Job ID = 4303120 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,020,514 reads read : 4,020,514 reads written : 4,020,514 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1552265.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: 00:00:55 4020514 reads; of these: 4020514 (100.00%) were unpaired; of these: 185297 (4.61%) aligned 0 times 3397938 (84.52%) aligned exactly 1 time 437279 (10.88%) aligned >1 times 95.39% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 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] 2395178 / 3835217 = 0.6245 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:46:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.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, 12 Dec 2019 00:46:53: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:46:53: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:47:00: 1000000 INFO @ Thu, 12 Dec 2019 00:47:04: #1 tag size is determined as 36 bps INFO @ Thu, 12 Dec 2019 00:47:04: #1 tag size = 36 INFO @ Thu, 12 Dec 2019 00:47:04: #1 total tags in treatment: 1440039 INFO @ Thu, 12 Dec 2019 00:47:04: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:47:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:47:04: #1 tags after filtering in treatment: 1440039 INFO @ Thu, 12 Dec 2019 00:47:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:47:04: #1 finished! INFO @ Thu, 12 Dec 2019 00:47:04: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:47:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:47:04: #2 number of paired peaks: 1249 INFO @ Thu, 12 Dec 2019 00:47:04: start model_add_line... INFO @ Thu, 12 Dec 2019 00:47:04: start X-correlation... INFO @ Thu, 12 Dec 2019 00:47:04: end of X-cor INFO @ Thu, 12 Dec 2019 00:47:04: #2 finished! INFO @ Thu, 12 Dec 2019 00:47:04: #2 predicted fragment length is 112 bps INFO @ Thu, 12 Dec 2019 00:47:04: #2 alternative fragment length(s) may be 112 bps INFO @ Thu, 12 Dec 2019 00:47:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.05_model.r INFO @ Thu, 12 Dec 2019 00:47:04: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:47:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:47:09: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:47:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:47:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.05_summits.bed INFO @ Thu, 12 Dec 2019 00:47:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1344 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:47:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.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, 12 Dec 2019 00:47:21: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:47:21: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:47:29: 1000000 INFO @ Thu, 12 Dec 2019 00:47:32: #1 tag size is determined as 36 bps INFO @ Thu, 12 Dec 2019 00:47:32: #1 tag size = 36 INFO @ Thu, 12 Dec 2019 00:47:32: #1 total tags in treatment: 1440039 INFO @ Thu, 12 Dec 2019 00:47:32: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:47:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:47:32: #1 tags after filtering in treatment: 1440039 INFO @ Thu, 12 Dec 2019 00:47:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:47:32: #1 finished! INFO @ Thu, 12 Dec 2019 00:47:32: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:47:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:47:33: #2 number of paired peaks: 1249 INFO @ Thu, 12 Dec 2019 00:47:33: start model_add_line... INFO @ Thu, 12 Dec 2019 00:47:33: start X-correlation... INFO @ Thu, 12 Dec 2019 00:47:33: end of X-cor INFO @ Thu, 12 Dec 2019 00:47:33: #2 finished! INFO @ Thu, 12 Dec 2019 00:47:33: #2 predicted fragment length is 112 bps INFO @ Thu, 12 Dec 2019 00:47:33: #2 alternative fragment length(s) may be 112 bps INFO @ Thu, 12 Dec 2019 00:47:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.10_model.r INFO @ Thu, 12 Dec 2019 00:47:33: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:47:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:47:37: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:47:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.10_summits.bed INFO @ Thu, 12 Dec 2019 00:47:41: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (775 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:47:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.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, 12 Dec 2019 00:47:51: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:47:51: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:47:58: 1000000 INFO @ Thu, 12 Dec 2019 00:48:02: #1 tag size is determined as 36 bps INFO @ Thu, 12 Dec 2019 00:48:02: #1 tag size = 36 INFO @ Thu, 12 Dec 2019 00:48:02: #1 total tags in treatment: 1440039 INFO @ Thu, 12 Dec 2019 00:48:02: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:48:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:48:02: #1 tags after filtering in treatment: 1440039 INFO @ Thu, 12 Dec 2019 00:48:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:48:02: #1 finished! INFO @ Thu, 12 Dec 2019 00:48:02: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:48:03: #2 number of paired peaks: 1249 INFO @ Thu, 12 Dec 2019 00:48:03: start model_add_line... INFO @ Thu, 12 Dec 2019 00:48:03: start X-correlation... INFO @ Thu, 12 Dec 2019 00:48:03: end of X-cor INFO @ Thu, 12 Dec 2019 00:48:03: #2 finished! INFO @ Thu, 12 Dec 2019 00:48:03: #2 predicted fragment length is 112 bps INFO @ Thu, 12 Dec 2019 00:48:03: #2 alternative fragment length(s) may be 112 bps INFO @ Thu, 12 Dec 2019 00:48:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.20_model.r INFO @ Thu, 12 Dec 2019 00:48:03: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:48:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:48:07: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:48:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:48:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681796/SRX681796.20_summits.bed INFO @ Thu, 12 Dec 2019 00:48:10: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (374 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。