Job ID = 9029558 sra ファイルのダウンロード中... Completed: 645345K bytes transferred in 9 seconds (582698K 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 7663 0 7663 0 0 1070 0 --:--:-- 0:00:07 --:--:-- 10043 100 30317 0 30317 0 0 3796 0 --:--:-- 0:00:07 --:--:-- 19031 100 86317 0 86317 0 0 9701 0 --:--:-- 0:00:08 --:--:-- 34457 100 165k 0 165k 0 0 17224 0 --:--:-- 0:00:09 --:--:-- 49068 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 11670353 spots for /home/okishinya/chipatlas/results/dm3/SRX1840071/SRR3661297.sra Written 11670353 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: 00:07:01 11670353 reads; of these: 11670353 (100.00%) were unpaired; of these: 2745650 (23.53%) aligned 0 times 6689612 (57.32%) aligned exactly 1 time 2235091 (19.15%) aligned >1 times 76.47% overall alignment rate Time searching: 00:07:01 Overall time: 00:07:01 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] 2280329 / 8924703 = 0.2555 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 14:19:32: # Command line: callpeak -t SRX1840071.bam -f BAM -g dm -n SRX1840071.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1840071.20 # format = BAM # ChIP-seq file = ['SRX1840071.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 14:19:32: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:19:32: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:19:32: # Command line: callpeak -t SRX1840071.bam -f BAM -g dm -n SRX1840071.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1840071.10 # format = BAM # ChIP-seq file = ['SRX1840071.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 14:19:32: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:19:32: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:19:32: # Command line: callpeak -t SRX1840071.bam -f BAM -g dm -n SRX1840071.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1840071.05 # format = BAM # ChIP-seq file = ['SRX1840071.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 14:19:32: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:19:32: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:19:40: 1000000 INFO @ Sat, 03 Jun 2017 14:19:40: 1000000 INFO @ Sat, 03 Jun 2017 14:19:40: 1000000 INFO @ Sat, 03 Jun 2017 14:19:49: 2000000 INFO @ Sat, 03 Jun 2017 14:19:49: 2000000 INFO @ Sat, 03 Jun 2017 14:19:49: 2000000 INFO @ Sat, 03 Jun 2017 14:19:57: 3000000 INFO @ Sat, 03 Jun 2017 14:19:57: 3000000 INFO @ Sat, 03 Jun 2017 14:19:57: 3000000 INFO @ Sat, 03 Jun 2017 14:20:06: 4000000 INFO @ Sat, 03 Jun 2017 14:20:06: 4000000 INFO @ Sat, 03 Jun 2017 14:20:06: 4000000 INFO @ Sat, 03 Jun 2017 14:20:14: 5000000 INFO @ Sat, 03 Jun 2017 14:20:14: 5000000 INFO @ Sat, 03 Jun 2017 14:20:14: 5000000 INFO @ Sat, 03 Jun 2017 14:20:23: 6000000 INFO @ Sat, 03 Jun 2017 14:20:23: 6000000 INFO @ Sat, 03 Jun 2017 14:20:23: 6000000 INFO @ Sat, 03 Jun 2017 14:20:29: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:20:29: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:20:29: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:20:29: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:20:29: #1 total tags in treatment: 6644374 INFO @ Sat, 03 Jun 2017 14:20:29: #1 total tags in treatment: 6644374 INFO @ Sat, 03 Jun 2017 14:20:29: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:20:29: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:20:29: #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 14:20:29: #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 14:20:29: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:20:29: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:20:29: #1 total tags in treatment: 6644374 INFO @ Sat, 03 Jun 2017 14:20:29: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:20:29: #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 14:20:30: #1 tags after filtering in treatment: 6637963 INFO @ Sat, 03 Jun 2017 14:20:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:20:30: #1 finished! INFO @ Sat, 03 Jun 2017 14:20:30: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:20:30: #1 tags after filtering in treatment: 6637963 INFO @ Sat, 03 Jun 2017 14:20:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:20:30: #1 finished! INFO @ Sat, 03 Jun 2017 14:20:30: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:20:30: #1 tags after filtering in treatment: 6637963 INFO @ Sat, 03 Jun 2017 14:20:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:20:30: #1 finished! INFO @ Sat, 03 Jun 2017 14:20:30: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:20:31: #2 number of paired peaks: 1715 INFO @ Sat, 03 Jun 2017 14:20:31: start model_add_line... INFO @ Sat, 03 Jun 2017 14:20:31: #2 number of paired peaks: 1715 INFO @ Sat, 03 Jun 2017 14:20:31: start model_add_line... INFO @ Sat, 03 Jun 2017 14:20:32: #2 number of paired peaks: 1715 INFO @ Sat, 03 Jun 2017 14:20:32: start model_add_line... INFO @ Sat, 03 Jun 2017 14:20:39: start X-correlation... INFO @ Sat, 03 Jun 2017 14:20:39: end of X-cor INFO @ Sat, 03 Jun 2017 14:20:39: #2 finished! INFO @ Sat, 03 Jun 2017 14:20:39: #2 predicted fragment length is 305 bps INFO @ Sat, 03 Jun 2017 14:20:39: #2 alternative fragment length(s) may be 305 bps INFO @ Sat, 03 Jun 2017 14:20:39: #2.2 Generate R script for model : SRX1840071.05_model.r INFO @ Sat, 03 Jun 2017 14:20:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:20:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:20:39: start X-correlation... INFO @ Sat, 03 Jun 2017 14:20:39: end of X-cor INFO @ Sat, 03 Jun 2017 14:20:39: #2 finished! INFO @ Sat, 03 Jun 2017 14:20:39: #2 predicted fragment length is 305 bps INFO @ Sat, 03 Jun 2017 14:20:39: #2 alternative fragment length(s) may be 305 bps INFO @ Sat, 03 Jun 2017 14:20:39: #2.2 Generate R script for model : SRX1840071.20_model.r INFO @ Sat, 03 Jun 2017 14:20:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:20:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:20:39: start X-correlation... INFO @ Sat, 03 Jun 2017 14:20:39: end of X-cor INFO @ Sat, 03 Jun 2017 14:20:39: #2 finished! INFO @ Sat, 03 Jun 2017 14:20:39: #2 predicted fragment length is 305 bps INFO @ Sat, 03 Jun 2017 14:20:39: #2 alternative fragment length(s) may be 305 bps INFO @ Sat, 03 Jun 2017 14:20:39: #2.2 Generate R script for model : SRX1840071.10_model.r INFO @ Sat, 03 Jun 2017 14:20:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:20:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:21:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:21:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:21:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:21:57: #4 Write output xls file... SRX1840071.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:21:57: #4 Write output xls file... SRX1840071.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:21:57: #4 Write peak in narrowPeak format file... SRX1840071.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:21:57: #4 Write peak in narrowPeak format file... SRX1840071.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:21:57: #4 Write summits bed file... SRX1840071.20_summits.bed INFO @ Sat, 03 Jun 2017 14:21:57: Done! INFO @ Sat, 03 Jun 2017 14:21:57: #4 Write summits bed file... SRX1840071.10_summits.bed INFO @ Sat, 03 Jun 2017 14:21:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1869 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3184 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:21:58: #4 Write output xls file... SRX1840071.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:21:58: #4 Write peak in narrowPeak format file... SRX1840071.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:21:58: #4 Write summits bed file... SRX1840071.05_summits.bed INFO @ Sat, 03 Jun 2017 14:21:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4736 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。