Job ID = 9035986 sra ファイルのダウンロード中... Completed: 361503K bytes transferred in 6 seconds (431031K 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 22318 0 22318 0 0 2785 0 --:--:-- 0:00:08 --:--:-- 14125 100 41142 0 41142 0 0 4652 0 --:--:-- 0:00:08 --:--:-- 17071 100 80863 0 80863 0 0 8618 0 --:--:-- 0:00:09 --:--:-- 27411 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 5571899 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1274609/SRR2485851.sra Written 5571899 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: 00:01:48 5571899 reads; of these: 5571899 (100.00%) were unpaired; of these: 696016 (12.49%) aligned 0 times 4285433 (76.91%) aligned exactly 1 time 590450 (10.60%) aligned >1 times 87.51% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 1533296 / 4875883 = 0.3145 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 02:05:16: # Command line: callpeak -t SRX1274609.bam -f BAM -g 12100000 -n SRX1274609.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1274609.05 # format = BAM # ChIP-seq file = ['SRX1274609.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 02:05:16: # Command line: callpeak -t SRX1274609.bam -f BAM -g 12100000 -n SRX1274609.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1274609.20 # format = BAM # ChIP-seq file = ['SRX1274609.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 02:05:16: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:05:16: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:05:16: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:05:16: # Command line: callpeak -t SRX1274609.bam -f BAM -g 12100000 -n SRX1274609.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1274609.10 # format = BAM # ChIP-seq file = ['SRX1274609.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 02:05:16: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:05:16: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:05:16: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:05:23: 1000000 INFO @ Sun, 04 Jun 2017 02:05:24: 1000000 INFO @ Sun, 04 Jun 2017 02:05:24: 1000000 INFO @ Sun, 04 Jun 2017 02:05:32: 2000000 INFO @ Sun, 04 Jun 2017 02:05:35: 2000000 INFO @ Sun, 04 Jun 2017 02:05:35: 2000000 INFO @ Sun, 04 Jun 2017 02:05:41: 3000000 INFO @ Sun, 04 Jun 2017 02:05:44: #1 tag size is determined as 101 bps INFO @ Sun, 04 Jun 2017 02:05:44: #1 tag size = 101 INFO @ Sun, 04 Jun 2017 02:05:44: #1 total tags in treatment: 3342587 INFO @ Sun, 04 Jun 2017 02:05:44: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:05:44: #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 02:05:45: #1 tags after filtering in treatment: 3338021 INFO @ Sun, 04 Jun 2017 02:05:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:05:45: #1 finished! INFO @ Sun, 04 Jun 2017 02:05:45: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:05:45: 3000000 INFO @ Sun, 04 Jun 2017 02:05:45: 3000000 INFO @ Sun, 04 Jun 2017 02:05:46: #2 number of paired peaks: 226 WARNING @ Sun, 04 Jun 2017 02:05:46: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Sun, 04 Jun 2017 02:05:46: start model_add_line... INFO @ Sun, 04 Jun 2017 02:05:49: #1 tag size is determined as 101 bps INFO @ Sun, 04 Jun 2017 02:05:49: #1 tag size = 101 INFO @ Sun, 04 Jun 2017 02:05:49: #1 total tags in treatment: 3342587 INFO @ Sun, 04 Jun 2017 02:05:49: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:05:49: #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 02:05:49: #1 tag size is determined as 101 bps INFO @ Sun, 04 Jun 2017 02:05:49: #1 tag size = 101 INFO @ Sun, 04 Jun 2017 02:05:49: #1 total tags in treatment: 3342587 INFO @ Sun, 04 Jun 2017 02:05:49: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:05:49: #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 02:05:49: #1 tags after filtering in treatment: 3338021 INFO @ Sun, 04 Jun 2017 02:05:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:05:49: #1 finished! INFO @ Sun, 04 Jun 2017 02:05:49: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:05:49: #1 tags after filtering in treatment: 3338021 INFO @ Sun, 04 Jun 2017 02:05:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:05:49: #1 finished! INFO @ Sun, 04 Jun 2017 02:05:49: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:05:50: start X-correlation... INFO @ Sun, 04 Jun 2017 02:05:50: end of X-cor INFO @ Sun, 04 Jun 2017 02:05:50: #2 finished! INFO @ Sun, 04 Jun 2017 02:05:50: #2 predicted fragment length is 430 bps INFO @ Sun, 04 Jun 2017 02:05:50: #2 alternative fragment length(s) may be 430 bps INFO @ Sun, 04 Jun 2017 02:05:50: #2.2 Generate R script for model : SRX1274609.10_model.r INFO @ Sun, 04 Jun 2017 02:05:50: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:05:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:05:50: #2 number of paired peaks: 226 WARNING @ Sun, 04 Jun 2017 02:05:50: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Sun, 04 Jun 2017 02:05:50: start model_add_line... INFO @ Sun, 04 Jun 2017 02:05:50: #2 number of paired peaks: 226 WARNING @ Sun, 04 Jun 2017 02:05:50: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Sun, 04 Jun 2017 02:05:50: start model_add_line... INFO @ Sun, 04 Jun 2017 02:05:54: start X-correlation... INFO @ Sun, 04 Jun 2017 02:05:54: end of X-cor INFO @ Sun, 04 Jun 2017 02:05:54: #2 finished! INFO @ Sun, 04 Jun 2017 02:05:54: #2 predicted fragment length is 430 bps INFO @ Sun, 04 Jun 2017 02:05:54: #2 alternative fragment length(s) may be 430 bps INFO @ Sun, 04 Jun 2017 02:05:54: #2.2 Generate R script for model : SRX1274609.20_model.r INFO @ Sun, 04 Jun 2017 02:05:54: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:05:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:05:54: start X-correlation... INFO @ Sun, 04 Jun 2017 02:05:54: end of X-cor INFO @ Sun, 04 Jun 2017 02:05:54: #2 finished! INFO @ Sun, 04 Jun 2017 02:05:54: #2 predicted fragment length is 430 bps INFO @ Sun, 04 Jun 2017 02:05:54: #2 alternative fragment length(s) may be 430 bps INFO @ Sun, 04 Jun 2017 02:05:54: #2.2 Generate R script for model : SRX1274609.05_model.r INFO @ Sun, 04 Jun 2017 02:05:54: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:05:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:06:25: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 02:06:29: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:06:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 02:06:39: #4 Write output xls file... SRX1274609.10_peaks.xls INFO @ Sun, 04 Jun 2017 02:06:39: #4 Write peak in narrowPeak format file... SRX1274609.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:06:39: #4 Write summits bed file... SRX1274609.10_summits.bed INFO @ Sun, 04 Jun 2017 02:06:39: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (813 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:06:42: #4 Write output xls file... SRX1274609.20_peaks.xls INFO @ Sun, 04 Jun 2017 02:06:42: #4 Write peak in narrowPeak format file... SRX1274609.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:06:42: #4 Write summits bed file... SRX1274609.20_summits.bed INFO @ Sun, 04 Jun 2017 02:06:42: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (577 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:06:44: #4 Write output xls file... SRX1274609.05_peaks.xls INFO @ Sun, 04 Jun 2017 02:06:44: #4 Write peak in narrowPeak format file... SRX1274609.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:06:44: #4 Write summits bed file... SRX1274609.05_summits.bed INFO @ Sun, 04 Jun 2017 02:06:44: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1084 records, 4 fields): 3 millis CompletedMACS2peakCalling