Job ID = 9029795 sra ファイルのダウンロード中... Completed: 362486K bytes transferred in 6 seconds (478119K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 7663 0 7663 0 0 1067 0 --:--:-- 0:00:07 --:--:-- 9774 100 30317 0 30317 0 0 3785 0 --:--:-- 0:00:08 --:--:-- 18783 100 69833 0 69833 0 0 8051 0 --:--:-- 0:00:08 --:--:-- 30668 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... Written 12127490 spots for /home/okishinya/chipatlas/results/dm3/SRX209931/SRR631786.sra Written 12127490 spots total rm: cannot remove `[DSE]RR*.fastq': 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:30 12127490 reads; of these: 12127490 (100.00%) were unpaired; of these: 1366047 (11.26%) aligned 0 times 8719660 (71.90%) aligned exactly 1 time 2041783 (16.84%) aligned >1 times 88.74% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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] 2356558 / 10761443 = 0.2190 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, 03 Jun 2017 15:20:49: # Command line: callpeak -t SRX209931.bam -f BAM -g dm -n SRX209931.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX209931.20 # format = BAM # ChIP-seq file = ['SRX209931.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 INFO @ Sat, 03 Jun 2017 15:20:49: # Command line: callpeak -t SRX209931.bam -f BAM -g dm -n SRX209931.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX209931.10 # format = BAM # ChIP-seq file = ['SRX209931.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 INFO @ Sat, 03 Jun 2017 15:20:49: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:20:49: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:20:49: # Command line: callpeak -t SRX209931.bam -f BAM -g dm -n SRX209931.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX209931.05 # format = BAM # ChIP-seq file = ['SRX209931.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 INFO @ Sat, 03 Jun 2017 15:20:49: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:20:49: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:20:49: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:20:49: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:20:56: 1000000 INFO @ Sat, 03 Jun 2017 15:20:56: 1000000 INFO @ Sat, 03 Jun 2017 15:20:56: 1000000 INFO @ Sat, 03 Jun 2017 15:21:03: 2000000 INFO @ Sat, 03 Jun 2017 15:21:03: 2000000 INFO @ Sat, 03 Jun 2017 15:21:03: 2000000 INFO @ Sat, 03 Jun 2017 15:21:10: 3000000 INFO @ Sat, 03 Jun 2017 15:21:10: 3000000 INFO @ Sat, 03 Jun 2017 15:21:10: 3000000 INFO @ Sat, 03 Jun 2017 15:21:17: 4000000 INFO @ Sat, 03 Jun 2017 15:21:17: 4000000 INFO @ Sat, 03 Jun 2017 15:21:17: 4000000 INFO @ Sat, 03 Jun 2017 15:21:23: 5000000 INFO @ Sat, 03 Jun 2017 15:21:24: 5000000 INFO @ Sat, 03 Jun 2017 15:21:25: 5000000 INFO @ Sat, 03 Jun 2017 15:21:31: 6000000 INFO @ Sat, 03 Jun 2017 15:21:32: 6000000 INFO @ Sat, 03 Jun 2017 15:21:34: 6000000 INFO @ Sat, 03 Jun 2017 15:21:40: 7000000 INFO @ Sat, 03 Jun 2017 15:21:40: 7000000 INFO @ Sat, 03 Jun 2017 15:21:43: 7000000 INFO @ Sat, 03 Jun 2017 15:21:48: 8000000 INFO @ Sat, 03 Jun 2017 15:21:48: 8000000 INFO @ Sat, 03 Jun 2017 15:21:51: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 15:21:51: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 15:21:51: #1 total tags in treatment: 8404885 INFO @ Sat, 03 Jun 2017 15:21:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:21:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 15:21:51: 8000000 INFO @ Sat, 03 Jun 2017 15:21:52: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 15:21:52: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 15:21:52: #1 total tags in treatment: 8404885 INFO @ Sat, 03 Jun 2017 15:21:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:21:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 15:21:53: #1 tags after filtering in treatment: 8402175 INFO @ Sat, 03 Jun 2017 15:21:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:21:53: #1 finished! INFO @ Sat, 03 Jun 2017 15:21:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:21:53: #1 tags after filtering in treatment: 8402175 INFO @ Sat, 03 Jun 2017 