Job ID = 2590550 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 43,124,394 reads read : 43,124,394 reads written : 43,124,394 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1141008.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: 00:05:37 43124394 reads; of these: 43124394 (100.00%) were unpaired; of these: 30599147 (70.96%) aligned 0 times 10071627 (23.35%) aligned exactly 1 time 2453620 (5.69%) aligned >1 times 29.04% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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_rmdupse_core] 3018968 / 12525247 = 0.2410 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 22:23:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.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 @ Mon, 12 Aug 2019 22:23:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:23:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:23:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.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 @ Mon, 12 Aug 2019 22:23:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:23:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:23:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.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 @ Mon, 12 Aug 2019 22:23:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:23:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:23:43: 1000000 INFO @ Mon, 12 Aug 2019 22:23:43: 1000000 INFO @ Mon, 12 Aug 2019 22:23:45: 1000000 INFO @ Mon, 12 Aug 2019 22:23:50: 2000000 INFO @ Mon, 12 Aug 2019 22:23:50: 2000000 INFO @ Mon, 12 Aug 2019 22:23:51: 2000000 INFO @ Mon, 12 Aug 2019 22:23:56: 3000000 INFO @ Mon, 12 Aug 2019 22:23:56: 3000000 INFO @ Mon, 12 Aug 2019 22:23:58: 3000000 INFO @ Mon, 12 Aug 2019 22:24:02: 4000000 INFO @ Mon, 12 Aug 2019 22:24:03: 4000000 INFO @ Mon, 12 Aug 2019 22:24:04: 4000000 INFO @ Mon, 12 Aug 2019 22:24:09: 5000000 INFO @ Mon, 12 Aug 2019 22:24:09: 5000000 INFO @ Mon, 12 Aug 2019 22:24:10: 5000000 INFO @ Mon, 12 Aug 2019 22:24:15: 6000000 INFO @ Mon, 12 Aug 2019 22:24:16: 6000000 INFO @ Mon, 12 Aug 2019 22:24:17: 6000000 INFO @ Mon, 12 Aug 2019 22:24:21: 7000000 INFO @ Mon, 12 Aug 2019 22:24:22: 7000000 INFO @ Mon, 12 Aug 2019 22:24:23: 7000000 INFO @ Mon, 12 Aug 2019 22:24:27: 8000000 INFO @ Mon, 12 Aug 2019 22:24:28: 8000000 INFO @ Mon, 12 Aug 2019 22:24:30: 8000000 INFO @ Mon, 12 Aug 2019 22:24:33: 9000000 INFO @ Mon, 12 Aug 2019 22:24:35: 9000000 INFO @ Mon, 12 Aug 2019 22:24:36: 9000000 INFO @ Mon, 12 Aug 2019 22:24:37: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 22:24:37: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 22:24:37: #1 total tags in treatment: 9506279 INFO @ Mon, 12 Aug 2019 22:24:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:24:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:24:37: #1 tags after filtering in treatment: 9506279 INFO @ Mon, 12 Aug 2019 22:24:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:24:37: #1 finished! INFO @ Mon, 12 Aug 2019 22:24:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:24:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:24:38: #2 number of paired peaks: 1086 INFO @ Mon, 12 Aug 2019 22:24:38: start model_add_line... INFO @ Mon, 12 Aug 2019 22:24:39: start X-correlation... INFO @ Mon, 12 Aug 2019 22:24:39: end of X-cor INFO @ Mon, 12 Aug 2019 22:24:39: #2 finished! INFO @ Mon, 12 Aug 2019 22:24:39: #2 predicted fragment length is 92 bps INFO @ Mon, 12 Aug 2019 22:24:39: #2 alternative fragment length(s) may be 92 bps INFO @ Mon, 12 Aug 2019 22:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.10_model.r INFO @ Mon, 12 Aug 2019 22:24:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:24:39: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 22:24:39: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 22:24:39: #1 total tags in treatment: 9506279 INFO @ Mon, 12 Aug 2019 22:24:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:24:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:24:39: #1 tags after filtering in treatment: 9506279 INFO @ Mon, 12 Aug 2019 22:24:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:24:39: #1 finished! INFO @ Mon, 12 Aug 2019 22:24:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:24:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:24:40: #2 number of paired peaks: 1086 INFO @ Mon, 12 Aug 2019 22:24:40: start model_add_line... INFO @ Mon, 12 Aug 2019 22:24:40: start X-correlation... INFO @ Mon, 12 Aug 2019 22:24:40: end of X-cor INFO @ Mon, 12 Aug 2019 22:24:40: #2 finished! INFO @ Mon, 12 Aug 2019 22:24:40: #2 predicted fragment length is 92 bps INFO @ Mon, 12 Aug 2019 22:24:40: #2 alternative fragment length(s) may be 92 bps INFO @ Mon, 12 Aug 2019 22:24:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.05_model.r INFO @ Mon, 12 Aug 2019 22:24:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:24:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:24:40: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 22:24:40: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 22:24:40: #1 total tags in treatment: 9506279 INFO @ Mon, 12 Aug 2019 22:24:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:24:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:24:40: #1 tags after filtering in treatment: 9506279 INFO @ Mon, 12 Aug 2019 22:24:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:24:40: #1 finished! INFO @ Mon, 12 Aug 2019 22:24:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:24:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:24:41: #2 number of paired peaks: 1086 INFO @ Mon, 12 Aug 2019 22:24:41: start model_add_line... INFO @ Mon, 12 Aug 2019 22:24:41: start X-correlation... INFO @ Mon, 12 Aug 2019 22:24:41: end of X-cor INFO @ Mon, 12 Aug 2019 22:24:41: #2 finished! INFO @ Mon, 12 Aug 2019 22:24:41: #2 predicted fragment length is 92 bps INFO @ Mon, 12 Aug 2019 22:24:41: #2 alternative fragment length(s) may be 92 bps INFO @ Mon, 12 Aug 2019 22:24:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.20_model.r INFO @ Mon, 12 Aug 2019 22:24:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:24:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:25:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:25:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:25:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:25:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:25:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:25:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.10_summits.bed INFO @ Mon, 12 Aug 2019 22:25:21: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3944 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:25:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:25:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:25:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.05_summits.bed INFO @ Mon, 12 Aug 2019 22:25:22: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6174 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:25:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX447392/SRX447392.20_summits.bed INFO @ Mon, 12 Aug 2019 22:25:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2419 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。