Job ID = 9028819 sra ファイルのダウンロード中... Completed: 287743K bytes transferred in 5 seconds (411146K 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 --:--:-- 0 100 22318 0 22318 0 0 2386 0 --:--:-- 0:00:09 --:--:-- 7544 100 48603 0 48603 0 0 4697 0 --:--:-- 0:00:10 --:--:-- 12295 100 50474 0 50474 0 0 4845 0 --:--:-- 0:00:10 --:--:-- 12546 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 9373615 spots for /home/okishinya/chipatlas/results/ce10/SRX982061/SRR1956537.sra Written 9373615 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: 00:02:12 9373615 reads; of these: 9373615 (100.00%) were unpaired; of these: 2028970 (21.65%) aligned 0 times 6125373 (65.35%) aligned exactly 1 time 1219272 (13.01%) aligned >1 times 78.35% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1870426 / 7344645 = 0.2547 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 @ Sat, 03 Jun 2017 11:56:36: # Command line: callpeak -t SRX982061.bam -f BAM -g ce -n SRX982061.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982061.05 # format = BAM # ChIP-seq file = ['SRX982061.bam'] # control file = None # effective genome size = 9.00e+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 @ Sat, 03 Jun 2017 11:56:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 11:56:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 11:56:36: # Command line: callpeak -t SRX982061.bam -f BAM -g ce -n SRX982061.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982061.10 # format = BAM # ChIP-seq file = ['SRX982061.bam'] # control file = None # effective genome size = 9.00e+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 @ Sat, 03 Jun 2017 11:56:36: # Command line: callpeak -t SRX982061.bam -f BAM -g ce -n SRX982061.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982061.20 # format = BAM # ChIP-seq file = ['SRX982061.bam'] # control file = None # effective genome size = 9.00e+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 @ Sat, 03 Jun 2017 11:56:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 11:56:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 11:56:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 11:56:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 11:56:42: 1000000 INFO @ Sat, 03 Jun 2017 11:56:43: 1000000 INFO @ Sat, 03 Jun 2017 11:56:43: 1000000 INFO @ Sat, 03 Jun 2017 11:56:49: 2000000 INFO @ Sat, 03 Jun 2017 11:56:50: 2000000 INFO @ Sat, 03 Jun 2017 11:56:50: 2000000 INFO @ Sat, 03 Jun 2017 11:56:55: 3000000 INFO @ Sat, 03 Jun 2017 11:56:57: 3000000 INFO @ Sat, 03 Jun 2017 11:56:57: 3000000 INFO @ Sat, 03 Jun 2017 11:57:02: 4000000 INFO @ Sat, 03 Jun 2017 11:57:03: 4000000 INFO @ Sat, 03 Jun 2017 11:57:04: 4000000 INFO @ Sat, 03 Jun 2017 11:57:09: 5000000 INFO @ Sat, 03 Jun 2017 11:57:10: 5000000 INFO @ Sat, 03 Jun 2017 11:57:12: 5000000 INFO @ Sat, 03 Jun 2017 11:57:12: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 11:57:12: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 11:57:12: #1 total tags in treatment: 5474219 INFO @ Sat, 03 Jun 2017 11:57:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 11:57:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 11:57:13: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 11:57:13: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 11:57:13: #1 total tags in treatment: 5474219 INFO @ Sat, 03 Jun 2017 11:57:13: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 11:57:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 11:57:13: #1 tags after filtering in treatment: 5473459 INFO @ Sat, 03 Jun 2017 11:57:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 11:57:13: #1 finished! INFO @ Sat, 03 Jun 2017 11:57:13: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 11:57:14: #1 tags after filtering in treatment: 5473459 INFO @ Sat, 03 Jun 2017 11:57:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 11:57:14: #1 finished! INFO @ Sat, 03 Jun 2017 11:57:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 11:57:14: #2 number of paired peaks: 781 WARNING @ Sat, 03 Jun 2017 11:57:14: Fewer paired peaks (781) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 781 pairs to build