Job ID = 9029284 sra ファイルのダウンロード中... Completed: 501178K bytes transferred in 7 seconds (553575K 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 --:--:-- 0 100 14324 0 14324 0 0 1887 0 --:--:-- 0:00:07 --:--:-- 14070 100 55544 0 55544 0 0 6565 0 --:--:-- 0:00:08 --:--:-- 29403 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 22460845 spots for /home/okishinya/chipatlas/results/dm3/SRX1531760/SRR3102818.sra Written 22460845 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: 00:02:08 22460845 reads; of these: 22460845 (100.00%) were unpaired; of these: 22317076 (99.36%) aligned 0 times 120174 (0.54%) aligned exactly 1 time 23595 (0.11%) aligned >1 times 0.64% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 19273 / 143769 = 0.1341 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 13:03:15: # Command line: callpeak -t SRX1531760.bam -f BAM -g dm -n SRX1531760.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1531760.20 # format = BAM # ChIP-seq file = ['SRX1531760.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 @ Sat, 03 Jun 2017 13:03:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:03:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:03:15: # Command line: callpeak -t SRX1531760.bam -f BAM -g dm -n SRX1531760.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1531760.10 # format = BAM # ChIP-seq file = ['SRX1531760.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 @ Sat, 03 Jun 2017 13:03:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:03:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:03:15: # Command line: callpeak -t SRX1531760.bam -f BAM -g dm -n SRX1531760.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1531760.05 # format = BAM # ChIP-seq file = ['SRX1531760.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 @ Sat, 03 Jun 2017 13:03:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:03:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:03:16: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:03:16: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:03:16: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:03:16: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:03:16: #1 total tags in treatment: 124496 INFO @ Sat, 03 Jun 2017 13:03:16: #1 total tags in treatment: 124496 INFO @ Sat, 03 Jun 2017 13:03:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:03:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:03:16: #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 13:03:16: #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 13:03:16: #1 tags after filtering in treatment: 124476 INFO @ Sat, 03 Jun 2017 13:03:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:03:16: #1 finished! INFO @ Sat, 03 Jun 2017 13:03:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:03:16: #1 tags after filtering in treatment: 124476 INFO @ Sat, 03 Jun 2017 13:03:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:03:16: #1 finished! INFO @ Sat, 03 Jun 2017 13:03:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:03:16: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:03:16: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:03:16: #1 total tags in treatment: 124496 INFO @ Sat, 03 Jun 2017 13:03:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:03:16: #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 13:03:16: #1 tags after filtering in treatment: 124476 INFO @ Sat, 03 Jun 2017 13:03:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:03:16: #1 finished! INFO @ Sat, 03 Jun 2017 13:03:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:03:16: #2 number of paired peaks: 2277 INFO @ Sat, 03 Jun 2017 13:03:16: start model_add_line... INFO @ Sat, 03 Jun 2017 13:03:16: #2 number of paired peaks: 2277 INFO @ Sat, 03 Jun 2017 13:03:16: start model_add_line... INFO @ Sat, 03 Jun 2017 13:03:17: #2 number of paired peaks: 2277 INFO @ Sat, 03 Jun 2017 13:03:17: start model_add_line... INFO @ Sat, 03 Jun 2017 13:03:17: start X-correlation... INFO @ Sat, 03 Jun 2017 13:03:17: end of X-cor INFO @ Sat, 03 Jun 2017 13:03:17: #2 finished! INFO @ Sat, 03 Jun 2017 13:03:17: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Jun 2017 13:03:17: #2 alternative fragment length(s) may be 128,596 bps INFO @ Sat, 03 Jun 2017 13:03:17: #2.2 Generate R script for model : SRX1531760.10_model.r INFO @ Sat, 03 Jun 2017 13:03:17: start X-correlation... INFO @ Sat, 03 Jun 2017 13:03:17: end of X-cor INFO @ Sat, 03 Jun 2017 13:03:17: #2 finished! INFO @ Sat, 03 Jun 2017 13:03:17: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Jun 2017 13:03:17: #2 alternative fragment length(s) may be 128,596 bps INFO @ Sat, 03 Jun 2017 13:03:17: #2.2 Generate R script for model : SRX1531760.20_model.r INFO @ Sat, 03 Jun 2017 13:03:17: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:03:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:03:17: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:03:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:03:17: start X-correlation... INFO @ Sat, 03 Jun 2017 13:03:17: end of X-cor INFO @ Sat, 03 Jun 2017 13:03:17: #2 finished! INFO @ Sat, 03 Jun 2017 13:03:17: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Jun 2017 13:03:17: #2 alternative fragment length(s) may be 128,596 bps INFO @ Sat, 03 Jun 2017 13:03:17: #2.2 Generate R script for model : SRX1531760.05_model.r INFO @ Sat, 03 Jun 2017 13:03:17: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:03:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:03:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:03:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:03:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:03:18: #4 Write output xls file... SRX1531760.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:03:18: #4 Write peak in narrowPeak format file... SRX1531760.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:03:18: #4 Write summits bed file... SRX1531760.20_summits.bed INFO @ Sat, 03 Jun 2017 13:03:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (32 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:03:18: #4 Write output xls file... SRX1531760.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:03:18: #4 Write peak in narrowPeak format file... SRX1531760.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:03:18: #4 Write summits bed file... SRX1531760.10_summits.bed INFO @ Sat, 03 Jun 2017 13:03:18: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (122 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 13:03:18: #4 Write output xls file... SRX1531760.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:03:18: #4 Write peak in narrowPeak format file... SRX1531760.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:03:18: #4 Write summits bed file... SRX1531760.05_summits.bed INFO @ Sat, 03 Jun 2017 13:03:18: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (313 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。