Job ID = 9035945 sra ファイルのダウンロード中... Completed: 178258K bytes transferred in 4 seconds (297083K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 14324 0 14324 0 0 1817 0 --:--:-- 0:00:07 --:--:-- 9804 100 38246 0 38246 0 0 4308 0 --:--:-- 0:00:08 --:--:-- 15566 100 65526 0 65526 0 0 6988 0 --:--:-- 0:00:09 --:--:-- 22167 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 8241742 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1142477/SRR2155472.sra Written 8241742 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:37 8241742 reads; of these: 8241742 (100.00%) were unpaired; of these: 1561978 (18.95%) aligned 0 times 5374651 (65.21%) aligned exactly 1 time 1305113 (15.84%) aligned >1 times 81.05% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 2533938 / 6679764 = 0.3793 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 @ Sun, 04 Jun 2017 01:59:24: # Command line: callpeak -t SRX1142477.bam -f BAM -g 12100000 -n SRX1142477.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1142477.20 # format = BAM # ChIP-seq file = ['SRX1142477.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sun, 04 Jun 2017 01:59:24: #1 read tag files... INFO @ Sun, 04 Jun 2017 01:59:24: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 01:59:24: # Command line: callpeak -t SRX1142477.bam -f BAM -g 12100000 -n SRX1142477.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1142477.05 # format = BAM # ChIP-seq file = ['SRX1142477.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sun, 04 Jun 2017 01:59:24: #1 read tag files... INFO @ Sun, 04 Jun 2017 01:59:24: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 01:59:24: # Command line: callpeak -t SRX1142477.bam -f BAM -g 12100000 -n SRX1142477.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1142477.10 # format = BAM # ChIP-seq file = ['SRX1142477.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sun, 04 Jun 2017 01:59:24: #1 read tag files... INFO @ Sun, 04 Jun 2017 01:59:24: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 01:59:30: 1000000 INFO @ Sun, 04 Jun 2017 01:59:30: 1000000 INFO @ Sun, 04 Jun 2017 01:59:30: 1000000 INFO @ Sun, 04 Jun 2017 01:59:35: 2000000 INFO @ Sun, 04 Jun 2017 01:59:37: 2000000 INFO @ Sun, 04 Jun 2017 01:59:37: 2000000 INFO @ Sun, 04 Jun 2017 01:59:41: 3000000 INFO @ Sun, 04 Jun 2017 01:59:43: 3000000 INFO @ Sun, 04 Jun 2017 01:59:43: 3000000 INFO @ Sun, 04 Jun 2017 01:59:47: 4000000 INFO @ Sun, 04 Jun 2017 01:59:48: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 01:59:48: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 01:59:48: #1 total tags in treatment: 4145826 INFO @ Sun, 04 Jun 2017 01:59:48: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 01:59:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 01:59:49: #1 tags after filtering in treatment: 4143818 INFO @ Sun, 04 Jun 2017 01:59:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 01:59:49: #1 finished! INFO @ Sun, 04 Jun 2017 01:59:49: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 01:59:49: #2 number of paired peaks: 101 WARNING @ Sun, 04 Jun 2017 01:59:49: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sun, 04 Jun 2017 01:59:49: start model_add_line... INFO @ Sun, 04 Jun 2017 01:59:49: 4000000 INFO @ Sun, 04 Jun 2017 01:59:50: 4000000 INFO @ Sun, 04 Jun 2017 01:59:50: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 01:59:50: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 01:59:50: #1 total tags in treatment: 4145826 INFO @ Sun, 04 Jun 2017 01:59:50: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 01:59:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 01:59:51: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 01:59:51: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 01:59:51: #1 total tags in treatment: 4145826 INFO @ Sun, 04 Jun 2017 01:59:51: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 01:59:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 01:59:51: #1 tags