15:21:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:21:53: #1 finished! INFO @ Sat, 03 Jun 2017 15:21:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:21:54: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 15:21:54: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 15:21:54: #1 total tags in treatment: 8404885 INFO @ Sat, 03 Jun 2017 15:21:54: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:21:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 15:21:55: #2 number of paired peaks: 313 WARNING @ Sat, 03 Jun 2017 15:21:55: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sat, 03 Jun 2017 15:21:55: start model_add_line... INFO @ Sat, 03 Jun 2017 15:21:55: #2 number of paired peaks: 313 WARNING @ Sat, 03 Jun 2017 15:21:55: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sat, 03 Jun 2017 15:21:55: start model_add_line... INFO @ Sat, 03 Jun 2017 15:21:56: #1 tags after filtering in treatment: 8402175 INFO @ Sat, 03 Jun 2017 15:21:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:21:56: #1 finished! INFO @ Sat, 03 Jun 2017 15:21:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:21:57: start X-correlation... INFO @ Sat, 03 Jun 2017 15:21:57: end of X-cor INFO @ Sat, 03 Jun 2017 15:21:57: #2 finished! INFO @ Sat, 03 Jun 2017 15:21:57: #2 predicted fragment length is 93 bps INFO @ Sat, 03 Jun 2017 15:21:57: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 03 Jun 2017 15:21:57: #2.2 Generate R script for model : SRX209931.20_model.r INFO @ Sat, 03 Jun 2017 15:21:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:21:57: start X-correlation... INFO @ Sat, 03 Jun 2017 15:21:57: end of X-cor INFO @ Sat, 03 Jun 2017 15:21:57: #2 finished! INFO @ Sat, 03 Jun 2017 15:21:57: #2 predicted fragment length is 93 bps INFO @ Sat, 03 Jun 2017 15:21:57: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 03 Jun 2017 15:21:57: #2.2 Generate R script for model : SRX209931.05_model.r INFO @ Sat, 03 Jun 2017 15:21:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:21:57: #2 number of paired peaks: 313 WARNING @ Sat, 03 Jun 2017 15:21:57: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sat, 03 Jun 2017 15:21:57: start model_add_line... INFO @ Sat, 03 Jun 2017 15:21:59: start X-correlation... INFO @ Sat, 03 Jun 2017 15:21:59: end of X-cor INFO @ Sat, 03 Jun 2017 15:21:59: #2 finished! INFO @ Sat, 03 Jun 2017 15:21:59: #2 predicted fragment length is 93 bps INFO @ Sat, 03 Jun 2017 15:21:59: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 03 Jun 2017 15:21:59: #2.2 Generate R script for model : SRX209931.10_model.r INFO @ Sat, 03 Jun 2017 15:21:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:21:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:22:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:22:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:22:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:23:17: #4 Write output xls file... SRX209931.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:23:17: #4 Write peak in narrowPeak format file... SRX209931.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:23:17: #4 Write summits bed file... SRX209931.20_summits.bed INFO @ Sat, 03 Jun 2017 15:23:17: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (750 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:23:21: #4 Write output xls file... SRX209931.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:23:21: #4 Write peak in narrowPeak format file... SRX209931.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:23:21: #4 Write summits bed file... SRX209931.05_summits.bed INFO @ Sat, 03 Jun 2017 15:23:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4680 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:23:23: #4 Write output xls file... SRX209931.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:23:23: #4 Write peak in narrowPeak format file... SRX209931.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:23:23: #4 Write summits bed file... SRX209931.10_summits.bed INFO @ Sat, 03 Jun 2017 15:23:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2040 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。