Job ID = 9029289 sra ファイルのダウンロード中... Completed: 751230K bytes transferred in 8 seconds (684166K 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 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1874 0 --:--:-- 0:00:07 --:--:-- 12520 100 54318 0 54318 0 0 6289 0 --:--:-- 0:00:08 --:--:-- 25382 100 75194 0 75194 0 0 8542 0 --:--:-- 0:00:08 --:--:-- 32593 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 26739196 spots for /home/okishinya/chipatlas/results/dm3/SRX1531765/SRR3102823.sra Written 26739196 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: 00:04:31 26739196 reads; of these: 26739196 (100.00%) were unpaired; of these: 17511211 (65.49%) aligned 0 times 7981982 (29.85%) aligned exactly 1 time 1246003 (4.66%) aligned >1 times 34.51% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 3543135 / 9227985 = 0.3840 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 13:08:55: # Command line: callpeak -t SRX1531765.bam -f BAM -g dm -n SRX1531765.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1531765.05 # format = BAM # ChIP-seq file = ['SRX1531765.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 13:08:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:08:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:08:55: # Command line: callpeak -t SRX1531765.bam -f BAM -g dm -n SRX1531765.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1531765.10 # format = BAM # ChIP-seq file = ['SRX1531765.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 13:08:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:08:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:08:55: # Command line: callpeak -t SRX1531765.bam -f BAM -g dm -n SRX1531765.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1531765.20 # format = BAM # ChIP-seq file = ['SRX1531765.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 13:08:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:08:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:09:02: 1000000 INFO @ Sat, 03 Jun 2017 13:09:02: 1000000 INFO @ Sat, 03 Jun 2017 13:09:02: 1000000 INFO @ Sat, 03 Jun 2017 13:09:09: 2000000 INFO @ Sat, 03 Jun 2017 13:09:10: 2000000 INFO @ Sat, 03 Jun 2017 13:09:10: 2000000 INFO @ Sat, 03 Jun 2017 13:09:16: 3000000 INFO @ Sat, 03 Jun 2017 13:09:18: 3000000 INFO @ Sat, 03 Jun 2017 13:09:19: 3000000 INFO @ Sat, 03 Jun 2017 13:09:24: 4000000 INFO @ Sat, 03 Jun 2017 13:09:27: 4000000 INFO @ Sat, 03 Jun 2017 13:09:27: 4000000 INFO @ Sat, 03 Jun 2017 13:09:31: 5000000 INFO @ Sat, 03 Jun 2017 13:09:35: 5000000 INFO @ Sat, 03 Jun 2017 13:09:35: 5000000 INFO @ Sat, 03 Jun 2017 13:09:36: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:09:36: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:09:36: #1 total tags in treatment: 5684850 INFO @ Sat, 03 Jun 2017 13:09:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:36: #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 13:09:37: #1 tags after filtering in treatment: 5683466 INFO @ Sat, 03 Jun 2017 13:09:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:37: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:37: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:38: #2 number of paired peaks: 3235 INFO @ Sat, 03 Jun 2017 13:09:38: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:40: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:09:40: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:09:40: #1 total tags in treatment: 5684850 INFO @ Sat, 03 Jun 2017 13:09:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:40: #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 13:09:41: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:09:41: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:09:41: #1 total tags in treatment: 5684850 INFO @ Sat, 03 Jun 2017 13:09:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:41: #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 13:09:41: #1 tags after filtering in treatment: 5683466 INFO @ Sat, 03 Jun 2017 13:09:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:41: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:42: #1 tags after filtering in treatment: 5683466 INFO @ Sat, 03 Jun 2017 13:09:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:42: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:43: #2 number of paired peaks: 3235 INFO @ Sat, 03 Jun 2017 13:09:43: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:44: #2 number of paired peaks: 3235 INFO @ Sat, 03 Jun 2017 13:09:44: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:50: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:50: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:50: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:50: #2 predicted fragment length is 191 bps INFO @ Sat, 03 Jun 2017 13:09:50: #2 alternative fragment length(s) may be 4,191 bps INFO @ Sat, 03 Jun 2017 13:09:50: #2.2 Generate R script for model : SRX1531765.05_model.r INFO @ Sat, 03 Jun 2017 13:09:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:09:54: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:54: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:54: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:54: #2 predicted fragment length is 191 bps INFO @ Sat, 03 Jun 2017 13:09:54: #2 alternative fragment length(s) may be 4,191 bps INFO @ Sat, 03 Jun 2017 13:09:54: #2.2 Generate R script for model : SRX1531765.20_model.r INFO @ Sat, 03 Jun 2017 13:09:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:09:55: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:55: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:55: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:55: #2 predicted fragment length is 191 bps INFO @ Sat, 03 Jun 2017 13:09:55: #2 alternative fragment length(s) may be 4,191 bps INFO @ Sat, 03 Jun 2017 13:09:55: #2.2 Generate R script for model : SRX1531765.10_model.r INFO @ Sat, 03 Jun 2017 13:09:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:10:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:10:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:10:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:10:50: #4 Write output xls file... SRX1531765.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:10:50: #4 Write peak in narrowPeak format file... SRX1531765.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:10:50: #4 Write summits bed file... SRX1531765.10_summits.bed INFO @ Sat, 03 Jun 2017 13:10:50: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (178 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:10:51: #4 Write output xls file... SRX1531765.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:10:51: #4 Write peak in narrowPeak format file... SRX1531765.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:10:51: #4 Write summits bed file... SRX1531765.05_summits.bed INFO @ Sat, 03 Jun 2017 13:10:51: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (378 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:10:51: #4 Write output xls file... SRX1531765.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:10:51: #4 Write peak in narrowPeak format file... SRX1531765.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:10:51: #4 Write summits bed file... SRX1531765.20_summits.bed INFO @ Sat, 03 Jun 2017 13:10:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (93 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。