Job ID = 2161356 sra ファイルのダウンロード中... Completed: 173766K bytes transferred in 5 seconds (283036K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0 100 4007 0 4007 0 0 1271 0 --:--:-- 0:00:03 --:--:-- 1354 100 36780 0 36780 0 0 11011 0 --:--:-- 0:00:03 --:--:-- 11683 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 9739953 spots for /home/okishinya/chipatlas/results/dm3/SRX022745/SRR059124.sra Written 9739953 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: 00:02:25 9739953 reads; of these: 9739953 (100.00%) were unpaired; of these: 970584 (9.96%) aligned 0 times 7005904 (71.93%) aligned exactly 1 time 1763465 (18.11%) aligned >1 times 90.04% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 946212 / 8769369 = 0.1079 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 @ Tue, 21 Apr 2015 12:32:04: # Command line: callpeak -t SRX022745.bam -f BAM -g dm -n SRX022745.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX022745.05 # format = BAM # ChIP-seq file = ['SRX022745.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:32:04: # Command line: callpeak -t SRX022745.bam -f BAM -g dm -n SRX022745.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX022745.10 # format = BAM # ChIP-seq file = ['SRX022745.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:32:04: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:32:04: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:32:04: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:32:04: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:32:04: # Command line: callpeak -t SRX022745.bam -f BAM -g dm -n SRX022745.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX022745.20 # format = BAM # ChIP-seq file = ['SRX022745.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:32:04: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:32:04: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:32:09: 1000000 INFO @ Tue, 21 Apr 2015 12:32:09: 1000000 INFO @ Tue, 21 Apr 2015 12:32:09: 1000000 INFO @ Tue, 21 Apr 2015 12:32:13: 2000000 INFO @ Tue, 21 Apr 2015 12:32:14: 2000000 INFO @ Tue, 21 Apr 2015 12:32:14: 2000000 INFO @ Tue, 21 Apr 2015 12:32:18: 3000000 INFO @ Tue, 21 Apr 2015 12:32:18: 3000000 INFO @ Tue, 21 Apr 2015 12:32:18: 3000000 INFO @ Tue, 21 Apr 2015 12:32:23: 4000000 INFO @ Tue, 21 Apr 2015 12:32:23: 4000000 INFO @ Tue, 21 Apr 2015 12:32:23: 4000000 INFO @ Tue, 21 Apr 2015 12:32:28: 5000000 INFO @ Tue, 21 Apr 2015 12:32:28: 5000000 INFO @ Tue, 21 Apr 2015 12:32:28: 5000000 INFO @ Tue, 21 Apr 2015 12:32:32: 6000000 INFO @ Tue, 21 Apr 2015 12:32:33: 6000000 INFO @ Tue, 21 Apr 2015 12:32:33: 6000000 INFO @ Tue, 21 Apr 2015 12:32:37: 7000000 INFO @ Tue, 21 Apr 2015 12:32:38: 7000000 INFO @ Tue, 21 Apr 2015 12:32:38: 7000000 INFO @ Tue, 21 Apr 2015 12:32:41: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:32:41: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:32:41: #1 total tags in treatment: 7823157 INFO @ Tue, 21 Apr 2015 12:32:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:32:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:32:42: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:32:42: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:32:42: #1 total tags in treatment: 7823157 INFO @ Tue, 21 Apr 2015 12:32:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:32:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:32:42: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:32:42: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:32:42: #1 total tags in treatment: 7823157 INFO @ Tue, 21 Apr 2015 12:32:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:32:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:32:43: #1 tags after filtering in treatment: 7822312 INFO @ Tue, 21 Apr 2015 12:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:32:43: #1 finished! INFO @ Tue, 21 Apr 2015 12:32:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:32:43: #1 tags after filtering in treatment: 7822312 INFO @ Tue, 21 Apr 2015 12:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:32:43: #1 finished! INFO @ Tue, 21 Apr 2015 12:32:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:32:43: #1 tags after filtering in treatment: 7822312 INFO @ Tue, 21 Apr 2015 12:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:32:43: #1 finished! INFO @ Tue, 21 Apr 2015 12:32:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:32:45: #2 number of paired peaks: 2525 INFO @ Tue, 21 Apr 2015 12:32:45: start model_add_line... INFO @ Tue, 21 Apr 2015 12:32:45: #2 number of paired peaks: 2525 INFO @ Tue, 21 Apr 2015 12:32:45: start model_add_line... INFO @ Tue, 21 Apr 2015 12:32:45: #2 number of paired peaks: 2525 INFO @ Tue, 21 Apr 2015 12:32:45: start model_add_line... INFO @ Tue, 21 Apr 2015 12:32:58: start X-correlation... INFO @ Tue, 21 Apr 2015 12:32:58: end of X-cor INFO @ Tue, 21 Apr 2015 12:32:58: #2 finished! INFO @ Tue, 21 Apr 2015 12:32:58: #2 predicted fragment length is 83 bps INFO @ Tue, 21 Apr 2015 12:32:58: #2 alternative fragment length(s) may be 83 bps INFO @ Tue, 21 Apr 2015 12:32:58: #2.2 Generate R script for model : SRX022745.20_model.r INFO @ Tue, 21 Apr 2015 12:32:58: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:32:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:32:58: start X-correlation... INFO @ Tue, 21 Apr 2015 12:32:58: end of X-cor INFO @ Tue, 21 Apr 2015 12:32:58: #2 finished! INFO @ Tue, 21 Apr 2015 12:32:58: #2 predicted fragment length is 83 bps INFO @ Tue, 21 Apr 2015 12:32:58: #2 alternative fragment length(s) may be 83 bps INFO @ Tue, 21 Apr 2015 12:32:58: #2.2 Generate R script for model : SRX022745.10_model.r INFO @ Tue, 21 Apr 2015 12:32:58: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:32:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:32:58: start X-correlation... INFO @ Tue, 21 Apr 2015 12:32:58: end of X-cor INFO @ Tue, 21 Apr 2015 12:32:58: #2 finished! INFO @ Tue, 21 Apr 2015 12:32:58: #2 predicted fragment length is 83 bps INFO @ Tue, 21 Apr 2015 12:32:58: #2 alternative fragment length(s) may be 83 bps INFO @ Tue, 21 Apr 2015 12:32:58: #2.2 Generate R script for model : SRX022745.05_model.r INFO @ Tue, 21 Apr 2015 12:32:58: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:32:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:33:40: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:33:43: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:33:44: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:34:13: #4 Write output xls file... SRX022745.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:34:13: #4 Write peak in narrowPeak format file... SRX022745.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:34:13: #4 Write summits bed file... SRX022745.20_summits.bed INFO @ Tue, 21 Apr 2015 12:34:13: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3422 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:34:15: #4 Write output xls file... SRX022745.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:34:15: #4 Write peak in narrowPeak format file... SRX022745.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:34:15: #4 Write summits bed file... SRX022745.10_summits.bed INFO @ Tue, 21 Apr 2015 12:34:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5513 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:34:22: #4 Write output xls file... SRX022745.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:34:22: #4 Write peak in narrowPeak format file... SRX022745.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:34:22: #4 Write summits bed file... SRX022745.05_summits.bed INFO @ Tue, 21 Apr 2015 12:34:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8153 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。