Job ID = 4303125 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,814,505 reads read : 36,814,505 reads written : 36,814,505 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1552291.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: 00:09:37 36814505 reads; of these: 36814505 (100.00%) were unpaired; of these: 16401669 (44.55%) aligned 0 times 15746741 (42.77%) aligned exactly 1 time 4666095 (12.67%) aligned >1 times 55.45% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 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 12 files... [bam_rmdupse_core] 14112402 / 20412836 = 0.6913 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 01:02:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.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 01:02:51: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:02:51: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:02:59: 1000000 INFO @ Thu, 12 Dec 2019 01:03:06: 2000000 INFO @ Thu, 12 Dec 2019 01:03:14: 3000000 INFO @ Thu, 12 Dec 2019 01:03:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.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 01:03:20: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:03:20: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:03:21: 4000000 INFO @ Thu, 12 Dec 2019 01:03:29: 5000000 INFO @ Thu, 12 Dec 2019 01:03:30: 1000000 INFO @ Thu, 12 Dec 2019 01:03:36: 6000000 INFO @ Thu, 12 Dec 2019 01:03:38: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:03:38: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:03:38: #1 total tags in treatment: 6300434 INFO @ Thu, 12 Dec 2019 01:03:38: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:03:38: #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 01:03:39: #1 tags after filtering in treatment: 6300434 INFO @ Thu, 12 Dec 2019 01:03:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:03:39: #1 finished! INFO @ Thu, 12 Dec 2019 01:03:39: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:03:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:03:39: #2 number of paired peaks: 1370 INFO @ Thu, 12 Dec 2019 01:03:39: start model_add_line... INFO @ Thu, 12 Dec 2019 01:03:39: start X-correlation... INFO @ Thu, 12 Dec 2019 01:03:39: end of X-cor INFO @ Thu, 12 Dec 2019 01:03:39: #2 finished! INFO @ Thu, 12 Dec 2019 01:03:39: #2 predicted fragment length is 145 bps INFO @ Thu, 12 Dec 2019 01:03:39: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 12 Dec 2019 01:03:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.05_model.r INFO @ Thu, 12 Dec 2019 01:03:39: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:03:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:03:40: 2000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 01:03:50: 3000000 INFO @ Thu, 12 Dec 2019 01:03:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.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 01:03:50: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:03:50: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:03:59: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:04:00: 4000000 INFO @ Thu, 12 Dec 2019 01:04:01: 1000000 INFO @ Thu, 12 Dec 2019 01:04:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.05_peaks.xls INFO @ Thu, 12 Dec 2019 01:04:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:04:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.05_summits.bed INFO @ Thu, 12 Dec 2019 01:04:09: Done! INFO @ Thu, 12 Dec 2019 01:04:10: 5000000 INFO @ Thu, 12 Dec 2019 01:04:12: 2000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4415 records, 4 fields): 85 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:04:20: 6000000 INFO @ Thu, 12 Dec 2019 01:04:23: 3000000 INFO @ Thu, 12 Dec 2019 01:04:23: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:04:23: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:04:23: #1 total tags in treatment: 6300434 INFO @ Thu, 12 Dec 2019 01:04:23: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:04:23: #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 01:04:23: #1 tags after filtering in treatment: 6300434 INFO @ Thu, 12 Dec 2019 01:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:04:23: #1 finished! INFO @ Thu, 12 Dec 2019 01:04:23: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:04:24: #2 number of paired peaks: 1370 INFO @ Thu, 12 Dec 2019 01:04:24: start model_add_line... INFO @ Thu, 12 Dec 2019 01:04:24: start X-correlation... INFO @ Thu, 12 Dec 2019 01:04:24: end of X-cor INFO @ Thu, 12 Dec 2019 01:04:24: #2 finished! INFO @ Thu, 12 Dec 2019 01:04:24: #2 predicted fragment length is 145 bps INFO @ Thu, 12 Dec 2019 01:04:24: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 12 Dec 2019 01:04:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.10_model.r INFO @ Thu, 12 Dec 2019 01:04:24: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:04:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:04:34: 4000000 INFO @ Thu, 12 Dec 2019 01:04:44: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:04:44: 5000000 INFO @ Thu, 12 Dec 2019 01:04:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.10_peaks.xls INFO @ Thu, 12 Dec 2019 01:04:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:04:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.10_summits.bed INFO @ Thu, 12 Dec 2019 01:04:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2436 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:04:55: 6000000 INFO @ Thu, 12 Dec 2019 01:04:59: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:04:59: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:04:59: #1 total tags in treatment: 6300434 INFO @ Thu, 12 Dec 2019 01:04:59: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:04:59: #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 01:04:59: #1 tags after filtering in treatment: 6300434 INFO @ Thu, 12 Dec 2019 01:04:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:04:59: #1 finished! INFO @ Thu, 12 Dec 2019 01:04:59: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:04:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:05:00: #2 number of paired peaks: 1370 INFO @ Thu, 12 Dec 2019 01:05:00: start model_add_line... INFO @ Thu, 12 Dec 2019 01:05:00: start X-correlation... INFO @ Thu, 12 Dec 2019 01:05:00: end of X-cor INFO @ Thu, 12 Dec 2019 01:05:00: #2 finished! INFO @ Thu, 12 Dec 2019 01:05:00: #2 predicted fragment length is 145 bps INFO @ Thu, 12 Dec 2019 01:05:00: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 12 Dec 2019 01:05:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.20_model.r INFO @ Thu, 12 Dec 2019 01:05:00: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:05:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:05:20: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:05:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.20_peaks.xls INFO @ Thu, 12 Dec 2019 01:05:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:05:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681822/SRX681822.20_summits.bed INFO @ Thu, 12 Dec 2019 01:05:30: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1419 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。