Job ID = 9025517 sra ファイルのダウンロード中... Completed: 84640K bytes transferred in 4 seconds (161118K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 100 14324 0 14324 0 0 1494 0 --:--:-- 0:00:09 --:--:-- 5340 100 47495 0 47495 0 0 4615 0 --:--:-- 0:00:10 --:--:-- 14026 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 3615269 spots for /home/okishinya/chipatlas/results/ce10/SRX1388766/SRR2832482.sra Written 3615269 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: 00:01:06 3615269 reads; of these: 3615269 (100.00%) were unpaired; of these: 399781 (11.06%) aligned 0 times 2725130 (75.38%) aligned exactly 1 time 490358 (13.56%) aligned >1 times 88.94% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 264466 / 3215488 = 0.0822 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 04:14:38: # Command line: callpeak -t SRX1388766.bam -f BAM -g ce -n SRX1388766.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388766.10 # format = BAM # ChIP-seq file = ['SRX1388766.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 04:14:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:14:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:14:38: # Command line: callpeak -t SRX1388766.bam -f BAM -g ce -n SRX1388766.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388766.20 # format = BAM # ChIP-seq file = ['SRX1388766.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 04:14:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:14:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:14:38: # Command line: callpeak -t SRX1388766.bam -f BAM -g ce -n SRX1388766.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388766.05 # format = BAM # ChIP-seq file = ['SRX1388766.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 04:14:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:14:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:14:44: 1000000 INFO @ Sat, 03 Jun 2017 04:14:44: 1000000 INFO @ Sat, 03 Jun 2017 04:14:44: 1000000 INFO @ Sat, 03 Jun 2017 04:14:49: 2000000 INFO @ Sat, 03 Jun 2017 04:14:50: 2000000 INFO @ Sat, 03 Jun 2017 04:14:50: 2000000 INFO @ Sat, 03 Jun 2017 04:14:55: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:14:55: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:14:55: #1 total tags in treatment: 2951022 INFO @ Sat, 03 Jun 2017 04:14:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:14:55: #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 04:14:55: #1 tags after filtering in treatment: 2950659 INFO @ Sat, 03 Jun 2017 04:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:14:55: #1 finished! INFO @ Sat, 03 Jun 2017 04:14:55: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:14:56: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:14:56: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:14:56: #1 total tags in treatment: 2951022 INFO @ Sat, 03 Jun 2017 04:14:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:14:56: #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 04:14:56: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:14:56: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:14:56: #1 total tags in treatment: 2951022 INFO @ Sat, 03 Jun 2017 04:14:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:14:56: #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 04:14:56: #2 number of paired peaks: 1789 INFO @ Sat, 03 Jun 2017 04:14:56: start model_add_line... INFO @ Sat, 03 Jun 2017 04:14:56: #1 tags after filtering in treatment: 2950659 INFO @ Sat, 03 Jun 2017 04:14:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:14:56: #1 finished! INFO @ Sat, 03 Jun 2017 04:14:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:14:56: #1 tags after filtering in treatment: 2950659 INFO @ Sat, 03 Jun 2017 04:14:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:14:56: #1 finished! INFO @ Sat, 03 Jun 2017 04:14:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:14:57: #2 number of paired peaks: 1789 INFO @ Sat, 03 Jun 2017 04:14:57: start model_add_line... INFO @ Sat, 03 Jun 2017 04:14:57: #2 number of paired peaks: 1789 INFO @ Sat, 03 Jun 2017 04:14:57: start model_add_line... INFO @ Sat, 03 Jun 2017 04:15:02: start X-correlation... INFO @ Sat, 03 Jun 2017 04:15:02: end of X-cor INFO @ Sat, 03 Jun 2017 04:15:02: #2 finished! INFO @ Sat, 03 Jun 2017 04:15:02: #2 predicted fragment length is 144 bps INFO @ Sat, 03 Jun 2017 04:15:02: #2 alternative fragment length(s) may be 144,151 bps INFO @ Sat, 03 Jun 2017 04:15:02: #2.2 Generate R script for model : SRX1388766.10_model.r INFO @ Sat, 03 Jun 2017 04:15:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:15:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:15:03: start X-correlation... INFO @ Sat, 03 Jun 2017 04:15:03: end of X-cor INFO @ Sat, 03 Jun 2017 04:15:03: #2 finished! INFO @ Sat, 03 Jun 2017 04:15:03: #2 predicted fragment length is 144 bps INFO @ Sat, 03 Jun 2017 04:15:03: #2 alternative fragment length(s) may be 144,151 bps INFO @ Sat, 03 Jun 2017 04:15:03: #2.2 Generate R script for model : SRX1388766.05_model.r INFO @ Sat, 03 Jun 2017 04:15:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:15:03: start X-correlation... INFO @ Sat, 03 Jun 2017 04:15:03: end of X-cor INFO @ Sat, 03 Jun 2017 04:15:03: #2 finished! INFO @ Sat, 03 Jun 2017 04:15:03: #2 predicted fragment length is 144 bps INFO @ Sat, 03 Jun 2017 04:15:03: #2 alternative fragment length(s) may be 144,151 bps INFO @ Sat, 03 Jun 2017 04:15:03: #2.2 Generate R script for model : SRX1388766.20_model.r INFO @ Sat, 03 Jun 2017 04:15:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:15:20: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:15:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:15:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:15:34: #4 Write output xls file... SRX1388766.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:15:34: #4 Write peak in narrowPeak format file... SRX1388766.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:15:34: #4 Write summits bed file... SRX1388766.10_summits.bed INFO @ Sat, 03 Jun 2017 04:15:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (784 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:15:35: #4 Write output xls file... SRX1388766.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:15:35: #4 Write peak in narrowPeak format file... SRX1388766.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:15:35: #4 Write summits bed file... SRX1388766.20_summits.bed INFO @ Sat, 03 Jun 2017 04:15:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (269 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:15:35: #4 Write output xls file... SRX1388766.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:15:35: #4 Write peak in narrowPeak format file... SRX1388766.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:15:35: #4 Write summits bed file... SRX1388766.05_summits.bed INFO @ Sat, 03 Jun 2017 04:15:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1957 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。