after filtering in treatment: 4143818 INFO @ Sun, 04 Jun 2017 01:59:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 01:59:51: #1 finished! INFO @ Sun, 04 Jun 2017 01:59:51: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 01:59:51: #1 tags after filtering in treatment: 4143818 INFO @ Sun, 04 Jun 2017 01:59:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 01:59:51: #1 finished! INFO @ Sun, 04 Jun 2017 01:59:51: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 01:59:52: start X-correlation... INFO @ Sun, 04 Jun 2017 01:59:52: end of X-cor INFO @ Sun, 04 Jun 2017 01:59:52: #2 finished! INFO @ Sun, 04 Jun 2017 01:59:52: #2 predicted fragment length is 140 bps INFO @ Sun, 04 Jun 2017 01:59:52: #2 alternative fragment length(s) may be 2,17,50,99,119,140,157,180,202,285 bps INFO @ Sun, 04 Jun 2017 01:59:52: #2.2 Generate R script for model : SRX1142477.05_model.r INFO @ Sun, 04 Jun 2017 01:59:52: #3 Call peaks... INFO @ Sun, 04 Jun 2017 01:59:52: #2 number of paired peaks: 101 WARNING @ Sun, 04 Jun 2017 01:59:52: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sun, 04 Jun 2017 01:59:52: start model_add_line... INFO @ Sun, 04 Jun 2017 01:59:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 01:59:52: #2 number of paired peaks: 101 WARNING @ Sun, 04 Jun 2017 01:59:52: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sun, 04 Jun 2017 01:59:52: start model_add_line... INFO @ Sun, 04 Jun 2017 01:59:54: start X-correlation... INFO @ Sun, 04 Jun 2017 01:59:54: end of X-cor INFO @ Sun, 04 Jun 2017 01:59:54: #2 finished! INFO @ Sun, 04 Jun 2017 01:59:54: #2 predicted fragment length is 140 bps INFO @ Sun, 04 Jun 2017 01:59:54: #2 alternative fragment length(s) may be 2,17,50,99,119,140,157,180,202,285 bps INFO @ Sun, 04 Jun 2017 01:59:54: #2.2 Generate R script for model : SRX1142477.20_model.r INFO @ Sun, 04 Jun 2017 01:59:54: #3 Call peaks... INFO @ Sun, 04 Jun 2017 01:59:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 01:59:54: start X-correlation... INFO @ Sun, 04 Jun 2017 01:59:54: end of X-cor INFO @ Sun, 04 Jun 2017 01:59:54: #2 finished! INFO @ Sun, 04 Jun 2017 01:59:54: #2 predicted fragment length is 140 bps INFO @ Sun, 04 Jun 2017 01:59:54: #2 alternative fragment length(s) may be 2,17,50,99,119,140,157,180,202,285 bps INFO @ Sun, 04 Jun 2017 01:59:54: #2.2 Generate R script for model : SRX1142477.10_model.r INFO @ Sun, 04 Jun 2017 01:59:54: #3 Call peaks... INFO @ Sun, 04 Jun 2017 01:59:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:00:14: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:00:16: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:00:17: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:00:29: #4 Write output xls file... SRX1142477.05_peaks.xls INFO @ Sun, 04 Jun 2017 02:00:29: #4 Write peak in narrowPeak format file... SRX1142477.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:00:29: #4 Write summits bed file... SRX1142477.05_summits.bed INFO @ Sun, 04 Jun 2017 02:00:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1085 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:00:29: #4 Write output xls file... SRX1142477.20_peaks.xls INFO @ Sun, 04 Jun 2017 02:00:29: #4 Write peak in narrowPeak format file... SRX1142477.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:00:29: #4 Write summits bed file... SRX1142477.20_summits.bed INFO @ Sun, 04 Jun 2017 02:00:29: Done! pass1 - making usageList (17 chroms): 5 millis pass2 - checking and writing primary data (389 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:00:31: #4 Write output xls file... SRX1142477.10_peaks.xls INFO @ Sun, 04 Jun 2017 02:00:31: #4 Write peak in narrowPeak format file... SRX1142477.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:00:31: #4 Write summits bed file... SRX1142477.10_summits.bed INFO @ Sun, 04 Jun 2017 02:00:31: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (702 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。