Job ID = 5720655 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,060,642 reads read : 25,060,642 reads written : 25,060,642 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289752.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: 00:06:08 25060642 reads; of these: 25060642 (100.00%) were unpaired; of these: 7131025 (28.46%) aligned 0 times 14818662 (59.13%) aligned exactly 1 time 3110955 (12.41%) aligned >1 times 71.54% overall alignment rate Time searching: 00:06:08 Overall time: 00:06:08 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] 5318484 / 17929617 = 0.2966 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 00:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.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 00:59:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:59:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:59:41: 1000000 INFO @ Thu, 16 Apr 2020 00:59:46: 2000000 INFO @ Thu, 16 Apr 2020 00:59:52: 3000000 INFO @ Thu, 16 Apr 2020 00:59:57: 4000000 INFO @ Thu, 16 Apr 2020 01:00:03: 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 01:00:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.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 01:00:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:08: 6000000 INFO @ Thu, 16 Apr 2020 01:00:10: 1000000 INFO @ Thu, 16 Apr 2020 01:00:14: 7000000 INFO @ Thu, 16 Apr 2020 01:00:15: 2000000 INFO @ Thu, 16 Apr 2020 01:00:20: 8000000 INFO @ Thu, 16 Apr 2020 01:00:20: 3000000 INFO @ Thu, 16 Apr 2020 01:00:25: 4000000 INFO @ Thu, 16 Apr 2020 01:00:25: 9000000 INFO @ Thu, 16 Apr 2020 01:00:30: 5000000 INFO @ Thu, 16 Apr 2020 01:00:31: 10000000 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 01:00:35: 6000000 INFO @ Thu, 16 Apr 2020 01:00:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.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 01:00:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:37: 11000000 INFO @ Thu, 16 Apr 2020 01:00:40: 7000000 INFO @ Thu, 16 Apr 2020 01:00:40: 1000000 INFO @ Thu, 16 Apr 2020 01:00:43: 12000000 INFO @ Thu, 16 Apr 2020 01:00:45: 8000000 INFO @ Thu, 16 Apr 2020 01:00:45: 2000000 INFO @ Thu, 16 Apr 2020 01:00:46: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:00:46: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:00:46: #1 total tags in treatment: 12611133 INFO @ Thu, 16 Apr 2020 01:00:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:00:46: #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 01:00:47: #1 tags after filtering in treatment: 12611133 INFO @ Thu, 16 Apr 2020 01:00:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:00:47: #1 finished! INFO @ Thu, 16 Apr 2020 01:00:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:00:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:00:48: #2 number of paired peaks: 7264 INFO @ Thu, 16 Apr 2020 01:00:48: start model_add_line... INFO @ Thu, 16 Apr 2020 01:00:48: start X-correlation... INFO @ Thu, 16 Apr 2020 01:00:48: end of X-cor INFO @ Thu, 16 Apr 2020 01:00:48: #2 finished! INFO @ Thu, 16 Apr 2020 01:00:48: #2 predicted fragment length is 198 bps INFO @ Thu, 16 Apr 2020 01:00:48: #2 alternative fragment length(s) may be 198 bps INFO @ Thu, 16 Apr 2020 01:00:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.05_model.r INFO @ Thu, 16 Apr 2020 01:00:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:00:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:00:49: 9000000 INFO @ Thu, 16 Apr 2020 01:00:50: 3000000 INFO @ Thu, 16 Apr 2020 01:00:54: 10000000 INFO @ Thu, 16 Apr 2020 01:00:55: 4000000 INFO @ Thu, 16 Apr 2020 01:00:59: 11000000 INFO @ Thu, 16 Apr 2020 01:01:00: 5000000 INFO @ Thu, 16 Apr 2020 01:01:04: 12000000 INFO @ Thu, 16 Apr 2020 01:01:05: 6000000 INFO @ Thu, 16 Apr 2020 01:01:07: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:01:07: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:01:07: #1 total tags in treatment: 12611133 INFO @ Thu, 16 Apr 2020 01:01:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:01:07: #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 01:01:07: #1 tags after filtering in treatment: 12611133 INFO @ Thu, 16 Apr 2020 01:01:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:01:07: #1 finished! INFO @ Thu, 16 Apr 2020 01:01:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:01:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:01:09: #2 number of paired peaks: 7264 INFO @ Thu, 16 Apr 2020 01:01:09: start model_add_line... INFO @ Thu, 16 Apr 2020 01:01:09: start X-correlation... INFO @ Thu, 16 Apr 2020 01:01:09: end of X-cor INFO @ Thu, 16 Apr 2020 01:01:09: #2 finished! INFO @ Thu, 16 Apr 2020 01:01:09: #2 predicted fragment length is 198 bps INFO @ Thu, 16 Apr 2020 01:01:09: #2 alternative fragment length(s) may be 198 bps INFO @ Thu, 16 Apr 2020 01:01:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.10_model.r INFO @ Thu, 16 Apr 2020 01:01:09: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:01:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:01:09: 7000000 INFO @ Thu, 16 Apr 2020 01:01:14: 8000000 INFO @ Thu, 16 Apr 2020 01:01:19: 9000000 INFO @ Thu, 16 Apr 2020 01:01:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:01:24: 10000000 INFO @ Thu, 16 Apr 2020 01:01:29: 11000000 INFO @ Thu, 16 Apr 2020 01:01:33: 12000000 INFO @ Thu, 16 Apr 2020 01:01:36: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:01:36: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:01:36: #1 total tags in treatment: 12611133 INFO @ Thu, 16 Apr 2020 01:01:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:01:36: #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 01:01:37: #1 tags after filtering in treatment: 12611133 INFO @ Thu, 16 Apr 2020 01:01:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:01:37: #1 finished! INFO @ Thu, 16 Apr 2020 01:01:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:01:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:01:38: #2 number of paired peaks: 7264 INFO @ Thu, 16 Apr 2020 01:01:38: start model_add_line... INFO @ Thu, 16 Apr 2020 01:01:38: start X-correlation... INFO @ Thu, 16 Apr 2020 01:01:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:01:38: end of X-cor INFO @ Thu, 16 Apr 2020 01:01:38: #2 finished! INFO @ Thu, 16 Apr 2020 01:01:38: #2 predicted fragment length is 198 bps INFO @ Thu, 16 Apr 2020 01:01:38: #2 alternative fragment length(s) may be 198 bps INFO @ Thu, 16 Apr 2020 01:01:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.20_model.r INFO @ Thu, 16 Apr 2020 01:01:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:01:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:01:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:01:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.05_summits.bed INFO @ Thu, 16 Apr 2020 01:01:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11173 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:01:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:02:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.10_summits.bed INFO @ Thu, 16 Apr 2020 01:02:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8792 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:02:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:02:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592475/SRX2592475.20_summits.bed INFO @ Thu, 16 Apr 2020 01:02:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6346 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。