Job ID = 9036413 sra ファイルのダウンロード中... Completed: 197837K bytes transferred in 5 seconds (317901K 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 --:--:-- 0:00:07 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 22317 0 22317 0 0 2602 0 --:--:-- 0:00:08 --:--:-- 18247 100 54038 0 54038 0 0 5746 0 --:--:-- 0:00:09 --:--:-- 26334 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 6352112 spots for /home/okishinya/chipatlas/results/sacCer3/SRX211424/SRR636675.sra Written 6352112 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: 00:00:56 6352112 reads; of these: 6352112 (100.00%) were unpaired; of these: 2749008 (43.28%) aligned 0 times 3107220 (48.92%) aligned exactly 1 time 495884 (7.81%) aligned >1 times 56.72% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 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] 3253081 / 3603104 = 0.9029 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 03:05:38: # Command line: callpeak -t SRX211424.bam -f BAM -g 12100000 -n SRX211424.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX211424.20 # format = BAM # ChIP-seq file = ['SRX211424.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 03:05:38: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:05:38: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:05:38: # Command line: callpeak -t SRX211424.bam -f BAM -g 12100000 -n SRX211424.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX211424.05 # format = BAM # ChIP-seq file = ['SRX211424.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 03:05:38: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:05:38: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:05:38: # Command line: callpeak -t SRX211424.bam -f BAM -g 12100000 -n SRX211424.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX211424.10 # format = BAM # ChIP-seq file = ['SRX211424.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 03:05:38: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:05:38: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:05:40: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:05:40: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:05:40: #1 total tags in treatment: 350023 INFO @ Sun, 04 Jun 2017 03:05:40: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:05:40: #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 03:05:40: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:05:40: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:05:40: #1 total tags in treatment: 350023 INFO @ Sun, 04 Jun 2017 03:05:40: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:05:40: #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 03:05:40: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:05:40: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:05:40: #1 total tags in treatment: 350023 INFO @ Sun, 04 Jun 2017 03:05:40: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:05:40: #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 03:05:40: #1 tags after filtering in treatment: 349628 INFO @ Sun, 04 Jun 2017 03:05:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:05:40: #1 tags after filtering in treatment: 349628 INFO @ Sun, 04 Jun 2017 03:05:40: #1 finished! INFO @ Sun, 04 Jun 2017 03:05:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:05:40: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:05:40: #1 finished! INFO @ Sun, 04 Jun 2017 03:05:40: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:05:40: #1 tags after filtering in treatment: 349628 INFO @ Sun, 04 Jun 2017 03:05:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:05:40: #1 finished! INFO @ Sun, 04 Jun 2017 03:05:40: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:05:41: #2 number of paired peaks: 467 WARNING @ Sun, 04 Jun 2017 03:05:41: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Sun, 04 Jun 2017 03:05:41: start model_add_line... INFO @ Sun, 04 Jun 2017 03:05:41: #2 number of paired peaks: 467 WARNING @ Sun, 04 Jun 2017 03:05:41: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Sun, 04 Jun 2017 03:05:41: start model_add_line... INFO @ Sun, 04 Jun 2017 03:05:41: #2 number of paired peaks: 467 WARNING @ Sun, 04 Jun 2017 03:05:41: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Sun, 04 Jun 2017 03:05:41: start model_add_line... INFO @ Sun, 04 Jun 2017 03:05:42: start X-correlation... INFO @ Sun, 04 Jun 2017 03:05:42: end of X-cor INFO @ Sun, 04 Jun 2017 03:05:42: #2 finished! INFO @ Sun, 04 Jun 2017 03:05:42: #2 predicted fragment length is 104 bps INFO @ Sun, 04 Jun 2017 03:05:42: #2 alternative fragment length(s) may be 4,104,125,194,216,238,244,251,278,475,496,501,520,537,561,574,594 bps INFO @ Sun, 04 Jun 2017 03:05:42: #2.2 Generate R script for model : SRX211424.10_model.r INFO @ Sun, 04 Jun 2017 03:05:42: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:05:42: start X-correlation... INFO @ Sun, 04 Jun 2017 03:05:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:05:42: end of X-cor INFO @ Sun, 04 Jun 2017 03:05:42: #2 finished! INFO @ Sun, 04 Jun 2017 03:05:42: #2 predicted fragment length is 104 bps INFO @ Sun, 04 Jun 2017 03:05:42: #2 alternative fragment length(s) may be 4,104,125,194,216,238,244,251,278,475,496,501,520,537,561,574,594 bps INFO @ Sun, 04 Jun 2017 03:05:42: #2.2 Generate R script for model : SRX211424.20_model.r INFO @ Sun, 04 Jun 2017 03:05:42: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:05:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:05:42: start X-correlation... INFO @ Sun, 04 Jun 2017 03:05:42: end of X-cor INFO @ Sun, 04 Jun 2017 03:05:42: #2 finished! INFO @ Sun, 04 Jun 2017 03:05:42: #2 predicted fragment length is 104 bps INFO @ Sun, 04 Jun 2017 03:05:42: #2 alternative fragment length(s) may be 4,104,125,194,216,238,244,251,278,475,496,501,520,537,561,574,594 bps INFO @ Sun, 04 Jun 2017 03:05:42: #2.2 Generate R script for model : SRX211424.05_model.r INFO @ Sun, 04 Jun 2017 03:05:42: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:05:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:05:45: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:05:45: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:05:45: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:05:46: #4 Write output xls file... SRX211424.05_peaks.xls INFO @ Sun, 04 Jun 2017 03:05:46: #4 Write peak in narrowPeak format file... SRX211424.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:05:46: #4 Write summits bed file... SRX211424.05_summits.bed INFO @ Sun, 04 Jun 2017 03:05:46: Done! INFO @ Sun, 04 Jun 2017 03:05:46: #4 Write output xls file... SRX211424.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:05:46: #4 Write output xls file... SRX211424.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:05:46: #4 Write peak in narrowPeak format file... SRX211424.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:05:46: #4 Write peak in narrowPeak format file... SRX211424.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:05:46: #4 Write summits bed file... SRX211424.20_summits.bed INFO @ Sun, 04 Jun 2017 03:05:46: #4 Write summits bed file... SRX211424.10_summits.bed INFO @ Sun, 04 Jun 2017 03:05:46: Done! pass1 - making usageList (17 chroms): 0 millis INFO @ Sun, 04 Jun 2017 03:05:46: Done! pass2 - checking and writing primary data (122 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 0 millis pass1 - making usageList (10 chroms)pass2 - checking and writing primary data (37 records, 4 fields): 0 millis : 2 millis pass2 - checking and writing primary data (19 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。