Job ID = 9025518 sra ファイルのダウンロード中... Completed: 124050K bytes transferred in 4 seconds (217531K 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 22318 0 22318 0 0 2692 0 --:--:-- 0:00:08 --:--:-- 11928 100 46618 0 46618 0 0 5305 0 --:--:-- 0:00:08 --:--:-- 19694 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 5332698 spots for /home/okishinya/chipatlas/results/ce10/SRX1388767/SRR2832483.sra Written 5332698 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: 00:01:19 5332698 reads; of these: 5332698 (100.00%) were unpaired; of these: 430802 (8.08%) aligned 0 times 4248843 (79.68%) aligned exactly 1 time 653053 (12.25%) aligned >1 times 91.92% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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_rmdupse_core] 482599 / 4901896 = 0.0985 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 04:15:35: # Command line: callpeak -t SRX1388767.bam -f BAM -g ce -n SRX1388767.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388767.10 # format = BAM # ChIP-seq file = ['SRX1388767.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 04:15:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:15:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:15:35: # Command line: callpeak -t SRX1388767.bam -f BAM -g ce -n SRX1388767.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388767.20 # format = BAM # ChIP-seq file = ['SRX1388767.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 04:15:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:15:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:15:35: # Command line: callpeak -t SRX1388767.bam -f BAM -g ce -n SRX1388767.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388767.05 # format = BAM # ChIP-seq file = ['SRX1388767.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 04:15:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:15:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:15:42: 1000000 INFO @ Sat, 03 Jun 2017 04:15:42: 1000000 INFO @ Sat, 03 Jun 2017 04:15:42: 1000000 INFO @ Sat, 03 Jun 2017 04:15:48: 2000000 INFO @ Sat, 03 Jun 2017 04:15:48: 2000000 INFO @ Sat, 03 Jun 2017 04:15:48: 2000000 INFO @ Sat, 03 Jun 2017 04:15:53: 3000000 INFO @ Sat, 03 Jun 2017 04:15:54: 3000000 INFO @ Sat, 03 Jun 2017 04:15:54: 3000000 INFO @ Sat, 03 Jun 2017 04:15:58: 4000000 INFO @ Sat, 03 Jun 2017 04:15:59: 4000000 INFO @ Sat, 03 Jun 2017 04:15:59: 4000000 INFO @ Sat, 03 Jun 2017 04:16:00: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:16:00: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:16:00: #1 total tags in treatment: 4419297 INFO @ Sat, 03 Jun 2017 04:16:00: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:16:00: #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 04:16:01: #1 tags after filtering in treatment: 4418485 INFO @ Sat, 03 Jun 2017 04:16:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:16:01: #1 finished! INFO @ Sat, 03 Jun 2017 04:16:01: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:16:01: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:16:01: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:16:01: #1 total tags in treatment: 4419297 INFO @ Sat, 03 Jun 2017 04:16:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:16:01: #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 04:16:02: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:16:02: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:16:02: #1 total tags in treatment: 4419297 INFO @ Sat, 03 Jun 2017 04:16:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:16:02: #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 04:16:02: #2 number of paired peaks: 2773 INFO @ Sat, 03 Jun 2017 04:16:02: start model_add_line... INFO @ Sat, 03 Jun 2017 04:16:02: #1 tags after filtering in treatment: 4418485 INFO @ Sat, 03 Jun 2017 04:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:16:02: #1 finished! INFO @ Sat, 03 Jun 2017 04:16:02: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:16:02: #1 tags after filtering in treatment: 4418485 INFO @ Sat, 03 Jun 2017 04:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:16:02: #1 finished! INFO @ Sat, 03 Jun 2017 04:16:02: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:16:03: #2 number of paired peaks: 2773 INFO @ Sat, 03 Jun 2017 04:16:03: start model_add_line... INFO @ Sat, 03 Jun 2017 04:16:03: #2 number of paired peaks: 2773 INFO @ Sat, 03 Jun 2017 04:16:03: start model_add_line... INFO @ Sat, 03 Jun 2017 04:16:15: start X-correlation... INFO @ Sat, 03 Jun 2017 04:16:15: end of X-cor INFO @ Sat, 03 Jun 2017 04:16:15: #2 finished! INFO @ Sat, 03 Jun 2017 04:16:15: #2 predicted fragment length is 174 bps INFO @ Sat, 03 Jun 2017 04:16:15: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 03 Jun 2017 04:16:15: #2.2 Generate R script for model : SRX1388767.05_model.r INFO @ Sat, 03 Jun 2017 04:16:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:16:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:16:16: start X-correlation... INFO @ Sat, 03 Jun 2017 04:16:16: end of X-cor INFO @ Sat, 03 Jun 2017 04:16:16: #2 finished! INFO @ Sat, 03 Jun 2017 04:16:16: #2 predicted fragment length is 174 bps INFO @ Sat, 03 Jun 2017 04:16:16: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 03 Jun 2017 04:16:16: #2.2 Generate R script for model : SRX1388767.20_model.r INFO @ Sat, 03 Jun 2017 04:16:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:16:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:16:17: start X-correlation... INFO @ Sat, 03 Jun 2017 04:16:17: end of X-cor INFO @ Sat, 03 Jun 2017 04:16:17: #2 finished! INFO @ Sat, 03 Jun 2017 04:16:17: #2 predicted fragment length is 174 bps INFO @ Sat, 03 Jun 2017 04:16:17: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 03 Jun 2017 04:16:17: #2.2 Generate R script for model : SRX1388767.10_model.r INFO @ Sat, 03 Jun 2017 04:16:17: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:16:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:16:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:16:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:17:03: #4 Write output xls file... SRX1388767.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:17:03: #4 Write peak in narrowPeak format file... SRX1388767.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:17:03: #4 Write summits bed file... SRX1388767.20_summits.bed INFO @ Sat, 03 Jun 2017 04:17:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (748 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:17:05: #4 Write output xls file... SRX1388767.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:17:05: #4 Write peak in narrowPeak format file... SRX1388767.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:17:05: #4 Write summits bed file... SRX1388767.10_summits.bed INFO @ Sat, 03 Jun 2017 04:17:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2038 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:17:08: #4 Write output xls file... SRX1388767.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:17:08: #4 Write peak in narrowPeak format file... SRX1388767.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:17:08: #4 Write summits bed file... SRX1388767.05_summits.bed INFO @ Sat, 03 Jun 2017 04:17:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3900 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。