Job ID = 9025545 sra ファイルのダウンロード中... Completed: 2378767K bytes transferred in 20 seconds (935189K 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 21557 0 21557 0 0 2622 0 --:--:-- 0:00:08 --:--:-- 13056 100 52725 0 52725 0 0 5722 0 --:--:-- 0:00:09 --:--:-- 19926 100 116k 0 116k 0 0 11792 0 --:--:-- 0:00:10 --:--:-- 33823 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 70154866 spots for /home/okishinya/chipatlas/results/ce10/SRX1674092/SRR3320138.sra Written 70154866 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: 00:15:32 70154866 reads; of these: 70154866 (100.00%) were unpaired; of these: 14915677 (21.26%) aligned 0 times 44941593 (64.06%) aligned exactly 1 time 10297596 (14.68%) aligned >1 times 78.74% overall alignment rate Time searching: 00:15:32 Overall time: 00:15:32 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_sort_core] merging from 24 files... [bam_rmdupse_core] 49292300 / 55239189 = 0.8923 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 04:46:14: # Command line: callpeak -t SRX1674092.bam -f BAM -g ce -n SRX1674092.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1674092.10 # format = BAM # ChIP-seq file = ['SRX1674092.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 04:46:14: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:46:14: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:46:14: # Command line: callpeak -t SRX1674092.bam -f BAM -g ce -n SRX1674092.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1674092.05 # format = BAM # ChIP-seq file = ['SRX1674092.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 04:46:14: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:46:14: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:46:14: # Command line: callpeak -t SRX1674092.bam -f BAM -g ce -n SRX1674092.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1674092.20 # format = BAM # ChIP-seq file = ['SRX1674092.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 04:46:14: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:46:14: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:46:21: 1000000 INFO @ Sat, 03 Jun 2017 04:46:21: 1000000 INFO @ Sat, 03 Jun 2017 04:46:21: 1000000 INFO @ Sat, 03 Jun 2017 04:46:28: 2000000 INFO @ Sat, 03 Jun 2017 04:46:28: 2000000 INFO @ Sat, 03 Jun 2017 04:46:28: 2000000 INFO @ Sat, 03 Jun 2017 04:46:36: 3000000 INFO @ Sat, 03 Jun 2017 04:46:36: 3000000 INFO @ Sat, 03 Jun 2017 04:46:36: 3000000 INFO @ Sat, 03 Jun 2017 04:46:43: 4000000 INFO @ Sat, 03 Jun 2017 04:46:43: 4000000 INFO @ Sat, 03 Jun 2017 04:46:43: 4000000 INFO @ Sat, 03 Jun 2017 04:46:50: 5000000 INFO @ Sat, 03 Jun 2017 04:46:50: 5000000 INFO @ Sat, 03 Jun 2017 04:46:50: 5000000 INFO @ Sat, 03 Jun 2017 04:46:57: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:46:57: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:46:57: #1 total tags in treatment: 5946889 INFO @ Sat, 03 Jun 2017 04:46:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:46:57: #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 04:46:57: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:46:57: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:46:57: #1 total tags in treatment: 5946889 INFO @ Sat, 03 Jun 2017 04:46:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:46:57: #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 04:46:58: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:46:58: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:46:58: #1 total tags in treatment: 5946889 INFO @ Sat, 03 Jun 2017 04:46:58: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:46:58: #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 04:46:58: #1 tags after filtering in treatment: 5943560 INFO @ Sat, 03 Jun 2017 04:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:46:58: #1 finished! INFO @ Sat, 03 Jun 2017 04:46:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:46:59: #1 tags after filtering in treatment: 5943560 INFO @ Sat, 03 Jun 2017 04:46:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:46:59: #1 finished! INFO @ Sat, 03 Jun 2017 04:46:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:46:59: #1 tags after filtering in treatment: 5943560 INFO @ Sat, 03 Jun 2017 04:46:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:46:59: #1 finished! INFO @ Sat, 03 Jun 2017 04:46:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:47:00: #2 number of paired peaks: 2405 INFO @ Sat, 03 Jun 2017 04:47:00: start model_add_line... INFO @ Sat, 03 Jun 2017 04:47:00: #2 number of paired peaks: 2405 INFO @ Sat, 03 Jun 2017 04:47:00: start model_add_line... INFO @ Sat, 03 Jun 2017 04:47:00: #2 number of paired peaks: 2405 INFO @ Sat, 03 Jun 2017 04:47:00: start model_add_line... INFO @ Sat, 03 Jun 2017 04:47:17: start X-correlation... INFO @ Sat, 03 Jun 2017 04:47:17: end of X-cor INFO @ Sat, 03 Jun 2017 04:47:17: #2 finished! INFO @ Sat, 03 Jun 2017 04:47:17: #2 predicted fragment length is 129 bps INFO @ Sat, 03 Jun 2017 04:47:17: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 03 Jun 2017 04:47:17: #2.2 Generate R script for model : SRX1674092.10_model.r INFO @ Sat, 03 Jun 2017 04:47:17: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:47:17: start X-correlation... INFO @ Sat, 03 Jun 2017 04:47:18: end of X-cor INFO @ Sat, 03 Jun 2017 04:47:18: #2 finished! INFO @ Sat, 03 Jun 2017 04:47:18: #2 predicted fragment length is 129 bps INFO @ Sat, 03 Jun 2017 04:47:18: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 03 Jun 2017 04:47:18: #2.2 Generate R script for model : SRX1674092.20_model.r INFO @ Sat, 03 Jun 2017 04:47:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:47:18: start X-correlation... INFO @ Sat, 03 Jun 2017 04:47:18: end of X-cor INFO @ Sat, 03 Jun 2017 04:47:18: #2 finished! INFO @ Sat, 03 Jun 2017 04:47:18: #2 predicted fragment length is 129 bps INFO @ Sat, 03 Jun 2017 04:47:18: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 03 Jun 2017 04:47:18: #2.2 Generate R script for model : SRX1674092.05_model.r INFO @ Sat, 03 Jun 2017 04:47:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:47:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:47:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:47:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:48:21: #4 Write output xls file... SRX1674092.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:48:21: #4 Write peak in narrowPeak format file... SRX1674092.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:48:21: #4 Write summits bed file... SRX1674092.20_summits.bed INFO @ Sat, 03 Jun 2017 04:48:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1954 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:48:24: #4 Write output xls file... SRX1674092.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:48:24: #4 Write peak in narrowPeak format file... SRX1674092.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:48:24: #4 Write summits bed file... SRX1674092.10_summits.bed INFO @ Sat, 03 Jun 2017 04:48:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4471 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:48:28: #4 Write output xls file... SRX1674092.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:48:28: #4 Write peak in narrowPeak format file... SRX1674092.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:48:28: #4 Write summits bed file... SRX1674092.05_summits.bed INFO @ Sat, 03 Jun 2017 04:48:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8905 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。