Job ID = 11171280 sra ファイルのダウンロード中... Completed: 136914K bytes transferred in 22 seconds (49982K bits/sec), in 1 file. Completed: 136751K bytes transferred in 5 seconds (213763K bits/sec), in 1 file. Completed: 137115K bytes transferred in 10 seconds (111988K bits/sec), in 1 file. Completed: 136002K bytes transferred in 8 seconds (126595K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 7133298 spots for /home/okishinya/chipatlas/results/dm3/SRX3020546/SRR5850447.sra Written 7133298 spots for /home/okishinya/chipatlas/results/dm3/SRX3020546/SRR5850447.sra Read 7197343 spots for /home/okishinya/chipatlas/results/dm3/SRX3020546/SRR5850444.sra Written 7197343 spots for /home/okishinya/chipatlas/results/dm3/SRX3020546/SRR5850444.sra Read 7177282 spots for /home/okishinya/chipatlas/results/dm3/SRX3020546/SRR5850445.sra Written 7177282 spots for /home/okishinya/chipatlas/results/dm3/SRX3020546/SRR5850445.sra Read 7207558 spots for /home/okishinya/chipatlas/results/dm3/SRX3020546/SRR5850446.sra Written 7207558 spots for /home/okishinya/chipatlas/results/dm3/SRX3020546/SRR5850446.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:08:46 28715481 reads; of these: 28715481 (100.00%) were unpaired; of these: 4942720 (17.21%) aligned 0 times 18921402 (65.89%) aligned exactly 1 time 4851359 (16.89%) aligned >1 times 82.79% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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 12 files... [bam_rmdupse_core] 6415444 / 23772761 = 0.2699 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 @ Sat, 08 Sep 2018 13:40:27: # Command line: callpeak -t SRX3020546.bam -f BAM -g dm -n SRX3020546.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020546.20 # format = BAM # ChIP-seq file = ['SRX3020546.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 @ Sat, 08 Sep 2018 13:40:27: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:40:27: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:40:27: # Command line: callpeak -t SRX3020546.bam -f BAM -g dm -n SRX3020546.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020546.05 # format = BAM # ChIP-seq file = ['SRX3020546.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 @ Sat, 08 Sep 2018 13:40:27: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:40:27: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:40:27: # Command line: callpeak -t SRX3020546.bam -f BAM -g dm -n SRX3020546.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020546.10 # format = BAM # ChIP-seq file = ['SRX3020546.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 @ Sat, 08 Sep 2018 13:40:27: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:40:27: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:40:36: 1000000 INFO @ Sat, 08 Sep 2018 13:40:36: 1000000 INFO @ Sat, 08 Sep 2018 13:40:36: 1000000 INFO @ Sat, 08 Sep 2018 13:40:44: 2000000 INFO @ Sat, 08 Sep 2018 13:40:44: 2000000 INFO @ Sat, 08 Sep 2018 13:40:44: 2000000 INFO @ Sat, 08 Sep 2018 13:40:52: 3000000 INFO @ Sat, 08 Sep 2018 13:40:52: 3000000 INFO @ Sat, 08 Sep 2018 13:40:52: 3000000 INFO @ Sat, 08 Sep 2018 13:41:00: 4000000 INFO @ Sat, 08 Sep 2018 13:41:00: 4000000 INFO @ Sat, 08 Sep 2018 13:41:00: 4000000 INFO @ Sat, 08 Sep 2018 13:41:09: 5000000 INFO @ Sat, 08 Sep 2018 13:41:09: 5000000 INFO @ Sat, 08 Sep 2018 13:41:09: 5000000 INFO @ Sat, 08 Sep 2018 13:41:17: 6000000 INFO @ Sat, 08 Sep 2018 13:41:17: 6000000 INFO @ Sat, 08 Sep 2018 13:41:17: 6000000 INFO @ Sat, 08 Sep 2018 13:41:25: 7000000 INFO @ Sat, 08 Sep 2018 13:41:25: 7000000 INFO @ Sat, 08 Sep 2018 13:41:25: 7000000 INFO @ Sat, 08 Sep 2018 13:41:34: 8000000 INFO @ Sat, 08 Sep 2018 13:41:34: 8000000 INFO @ Sat, 08 Sep 2018 13:41:34: 8000000 INFO @ Sat, 08 Sep 2018 13:41:42: 9000000 INFO @ Sat, 08 Sep 2018 13:41:42: 9000000 INFO @ Sat, 08 Sep 2018 13:41:42: 9000000 INFO @ Sat, 08 Sep 2018 13:41:50: 10000000 INFO @ Sat, 08 Sep 2018 13:41:50: 10000000 INFO @ Sat, 08 Sep 2018 13:41:50: 10000000 INFO @ Sat, 08 Sep 2018 13:41:58: 11000000 INFO @ Sat, 08 Sep 2018 13:41:58: 11000000 INFO @ Sat, 08 Sep 2018 13:41:58: 11000000 INFO @ Sat, 08 Sep 2018 13:42:06: 12000000 INFO @ Sat, 08 Sep 2018 13:42:06: 12000000 INFO @ Sat, 08 Sep 2018 13:42:06: 12000000 INFO @ Sat, 08 Sep 2018 13:42:14: 13000000 INFO @ Sat, 08 Sep 2018 13:42:14: 13000000 INFO @ Sat, 08 Sep 2018 13:42:14: 13000000 INFO @ Sat, 08 Sep 2018 13:42:23: 14000000 INFO @ Sat, 08 Sep 2018 13:42:23: 14000000 INFO @ Sat, 08 Sep 2018 13:42:23: 14000000 INFO @ Sat, 08 Sep 2018 13:42:31: 15000000 INFO @ Sat, 08 Sep 2018 13:42:31: 15000000 INFO @ Sat, 08 Sep 2018 13:42:31: 15000000 INFO @ Sat, 08 Sep 2018 13:42:39: 16000000 INFO @ Sat, 08 Sep 2018 13:42:39: 16000000 INFO @ Sat, 08 Sep 2018 13:42:39: 16000000 INFO @ Sat, 08 Sep 2018 13:42:47: 17000000 INFO @ Sat, 08 Sep 2018 13:42:47: 17000000 INFO @ Sat, 08 Sep 2018 13:42:47: 17000000 INFO @ Sat, 08 Sep 2018 