in treatment: 10869040 INFO @ Thu, 16 Apr 2020 01:03:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:03:19: #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 01:03:19: #1 tags after filtering in treatment: 10869040 INFO @ Thu, 16 Apr 2020 01:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:03:19: #1 finished! INFO @ Thu, 16 Apr 2020 01:03:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:03:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:03:21: #2 number of paired peaks: 9019 INFO @ Thu, 16 Apr 2020 01:03:21: start model_add_line... INFO @ Thu, 16 Apr 2020 01:03:21: start X-correlation... INFO @ Thu, 16 Apr 2020 01:03:21: end of X-cor INFO @ Thu, 16 Apr 2020 01:03:21: #2 finished! INFO @ Thu, 16 Apr 2020 01:03:21: #2 predicted fragment length is 210 bps INFO @ Thu, 16 Apr 2020 01:03:21: #2 alternative fragment length(s) may be 210 bps INFO @ Thu, 16 Apr 2020 01:03:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.20_model.r INFO @ Thu, 16 Apr 2020 01:03:21: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:03:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:03:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:03:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:03:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.10_summits.bed INFO @ Thu, 16 Apr 2020 01:03:34: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9381 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:03:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:04:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:04:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:04:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592499/SRX2592499.20_summits.bed INFO @ Thu, 16 Apr 2020 01:04:07: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6826 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。