Job ID = 9037635 sra ファイルのダウンロード中... Completed: 464841K bytes transferred in 7 seconds (537516K 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 22317 0 22317 0 0 2918 0 --:--:-- 0:00:07 --:--:-- 18188 100 60653 0 60653 0 0 7017 0 --:--:-- 0:00:08 --:--:-- 27284 100 137k 0 137k 0 0 14656 0 --:--:-- 0:00:09 --:--:-- 43902 100 139k 0 139k 0 0 14849 0 --:--:-- 0:00:09 --:--:-- 44470 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 16667804 spots for /home/okishinya/chipatlas/results/sacCer3/SRX966748/SRR1927164.sra Written 16667804 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: 00:01:23 16667804 reads; of these: 16667804 (100.00%) were unpaired; of these: 15038170 (90.22%) aligned 0 times 1470010 (8.82%) aligned exactly 1 time 159624 (0.96%) aligned >1 times 9.78% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 219957 / 1629634 = 0.1350 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 05:05:02: # Command line: callpeak -t SRX966748.bam -f BAM -g 12100000 -n SRX966748.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX966748.05 # format = BAM # ChIP-seq file = ['SRX966748.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 05:05:02: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:05:02: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:05:02: # Command line: callpeak -t SRX966748.bam -f BAM -g 12100000 -n SRX966748.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX966748.10 # format = BAM # ChIP-seq file = ['SRX966748.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 05:05:02: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:05:02: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:05:02: # Command line: callpeak -t SRX966748.bam -f BAM -g 12100000 -n SRX966748.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX966748.20 # format = BAM # ChIP-seq file = ['SRX966748.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 05:05:02: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:05:02: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:05:09: 1000000 INFO @ Sun, 04 Jun 2017 05:05:09: 1000000 INFO @ Sun, 04 Jun 2017 05:05:09: 1000000 INFO @ Sun, 04 Jun 2017 05:05:12: #1 tag size is determined as 48 bps INFO @ Sun, 04 Jun 2017 05:05:12: #1 tag size = 48 INFO @ Sun, 04 Jun 2017 05:05:12: #1 total tags in treatment: 1409677 INFO @ Sun, 04 Jun 2017 05:05:12: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:05:12: #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 05:05:12: #1 tag size is determined as 48 bps INFO @ Sun, 04 Jun 2017 05:05:12: #1 tag size = 48 INFO @ Sun, 04 Jun 2017 05:05:12: #1 total tags in treatment: 1409677 INFO @ Sun, 04 Jun 2017 05:05:12: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:05:12: #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 05:05:12: #1 tag size is determined as 48 bps INFO @ Sun, 04 Jun 2017 05:05:12: #1 tag size = 48 INFO @ Sun, 04 Jun 2017 05:05:12: #1 total tags in treatment: 1409677 INFO @ Sun, 04 Jun 2017 05:05:12: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:05:12: #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 05:05:12: #1 tags after filtering in treatment: 1409391 INFO @ Sun, 04 Jun 2017 05:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:05:12: #1 finished! INFO @ Sun, 04 Jun 2017 05:05:12: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:05:12: #1 tags after filtering in treatment: 1409391 INFO @ Sun, 04 Jun 2017 05:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:05:12: #1 finished! INFO @ Sun, 04 Jun 2017 05:05:12: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:05:12: #1 tags after filtering in treatment: 1409391 INFO @ Sun, 04 Jun 2017 05:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:05:12: #1 finished! INFO @ Sun, 04 Jun 2017 05:05:12: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:05:12: #2 number of paired peaks: 212 WARNING @ Sun, 04 Jun 2017 05:05:12: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sun, 04 Jun 2017 05:05:12: start model_add_line... INFO @ Sun, 04 Jun 2017 05:05:12: #2 number of paired peaks: 212 WARNING @ Sun, 04 Jun 2017 05:05:12: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sun, 04 Jun 2017 05:05:12: start model_add_line... INFO @ Sun, 04 Jun 2017 05:05:12: #2 number of paired peaks: 212 WARNING @ Sun, 04 Jun 2017 05:05:12: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sun, 04 Jun 2017 05:05:12: start model_add_line... INFO @ Sun, 04 Jun 2017 05:05:14: start X-correlation... INFO @ Sun, 04 Jun 2017 05:05:14: start X-correlation... INFO @ Sun, 04 Jun 2017 05:05:14: end of X-cor INFO @ Sun, 04 Jun 2017 05:05:14: #2 finished! INFO @ Sun, 04 Jun 2017 05:05:14: #2 predicted fragment length is 169 bps INFO @ Sun, 04 Jun 2017 05:05:14: #2 alternative fragment length(s) may be 4,146,169,200 bps INFO @ Sun, 04 Jun 2017 05:05:14: #2.2 Generate R script for model : SRX966748.05_model.r INFO @ Sun, 04 Jun 2017 05:05:14: end of X-cor INFO @ Sun, 04 Jun 2017 05:05:14: #2 finished! INFO @ Sun, 04 Jun 2017 05:05:14: #2 predicted fragment length is 169 bps INFO @ Sun, 04 Jun 2017 05:05:14: #2 alternative fragment length(s) may be 4,146,169,200 bps INFO @ Sun, 04 Jun 2017 05:05:14: #2.2 Generate R script for model : SRX966748.10_model.r INFO @ Sun, 04 Jun 2017 05:05:14: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:05:14: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:05:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:05:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:05:14: start X-correlation... INFO @ Sun, 04 Jun 2017 05:05:14: end of X-cor INFO @ Sun, 04 Jun 2017 05:05:14: #2 finished! INFO @ Sun, 04 Jun 2017 05:05:14: #2 predicted fragment length is 169 bps INFO @ Sun, 04 Jun 2017 05:05:14: #2 alternative fragment length(s) may be 4,146,169,200 bps INFO @ Sun, 04 Jun 2017 05:05:14: #2.2 Generate R script for model : SRX966748.20_model.r INFO @ Sun, 04 Jun 2017 05:05:14: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:05:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:05:23: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:05:24: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:05:24: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:05:30: #4 Write output xls file... SRX966748.20_peaks.xls INFO @ Sun, 04 Jun 2017 05:05:30: #4 Write peak in narrowPeak format file... SRX966748.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:05:30: #4 Write summits bed file... SRX966748.20_summits.bed INFO @ Sun, 04 Jun 2017 05:05:30: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (283 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 05:05:30: #4 Write output xls file... SRX966748.10_peaks.xls INFO @ Sun, 04 Jun 2017 05:05:30: #4 Write peak in narrowPeak format file... SRX966748.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:05:30: #4 Write summits bed file... SRX966748.10_summits.bed INFO @ Sun, 04 Jun 2017 05:05:30: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (530 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 05:05:32: #4 Write output xls file... SRX966748.05_peaks.xls INFO @ Sun, 04 Jun 2017 05:05:32: #4 Write peak in narrowPeak format file... SRX966748.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:05:32: #4 Write summits bed file... SRX966748.05_summits.bed INFO @ Sun, 04 Jun 2017 05:05:32: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (847 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。