Job ID = 9035989 sra ファイルのダウンロード中... Completed: 733335K bytes transferred in 9 seconds (626513K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 100 14324 0 14324 0 0 1401 0 --:--:-- 0:00:10 --:--:-- 3843 100 62101 0 62101 0 0 5536 0 --:--:-- 0:00:11 --:--:-- 13145 100 94402 0 94402 0 0 8058 0 --:--:-- 0:00:11 --:--:-- 22380 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 28256174 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1301576/SRR2568523.sra Written 28256174 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: 00:04:43 28256174 reads; of these: 28256174 (100.00%) were unpaired; of these: 8839682 (31.28%) aligned 0 times 13925337 (49.28%) aligned exactly 1 time 5491155 (19.43%) aligned >1 times 68.72% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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_sort_core] merging from 8 files... [bam_rmdupse_core] 18809461 / 19416492 = 0.9687 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 02:10:25: # Command line: callpeak -t SRX1301576.bam -f BAM -g 12100000 -n SRX1301576.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1301576.20 # format = BAM # ChIP-seq file = ['SRX1301576.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 02:10:25: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:10:25: # Command line: callpeak -t SRX1301576.bam -f BAM -g 12100000 -n SRX1301576.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1301576.05 # format = BAM # ChIP-seq file = ['SRX1301576.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 02:10:25: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:10:25: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:10:25: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:10:25: # Command line: callpeak -t SRX1301576.bam -f BAM -g 12100000 -n SRX1301576.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1301576.10 # format = BAM # ChIP-seq file = ['SRX1301576.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 02:10:25: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:10:25: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:10:29: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 02:10:29: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 02:10:29: #1 total tags in treatment: 607031 INFO @ Sun, 04 Jun 2017 02:10:29: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:10:29: #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 02:10:29: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 02:10:29: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 02:10:29: #1 total tags in treatment: 607031 INFO @ Sun, 04 Jun 2017 02:10:29: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:10:29: #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 02:10:29: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 02:10:29: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 02:10:29: #1 total tags in treatment: 607031 INFO @ Sun, 04 Jun 2017 02:10:29: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:10:29: #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 02:10:30: #1 tags after filtering in treatment: 605899 INFO @ Sun, 04 Jun 2017 02:10:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:10:30: #1 finished! INFO @ Sun, 04 Jun 2017 02:10:30: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:10:30: #1 tags after filtering in treatment: 605899 INFO @ Sun, 04 Jun 2017 02:10:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:10:30: #1 finished! INFO @ Sun, 04 Jun 2017 02:10:30: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:10:30: #1 tags after filtering in treatment: 605899 INFO @ Sun, 04 Jun 2017 02:10:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:10:30: #1 finished! INFO @ Sun, 04 Jun 2017 02:10:30: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:10:30: #2 number of paired peaks: 506 WARNING @ Sun, 04 Jun 2017 02:10:30: Fewer paired peaks (506) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 506 pairs to build model! INFO @ Sun, 04 Jun 2017 02:10:30: start model_add_line... INFO @ Sun, 04 Jun 2017 02:10:30: #2 number of paired peaks: 506 WARNING @ Sun, 04 Jun 2017 02:10:30: Fewer paired peaks (506) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 506 pairs to build model! INFO @ Sun, 04 Jun 2017 02:10:30: start model_add_line... INFO @ Sun, 04 Jun 2017 02:10:30: #2 number of paired peaks: 506 WARNING @ Sun, 04 Jun 2017 02:10:30: Fewer paired peaks (506) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 506 pairs to build model! INFO @ Sun, 04 Jun 2017 02:10:30: start model_add_line... INFO @ Sun, 04 Jun 2017 02:10:33: start X-correlation... INFO @ Sun, 04 Jun 2017 02:10:33: end of X-cor INFO @ Sun, 04 Jun 2017 02:10:33: #2 finished! INFO @ Sun, 04 Jun 2017 02:10:33: #2 predicted fragment length is 159 bps INFO @ Sun, 04 Jun 2017 02:10:33: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 04 Jun 2017 02:10:33: #2.2 Generate R script for model : SRX1301576.05_model.r INFO @ Sun, 04 Jun 2017 02:10:33: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:10:33: start X-correlation... INFO @ Sun, 04 Jun 2017 02:10:33: end of X-cor INFO @ Sun, 04 Jun 2017 02:10:33: #2 finished! INFO @ Sun, 04 Jun 2017 02:10:33: #2 predicted fragment length is 159 bps INFO @ Sun, 04 Jun 2017 02:10:33: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 04 Jun 2017 02:10:33: #2.2 Generate R script for model : SRX1301576.10_model.r INFO @ Sun, 04 Jun 2017 02:10:33: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:10:33: start X-correlation... INFO @ Sun, 04 Jun 2017 02:10:33: end of X-cor INFO @ Sun, 04 Jun 2017 02:10:33: #2 finished! INFO @ Sun, 04 Jun 2017 02:10:33: #2 predicted fragment length is 159 bps INFO @ Sun, 04 Jun 2017 02:10:33: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 04 Jun 2017 02:10:33: #2.2 Generate R script for model : SRX1301576.20_model.r INFO @ Sun, 04 Jun 2017 02:10:33: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:10:37: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:10:37: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:10:37: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 02:10:39: #4 Write output xls file... SRX1301576.20_peaks.xls INFO @ Sun, 04 Jun 2017 02:10:39: #4 Write peak in narrowPeak format file... SRX1301576.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:10:39: #4 Write summits bed file... SRX1301576.20_summits.bed INFO @ Sun, 04 Jun 2017 02:10:39: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (224 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:10:40: #4 Write output xls file... SRX1301576.10_peaks.xls INFO @ Sun, 04 Jun 2017 02:10:40: #4 Write peak in narrowPeak format file... SRX1301576.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:10:40: #4 Write summits bed file... SRX1301576.10_summits.bed INFO @ Sun, 04 Jun 2017 02:10:40: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (433 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:10:40: #4 Write output xls file... SRX1301576.05_peaks.xls INFO @ Sun, 04 Jun 2017 02:10:40: #4 Write peak in narrowPeak format file... SRX1301576.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:10:40: #4 Write summits bed file... SRX1301576.05_summits.bed INFO @ Sun, 04 Jun 2017 02:10:40: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (764 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。