Job ID = 11171320 sra ファイルのダウンロード中... Completed: 125920K bytes transferred in 5 seconds (189837K bits/sec), in 1 file. Completed: 125812K bytes transferred in 6 seconds (168248K bits/sec), in 1 file. Completed: 125861K bytes transferred in 13 seconds (76942K bits/sec), in 1 file. Completed: 125317K bytes transferred in 6 seconds (153657K 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 6629120 spots for /home/okishinya/chipatlas/results/dm3/SRX3020538/SRR5850415.sra Written 6629120 spots for /home/okishinya/chipatlas/results/dm3/SRX3020538/SRR5850415.sra Read 6659521 spots for /home/okishinya/chipatlas/results/dm3/SRX3020538/SRR5850413.sra Written 6659521 spots for /home/okishinya/chipatlas/results/dm3/SRX3020538/SRR5850413.sra Read 6682155 spots for /home/okishinya/chipatlas/results/dm3/SRX3020538/SRR5850412.sra Written 6682155 spots for /home/okishinya/chipatlas/results/dm3/SRX3020538/SRR5850412.sra Read 6675761 spots for /home/okishinya/chipatlas/results/dm3/SRX3020538/SRR5850414.sra Written 6675761 spots for /home/okishinya/chipatlas/results/dm3/SRX3020538/SRR5850414.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: 00:07:55 26646557 reads; of these: 26646557 (100.00%) were unpaired; of these: 6785471 (25.46%) aligned 0 times 15453896 (58.00%) aligned exactly 1 time 4407190 (16.54%) aligned >1 times 74.54% overall alignment rate Time searching: 00:07:55 Overall time: 00:07:55 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_sort_core] merging from 12 files... [bam_rmdupse_core] 4639450 / 19861086 = 0.2336 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 13:54:07: # Command line: callpeak -t SRX3020538.bam -f BAM -g dm -n SRX3020538.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020538.05 # format = BAM # ChIP-seq file = ['SRX3020538.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 13:54:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:54:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:54:07: # Command line: callpeak -t SRX3020538.bam -f BAM -g dm -n SRX3020538.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020538.20 # format = BAM # ChIP-seq file = ['SRX3020538.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 13:54:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:54:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:54:07: # Command line: callpeak -t SRX3020538.bam -f BAM -g dm -n SRX3020538.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020538.10 # format = BAM # ChIP-seq file = ['SRX3020538.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 13:54:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:54:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:54:13: 1000000 INFO @ Sat, 08 Sep 2018 13:54:13: 1000000 INFO @ Sat, 08 Sep 2018 13:54:13: 1000000 INFO @ Sat, 08 Sep 2018 13:54:19: 2000000 INFO @ Sat, 08 Sep 2018 13:54:19: 2000000 INFO @ Sat, 08 Sep 2018 13:54:19: 2000000 INFO @ Sat, 08 Sep 2018 13:54:25: 3000000 INFO @ Sat, 08 Sep 2018 13:54:25: 3000000 INFO @ Sat, 08 Sep 2018 13:54:26: 3000000 INFO @ Sat, 08 Sep 2018 13:54:31: 4000000 INFO @ Sat, 08 Sep 2018 13:54:31: 4000000 INFO @ Sat, 08 Sep 2018 13:54:32: 4000000 INFO @ Sat, 08 Sep 2018 13:54:37: 5000000 INFO @ Sat, 08 Sep 2018 13:54:37: 5000000 INFO @ Sat, 08 Sep 2018 13:54:38: 5000000 INFO @ Sat, 08 Sep 2018 13:54:43: 6000000 INFO @ Sat, 08 Sep 2018 13:54:43: 6000000 INFO @ Sat, 08 Sep 2018 13:54:44: 6000000 INFO @ Sat, 08 Sep 2018 13:54:49: 7000000 INFO @ Sat, 08 Sep 2018 13:54:49: 7000000 INFO @ Sat, 08 Sep 2018 13:54:51: 7000000 INFO @ Sat, 08 Sep 2018 13:54:55: 8000000 INFO @ Sat, 08 Sep 2018 13:54:56: 8000000 INFO @ Sat, 08 Sep 2018 13:54:58: 8000000 INFO @ Sat, 08 Sep 2018 13:55:02: 9000000 INFO @ Sat, 08 Sep 2018 13:55:04: 9000000 INFO @ Sat, 08 Sep 2018 13:55:05: 9000000 INFO @ Sat, 08 Sep 2018 13:55:09: 10000000 INFO @ Sat, 08 Sep 2018 13:55:11: 10000000 INFO @ Sat, 08 Sep 2018 13:55:12: 10000000 INFO @ Sat, 08 Sep 2018 13:55:15: 11000000 INFO @ Sat, 08 Sep 2018 13:55:18: 11000000 INFO @ Sat, 08 Sep 2018 13:55:19: 11000000 INFO @ Sat, 08 Sep 2018 13:55:22: 12000000 INFO @ Sat, 08 Sep 2018 13:55:25: 12000000 INFO @ Sat, 08 Sep 2018 13:55:25: 12000000 INFO @ Sat, 08 Sep 2018 13:55:28: 13000000 INFO @ Sat, 08 Sep 2018 13:55:32: 13000000 INFO @ Sat, 08 Sep 2018 13:55:32: 13000000 INFO @ Sat, 08 Sep 2018 13:55:35: 14000000 INFO @ Sat, 08 Sep 2018 13:55:39: 14000000 INFO @ Sat, 08 Sep 2018 13:55:39: 14000000 INFO @ Sat, 08 Sep 2018 13:55:41: 15000000 INFO @ Sat, 08 Sep 2018 13:55:43: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:55:43: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:55:43: #1 total tags in treatment: 15221636 INFO @ Sat, 08 Sep 2018 13:55:43: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:55:43: #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 