Job ID = 9041706 sra ファイルのダウンロード中... Completed: 1332699K bytes transferred in 13 seconds (797104K 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 --:--:-- 0 100 22317 0 22317 0 0 2772 0 --:--:-- 0:00:08 --:--:-- 14828 100 46173 0 46173 0 0 5200 0 --:--:-- 0:00:08 --:--:-- 19774 100 94802 0 94802 0 0 10067 0 --:--:-- 0:00:09 --:--:-- 32986 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 38750446 spots for /home/okishinya/chipatlas/results/dm3/SRX1361354/SRR2749792.sra Written 38750446 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: 00:05:29 38750446 reads; of these: 38750446 (100.00%) were unpaired; of these: 3190656 (8.23%) aligned 0 times 28939513 (74.68%) aligned exactly 1 time 6620277 (17.08%) aligned >1 times 91.77% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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_sort_core] merging from 16 files... [bam_rmdupse_core] 28776513 / 35559790 = 0.8092 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 @ Mon, 05 Jun 2017 01:44:59: # Command line: callpeak -t SRX1361354.bam -f BAM -g dm -n SRX1361354.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1361354.20 # format = BAM # ChIP-seq file = ['SRX1361354.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 @ Mon, 05 Jun 2017 01:44:59: # Command line: callpeak -t SRX1361354.bam -f BAM -g dm -n SRX1361354.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1361354.10 # format = BAM # ChIP-seq file = ['SRX1361354.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 @ Mon, 05 Jun 2017 01:44:59: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:44:59: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:44:59: # Command line: callpeak -t SRX1361354.bam -f BAM -g dm -n SRX1361354.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1361354.05 # format = BAM # ChIP-seq file = ['SRX1361354.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 @ Mon, 05 Jun 2017 01:44:59: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:44:59: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:44:59: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:44:59: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:45:06: 1000000 INFO @ Mon, 05 Jun 2017 01:45:06: 1000000 INFO @ Mon, 05 Jun 2017 01:45:06: 1000000 INFO @ Mon, 05 Jun 2017 01:45:13: 2000000 INFO @ Mon, 05 Jun 2017 01:45:13: 2000000 INFO @ Mon, 05 Jun 2017 01:45:13: 2000000 INFO @ Mon, 05 Jun 2017 01:45:20: 3000000 INFO @ Mon, 05 Jun 2017 01:45:20: 3000000 INFO @ Mon, 05 Jun 2017 01:45:20: 3000000 INFO @ Mon, 05 Jun 2017 01:45:27: 4000000 INFO @ Mon, 05 Jun 2017 01:45:27: 4000000 INFO @ Mon, 05 Jun 2017 01:45:27: 4000000 INFO @ Mon, 05 Jun 2017 01:45:35: 5000000 INFO @ Mon, 05 Jun 2017 01:45:35: 5000000 INFO @ Mon, 05 Jun 2017 01:45:35: 5000000 INFO @ Mon, 05 Jun 2017 01:45:42: 6000000 INFO @ Mon, 05 Jun 2017 01:45:42: 6000000 INFO @ Mon, 05 Jun 2017 01:45:42: 6000000 INFO @ Mon, 05 Jun 2017 01:45:47: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:45:47: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:45:47: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:45:47: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:45:47: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:45:47: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:45:47: #1 total tags in treatment: 6783277 INFO @ Mon, 05 Jun 2017 01:45:47: #1 total tags in treatment: 6783277 INFO @ Mon, 05 Jun 2017 01:45:47: #1 total tags in treatment: 6783277 INFO @ Mon, 05 Jun 2017 01:45:47: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:45:47: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:45:47: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:45:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:45:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:45:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:45:48: #1 tags after filtering in treatment: 6779902 INFO @ Mon, 05 Jun 2017 01:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:45:48: #1 finished! INFO @ Mon, 05 Jun 2017 01:45:48: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:45:48: #1 tags after filtering in treatment: 6779902 INFO @ Mon, 05 Jun 2017 01:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:45:48: #1 finished! INFO @ Mon, 05 Jun 2017 01:45:48: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:45:48: #1 tags after filtering in treatment: 6779902 INFO @ Mon, 05 Jun 2017 01:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:45:48: #1 finished! INFO @ Mon, 05 Jun 2017 01:45:48: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:45:50: #2 number of paired peaks: 5250 INFO @ Mon, 05 Jun 2017 01:45:50: start model_add_line... INFO @ Mon, 05 Jun 2017 01:45:50: #2 number of paired peaks: 5250 INFO @ Mon, 05 Jun 2017 01:45:50: start model_add_line... INFO @ Mon, 05 Jun 2017 01:45:50: #2 number of paired peaks: 5250 INFO @ Mon, 05 Jun 2017 01:45:50: start model_add_line... INFO @ Mon, 05 Jun 2017 01:46:18: start X-correlation... INFO @ Mon, 05 Jun 2017 01:46:18: end of X-cor INFO @ Mon, 05 Jun 2017 01:46:18: #2 finished! INFO @ Mon, 05 Jun 2017 01:46:18: #2 predicted fragment length is 194 bps INFO @ Mon, 05 Jun 2017 01:46:18: #2 alternative fragment length(s) may be 194 bps INFO @ Mon, 05 Jun 2017 01:46:18: #2.2 Generate R script for model : SRX1361354.05_model.r INFO @ Mon, 05 Jun 2017 01:46:18: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:46:18: start X-correlation... INFO @ Mon, 05 Jun 2017 01:46:18: end of X-cor INFO @ Mon, 05 Jun 2017 01:46:18: #2 finished! INFO @ Mon, 05 Jun 2017 01:46:18: #2 predicted fragment length is 194 bps INFO @ Mon, 05 Jun 2017 01:46:18: #2 alternative fragment length(s) may be 194 bps INFO @ Mon, 05 Jun 2017 01:46:18: #2.2 Generate R script for model : SRX1361354.10_model.r INFO @ Mon, 05 Jun 2017 01:46:18: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:46:19: start X-correlation... INFO @ Mon, 05 Jun 2017 01:46:19: end of X-cor INFO @ Mon, 05 Jun 2017 01:46:19: #2 finished! INFO @ Mon, 05 Jun 2017 01:46:19: #2 predicted fragment length is 194 bps INFO @ Mon, 05 Jun 2017 01:46:19: #2 alternative fragment length(s) may be 194 bps INFO @ Mon, 05 Jun 2017 01:46:19: #2.2 Generate R script for model : SRX1361354.20_model.r INFO @ Mon, 05 Jun 2017 01:46:19: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:46:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:47:03: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 01:47:04: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 01:47:06: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Mon, 05 Jun 2017 01:47:43: #4 Write output xls file... SRX1361354.20_peaks.xls INFO @ Mon, 05 Jun 2017 01:47:43: #4 Write peak in narrowPeak format file... SRX1361354.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 01:47:43: #4 Write summits bed file... SRX1361354.20_summits.bed INFO @ Mon, 05 Jun 2017 01:47:43: Done! pass1 - making usageList (14 chroms): 2 millis INFO @ Mon, 05 Jun 2017 01:47:43: #4 Write output xls file... SRX1361354.10_peaks.xls pass2 - checking and writing primary data (5133 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 01:47:43: #4 Write peak in narrowPeak format file... SRX1361354.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 01:47:43: #4 Write summits bed file... SRX1361354.10_summits.bed INFO @ Mon, 05 Jun 2017 01:47:43: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6891 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 01:47:49: #4 Write output xls file... SRX1361354.05_peaks.xls INFO @ Mon, 05 Jun 2017 01:47:49: #4 Write peak in narrowPeak format file... SRX1361354.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 01:47:50: #4 Write summits bed file... SRX1361354.05_summits.bed INFO @ Mon, 05 Jun 2017 01:47:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9159 records, 4 fields): 13 millis CompletedMACS2peakCalling