Job ID = 9036272 sra ファイルのダウンロード中... Completed: 208528K bytes transferred in 4 seconds (347530K 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 --:--:-- 0:00:06 --:--:-- 0 100 24454 0 24454 0 0 3035 0 --:--:-- 0:00:08 --:--:-- 14376 100 56240 0 56240 0 0 6329 0 --:--:-- 0:00:08 --:--:-- 22211 100 58111 0 58111 0 0 6539 0 --:--:-- 0:00:08 --:--:-- 22941 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 9677330 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1738698/SRR3471229.sra Written 9677330 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: 00:02:19 9677330 reads; of these: 9677330 (100.00%) were unpaired; of these: 869337 (8.98%) aligned 0 times 5084909 (52.54%) aligned exactly 1 time 3723084 (38.47%) aligned >1 times 91.02% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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] 6079335 / 8807993 = 0.6902 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 02:48:22: # Command line: callpeak -t SRX1738698.bam -f BAM -g 12100000 -n SRX1738698.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1738698.10 # format = BAM # ChIP-seq file = ['SRX1738698.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 02:48:22: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:48:22: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:48:22: # Command line: callpeak -t SRX1738698.bam -f BAM -g 12100000 -n SRX1738698.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1738698.20 # format = BAM # ChIP-seq file = ['SRX1738698.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 02:48:22: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:48:22: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:48:22: # Command line: callpeak -t SRX1738698.bam -f BAM -g 12100000 -n SRX1738698.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1738698.05 # format = BAM # ChIP-seq file = ['SRX1738698.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 02:48:22: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:48:22: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:48:28: 1000000 INFO @ Sun, 04 Jun 2017 02:48:29: 1000000 INFO @ Sun, 04 Jun 2017 02:48:29: 1000000 INFO @ Sun, 04 Jun 2017 02:48:34: 2000000 INFO @ Sun, 04 Jun 2017 02:48:35: 2000000 INFO @ Sun, 04 Jun 2017 02:48:35: 2000000 INFO @ Sun, 04 Jun 2017 02:48:39: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 02:48:39: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 02:48:39: #1 total tags in treatment: 2728658 INFO @ Sun, 04 Jun 2017 02:48:39: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:48:39: #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 02:48:39: #1 tags after filtering in treatment: 2709610 INFO @ Sun, 04 Jun 2017 02:48:39: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 04 Jun 2017 02:48:39: #1 finished! INFO @ Sun, 04 Jun 2017 02:48:39: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:48:39: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 02:48:39: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 02:48:39: #1 total tags in treatment: 2728658 INFO @ Sun, 04 Jun 2017 02:48:39: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:48:39: #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 02:48:39: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 02:48:39: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 02:48:39: #1 total tags in treatment: 2728658 INFO @ Sun, 04 Jun 2017 02:48:39: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:48:39: #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 02:48:40: #2 number of paired peaks: 567 WARNING @ Sun, 04 Jun 2017 02:48:40: Fewer paired peaks (567) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 567 pairs to build model! INFO @ Sun, 04 Jun 2017 02:48:40: start model_add_line... INFO @ Sun, 04 Jun 2017 02:48:40: #1 tags after filtering in treatment: 2709610 INFO @ Sun, 04 Jun 2017 02:48:40: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 04 Jun 2017 02:48:40: #1 finished! INFO @ Sun, 04 Jun 2017 02:48:40: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:48:40: #1 tags after filtering in treatment: 2709610 INFO @ Sun, 04 Jun 2017 02:48:40: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 04 Jun 2017 02:48:40: #1 finished! INFO @ Sun, 04 Jun 2017 02:48:40: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:48:40: #2 number of paired peaks: 567 WARNING @ Sun, 04 Jun 2017 02:48:40: Fewer paired peaks (567) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 567 pairs to build model! INFO @ Sun, 04 Jun 2017 02:48:40: start model_add_line... INFO @ Sun, 04 Jun 2017 02:48:41: #2 number of paired peaks: 567 WARNING @ Sun, 04 Jun 2017 02:48:41: Fewer paired peaks (567) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 567 pairs to build model! INFO @ Sun, 04 Jun 2017 02:48:41: start model_add_line... INFO @ Sun, 04 Jun 2017 02:48:50: start X-correlation... INFO @ Sun, 04 Jun 2017 02:48:50: end of X-cor INFO @ Sun, 04 Jun 2017 02:48:50: #2 finished! INFO @ Sun, 04 Jun 2017 02:48:50: #2 predicted fragment length is 171 bps INFO @ Sun, 04 Jun 2017 02:48:50: #2 alternative fragment length(s) may be 0,171,236,594 bps INFO @ Sun, 04 Jun 2017 02:48:50: #2.2 Generate R script for model : SRX1738698.20_model.r INFO @ Sun, 04 Jun 2017 02:48:50: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:48:50: start X-correlation... INFO @ Sun, 04 Jun 2017 02:48:50: end of X-cor INFO @ Sun, 04 Jun 2017 02:48:50: #2 finished! INFO @ Sun, 04 Jun 2017 02:48:50: #2 predicted fragment length is 171 bps INFO @ Sun, 04 Jun 2017 02:48:50: #2 alternative fragment length(s) may be 0,171,236,594 bps INFO @ Sun, 04 Jun 2017 02:48:50: #2.2 Generate R script for model : SRX1738698.05_model.r INFO @ Sun, 04 Jun 2017 02:48:50: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:48:51: start X-correlation... INFO @ Sun, 04 Jun 2017 02:48:51: end of X-cor INFO @ Sun, 04 Jun 2017 02:48:51: #2 finished! INFO @ Sun, 04 Jun 2017 02:48:51: #2 predicted fragment length is 171 bps INFO @ Sun, 04 Jun 2017 02:48:51: #2 alternative fragment length(s) may be 0,171,236,594 bps INFO @ Sun, 04 Jun 2017 02:48:51: #2.2 Generate R script for model : SRX1738698.10_model.r INFO @ Sun, 04 Jun 2017 02:48:51: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:48:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 02:49:10: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:49:11: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:49:11: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:49:17: #4 Write output xls file... SRX1738698.20_peaks.xls INFO @ Sun, 04 Jun 2017 02:49:17: #4 Write peak in narrowPeak format file... SRX1738698.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:49:17: #4 Write summits bed file... SRX1738698.20_summits.bed INFO @ Sun, 04 Jun 2017 02:49:17: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (81 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:49:19: #4 Write output xls file... SRX1738698.10_peaks.xls INFO @ Sun, 04 Jun 2017 02:49:19: #4 Write peak in narrowPeak format file... SRX1738698.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:49:19: #4 Write summits bed file... SRX1738698.10_summits.bed INFO @ Sun, 04 Jun 2017 02:49:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:49:19: #4 Write output xls file... SRX1738698.05_peaks.xls INFO @ Sun, 04 Jun 2017 02:49:19: #4 Write peak in narrowPeak format file... SRX1738698.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:49:19: #4 Write summits bed file... SRX1738698.05_summits.bed INFO @ Sun, 04 Jun 2017 02:49:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 2 millis CompletedMACS2peakCalling