13:55:43: #1 tags after filtering in treatment: 15221636 INFO @ Sat, 08 Sep 2018 13:55:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:55:43: #1 finished! INFO @ Sat, 08 Sep 2018 13:55:43: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:55:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:55:45: #2 number of paired peaks: 5896 INFO @ Sat, 08 Sep 2018 13:55:45: start model_add_line... INFO @ Sat, 08 Sep 2018 13:55:45: start X-correlation... INFO @ Sat, 08 Sep 2018 13:55:45: end of X-cor INFO @ Sat, 08 Sep 2018 13:55:45: #2 finished! INFO @ Sat, 08 Sep 2018 13:55:45: #2 predicted fragment length is 159 bps INFO @ Sat, 08 Sep 2018 13:55:45: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 08 Sep 2018 13:55:45: #2.2 Generate R script for model : SRX3020538.20_model.r INFO @ Sat, 08 Sep 2018 13:55:45: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:55:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:55:45: 15000000 INFO @ Sat, 08 Sep 2018 13:55:46: 15000000 INFO @ Sat, 08 Sep 2018 13:55:46: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:55:46: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:55:46: #1 total tags in treatment: 15221636 INFO @ Sat, 08 Sep 2018 13:55:46: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:55:46: #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 13:55:47: #1 tags after filtering in treatment: 15221636 INFO @ Sat, 08 Sep 2018 13:55:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:55:47: #1 finished! INFO @ Sat, 08 Sep 2018 13:55:47: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:55:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:55:47: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:55:47: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:55:47: #1 total tags in treatment: 15221636 INFO @ Sat, 08 Sep 2018 13:55:47: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:55:47: #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 13:55:48: #1 tags after filtering in treatment: 15221636 INFO @ Sat, 08 Sep 2018 13:55:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:55:48: #1 finished! INFO @ Sat, 08 Sep 2018 13:55:48: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:55:48: #2 number of paired peaks: 5896 INFO @ Sat, 08 Sep 2018 13:55:48: start model_add_line... INFO @ Sat, 08 Sep 2018 13:55:49: start X-correlation... INFO @ Sat, 08 Sep 2018 13:55:49: end of X-cor INFO @ Sat, 08 Sep 2018 13:55:49: #2 finished! INFO @ Sat, 08 Sep 2018 13:55:49: #2 predicted fragment length is 159 bps INFO @ Sat, 08 Sep 2018 13:55:49: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 08 Sep 2018 13:55:49: #2.2 Generate R script for model : SRX3020538.05_model.r INFO @ Sat, 08 Sep 2018 13:55:49: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:55:50: #2 number of paired peaks: 5896 INFO @ Sat, 08 Sep 2018 13:55:50: start model_add_line... INFO @ Sat, 08 Sep 2018 13:55:50: start X-correlation... INFO @ Sat, 08 Sep 2018 13:55:50: end of X-cor INFO @ Sat, 08 Sep 2018 13:55:50: #2 finished! INFO @ Sat, 08 Sep 2018 13:55:50: #2 predicted fragment length is 159 bps INFO @ Sat, 08 Sep 2018 13:55:50: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 08 Sep 2018 13:55:50: #2.2 Generate R script for model : SRX3020538.10_model.r INFO @ Sat, 08 Sep 2018 13:55:50: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:56:29: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:56:33: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:56:35: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:56:49: #4 Write output xls file... SRX3020538.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:56:49: #4 Write peak in narrowPeak format file... SRX3020538.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:56:49: #4 Write summits bed file... SRX3020538.20_summits.bed INFO @ Sat, 08 Sep 2018 13:56:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6134 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:56:54: #4 Write output xls file... SRX3020538.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:56:54: #4 Write output xls file... SRX3020538.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:56:54: #4 Write peak in narrowPeak format file... SRX3020538.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:56:54: #4 Write peak in narrowPeak format file... SRX3020538.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:56:54: #4 Write summits bed file... SRX3020538.10_summits.bed INFO @ Sat, 08 Sep 2018 13:56:54: Done! INFO @ Sat, 08 Sep 2018 13:56:54: #4 Write summits bed file... SRX3020538.05_summits.bed INFO @ Sat, 08 Sep 2018 13:56:54: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10094 records, 4 fields): 13 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12766 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。