13:42:50: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:42:50: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:42:50: #1 total tags in treatment: 17357317 INFO @ Sat, 08 Sep 2018 13:42:50: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:42:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:42:50: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:42:50: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:42:50: #1 total tags in treatment: 17357317 INFO @ Sat, 08 Sep 2018 13:42:50: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:42:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:42:50: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:42:50: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:42:50: #1 total tags in treatment: 17357317 INFO @ Sat, 08 Sep 2018 13:42:50: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:42:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:42:51: #1 tags after filtering in treatment: 17357317 INFO @ Sat, 08 Sep 2018 13:42:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:42:51: #1 finished! INFO @ Sat, 08 Sep 2018 13:42:51: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:42:51: #1 tags after filtering in treatment: 17357317 INFO @ Sat, 08 Sep 2018 13:42:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:42:51: #1 finished! INFO @ Sat, 08 Sep 2018 13:42:51: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:42:51: #1 tags after filtering in treatment: 17357317 INFO @ Sat, 08 Sep 2018 13:42:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:42:51: #1 finished! INFO @ Sat, 08 Sep 2018 13:42:51: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:42:53: #2 number of paired peaks: 7553 INFO @ Sat, 08 Sep 2018 13:42:53: start model_add_line... INFO @ Sat, 08 Sep 2018 13:42:53: #2 number of paired peaks: 7553 INFO @ Sat, 08 Sep 2018 13:42:53: start model_add_line... INFO @ Sat, 08 Sep 2018 13:42:53: #2 number of paired peaks: 7553 INFO @ Sat, 08 Sep 2018 13:42:53: start model_add_line... INFO @ Sat, 08 Sep 2018 13:42:53: start X-correlation... INFO @ Sat, 08 Sep 2018 13:42:53: start X-correlation... INFO @ Sat, 08 Sep 2018 13:42:53: start X-correlation... INFO @ Sat, 08 Sep 2018 13:42:53: end of X-cor INFO @ Sat, 08 Sep 2018 13:42:53: end of X-cor INFO @ Sat, 08 Sep 2018 13:42:53: end of X-cor INFO @ Sat, 08 Sep 2018 13:42:53: #2 finished! INFO @ Sat, 08 Sep 2018 13:42:53: #2 finished! INFO @ Sat, 08 Sep 2018 13:42:53: #2 finished! INFO @ Sat, 08 Sep 2018 13:42:53: #2 predicted fragment length is 172 bps INFO @ Sat, 08 Sep 2018 13:42:53: #2 predicted fragment length is 172 bps INFO @ Sat, 08 Sep 2018 13:42:53: #2 predicted fragment length is 172 bps INFO @ Sat, 08 Sep 2018 13:42:53: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 08 Sep 2018 13:42:53: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 08 Sep 2018 13:42:53: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 08 Sep 2018 13:42:53: #2.2 Generate R script for model : SRX3020546.20_model.r INFO @ Sat, 08 Sep 2018 13:42:53: #2.2 Generate R script for model : SRX3020546.05_model.r INFO @ Sat, 08 Sep 2018 13:42:53: #2.2 Generate R script for model : SRX3020546.10_model.r INFO @ Sat, 08 Sep 2018 13:42:53: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:42:53: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:42:53: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:42:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:42:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:42:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:43:44: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:43:44: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:43:44: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:44:06: #4 Write output xls file... SRX3020546.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:44:07: #4 Write peak in narrowPeak format file... SRX3020546.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:44:07: #4 Write summits bed file... SRX3020546.10_summits.bed INFO @ Sat, 08 Sep 2018 13:44:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8012 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:44:08: #4 Write output xls file... SRX3020546.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:44:08: #4 Write peak in narrowPeak format file... SRX3020546.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:44:08: #4 Write summits bed file... SRX3020546.05_summits.bed INFO @ Sat, 08 Sep 2018 13:44:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9150 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:44:08: #4 Write output xls file... SRX3020546.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:44:08: #4 Write peak in narrowPeak format file... SRX3020546.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:44:08: #4 Write summits bed file... SRX3020546.20_summits.bed INFO @ Sat, 08 Sep 2018 13:44:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6592 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。