model! INFO @ Sat, 03 Jun 2017 11:57:14: start model_add_line... INFO @ Sat, 03 Jun 2017 11:57:15: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 11:57:15: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 11:57:15: #1 total tags in treatment: 5474219 INFO @ Sat, 03 Jun 2017 11:57:15: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 11:57:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 11:57:15: #2 number of paired peaks: 781 WARNING @ Sat, 03 Jun 2017 11:57:15: Fewer paired peaks (781) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 781 pairs to build model! INFO @ Sat, 03 Jun 2017 11:57:15: start model_add_line... INFO @ Sat, 03 Jun 2017 11:57:16: #1 tags after filtering in treatment: 5473459 INFO @ Sat, 03 Jun 2017 11:57:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 11:57:16: #1 finished! INFO @ Sat, 03 Jun 2017 11:57:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 11:57:17: #2 number of paired peaks: 781 WARNING @ Sat, 03 Jun 2017 11:57:17: Fewer paired peaks (781) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 781 pairs to build model! INFO @ Sat, 03 Jun 2017 11:57:17: start model_add_line... INFO @ Sat, 03 Jun 2017 11:57:20: start X-correlation... INFO @ Sat, 03 Jun 2017 11:57:20: end of X-cor INFO @ Sat, 03 Jun 2017 11:57:20: #2 finished! INFO @ Sat, 03 Jun 2017 11:57:20: #2 predicted fragment length is 131 bps INFO @ Sat, 03 Jun 2017 11:57:20: #2 alternative fragment length(s) may be 131,135 bps INFO @ Sat, 03 Jun 2017 11:57:20: #2.2 Generate R script for model : SRX982061.10_model.r INFO @ Sat, 03 Jun 2017 11:57:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 11:57:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 11:57:21: start X-correlation... INFO @ Sat, 03 Jun 2017 11:57:21: end of X-cor INFO @ Sat, 03 Jun 2017 11:57:21: #2 finished! INFO @ Sat, 03 Jun 2017 11:57:21: #2 predicted fragment length is 131 bps INFO @ Sat, 03 Jun 2017 11:57:21: #2 alternative fragment length(s) may be 131,135 bps INFO @ Sat, 03 Jun 2017 11:57:21: #2.2 Generate R script for model : SRX982061.05_model.r INFO @ Sat, 03 Jun 2017 11:57:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 11:57:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 11:57:23: start X-correlation... INFO @ Sat, 03 Jun 2017 11:57:23: end of X-cor INFO @ Sat, 03 Jun 2017 11:57:23: #2 finished! INFO @ Sat, 03 Jun 2017 11:57:23: #2 predicted fragment length is 131 bps INFO @ Sat, 03 Jun 2017 11:57:23: #2 alternative fragment length(s) may be 131,135 bps INFO @ Sat, 03 Jun 2017 11:57:23: #2.2 Generate R script for model : SRX982061.20_model.r INFO @ Sat, 03 Jun 2017 11:57:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 11:57:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 11:57:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 11:57:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 11:57:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 11:58:14: #4 Write output xls file... SRX982061.10_peaks.xls INFO @ Sat, 03 Jun 2017 11:58:14: #4 Write peak in narrowPeak format file... SRX982061.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 11:58:14: #4 Write summits bed file... SRX982061.10_summits.bed INFO @ Sat, 03 Jun 2017 11:58:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (873 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 11:58:17: #4 Write output xls file... SRX982061.20_peaks.xls INFO @ Sat, 03 Jun 2017 11:58:17: #4 Write peak in narrowPeak format file... SRX982061.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 11:58:17: #4 Write summits bed file... SRX982061.20_summits.bed INFO @ Sat, 03 Jun 2017 11:58:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (523 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 11:58:20: #4 Write output xls file... SRX982061.05_peaks.xls INFO @ Sat, 03 Jun 2017 11:58:20: #4 Write peak in narrowPeak format file... SRX982061.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 11:58:20: #4 Write summits bed file... SRX982061.05_summits.bed INFO @ Sat, 03 Jun 2017 11:58:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1312 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。