Job ID = 9029891 sra ファイルのダウンロード中... Completed: 948723K bytes transferred in 14 seconds (553610K 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 --:--:-- 0 100 7663 0 7663 0 0 1072 0 --:--:-- 0:00:07 --:--:-- 10327 100 29582 0 29582 0 0 3633 0 --:--:-- 0:00:08 --:--:-- 17030 100 31453 0 31453 0 0 3862 0 --:--:-- 0:00:08 --:--:-- 18097 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 12752083 spots for /home/okishinya/chipatlas/results/dm3/SRX2551009/SRR5244306.sra Written 12752083 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: 00:08:22 12752083 reads; of these: 12752083 (100.00%) were unpaired; of these: 867066 (6.80%) aligned 0 times 9045779 (70.94%) aligned exactly 1 time 2839238 (22.26%) aligned >1 times 93.20% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 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 8 files... [bam_rmdupse_core] 6146172 / 11885017 = 0.5171 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 15:49:55: # Command line: callpeak -t SRX2551009.bam -f BAM -g dm -n SRX2551009.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2551009.20 # format = BAM # ChIP-seq file = ['SRX2551009.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 15:49:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:49:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:49:55: # Command line: callpeak -t SRX2551009.bam -f BAM -g dm -n SRX2551009.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2551009.10 # format = BAM # ChIP-seq file = ['SRX2551009.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 15:49:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:49:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:49:55: # Command line: callpeak -t SRX2551009.bam -f BAM -g dm -n SRX2551009.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2551009.05 # format = BAM # ChIP-seq file = ['SRX2551009.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 15:49:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:49:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:50:03: 1000000 INFO @ Sat, 03 Jun 2017 15:50:03: 1000000 INFO @ Sat, 03 Jun 2017 15:50:03: 1000000 INFO @ Sat, 03 Jun 2017 15:50:11: 2000000 INFO @ Sat, 03 Jun 2017 15:50:11: 2000000 INFO @ Sat, 03 Jun 2017 15:50:13: 2000000 INFO @ Sat, 03 Jun 2017 15:50:19: 3000000 INFO @ Sat, 03 Jun 2017 15:50:19: 3000000 INFO @ Sat, 03 Jun 2017 15:50:24: 3000000 INFO @ Sat, 03 Jun 2017 15:50:27: 4000000 INFO @ Sat, 03 Jun 2017 15:50:27: 4000000 INFO @ Sat, 03 Jun 2017 15:50:35: 4000000 INFO @ Sat, 03 Jun 2017 15:50:35: 5000000 INFO @ Sat, 03 Jun 2017 15:50:35: 5000000 INFO @ Sat, 03 Jun 2017 15:50:41: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 15:50:41: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 15:50:41: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 15:50:41: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 15:50:41: #1 total tags in treatment: 5738845 INFO @ Sat, 03 Jun 2017 15:50:41: #1 total tags in treatment: 5738845 INFO @ Sat, 03 Jun 2017 15:50:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:50:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:50:41: #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 15:50:41: #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 15:50:42: #1 tags after filtering in treatment: 5735838 INFO @ Sat, 03 Jun 2017 15:50:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:50:42: #1 finished! INFO @ Sat, 03 Jun 2017 15:50:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:50:42: #1 tags after filtering in treatment: 5735838 INFO @ Sat, 03 Jun 2017 15:50:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:50:42: #1 finished! INFO @ Sat, 03 Jun 2017 15:50:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:50:43: #2 number of paired peaks: 496 WARNING @ Sat, 03 Jun 2017 15:50:43: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Sat, 03 Jun 2017 15:50:43: start model_add_line... INFO @ Sat, 03 Jun 2017 15:50:43: #2 number of paired peaks: 496 WARNING @ Sat, 03 Jun 2017 15:50:43: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Sat, 03 Jun 2017 15:50:43: start model_add_line... INFO @ Sat, 03 Jun 2017 15:50:45: start X-correlation... INFO @ Sat, 03 Jun 2017 15:50:45: end of X-cor INFO @ Sat, 03 Jun 2017 15:50:45: #2 finished! INFO @ Sat, 03 Jun 2017 15:50:45: #2 predicted fragment length is 238 bps INFO @ Sat, 03 Jun 2017 15:50:45: #2 alternative fragment length(s) may be 238 bps INFO @ Sat, 03 Jun 2017 15:50:45: #2.2 Generate R script for model : SRX2551009.20_model.r INFO @ Sat, 03 Jun 2017 15:50:45: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:50:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:50:46: 5000000 INFO @ Sat, 03 Jun 2017 15:50:46: start X-correlation... INFO @ Sat, 03 Jun 2017 15:50:46: end of X-cor INFO @ Sat, 03 Jun 2017 15:50:46: #2 finished! INFO @ Sat, 03 Jun 2017 15:50:46: #2 predicted fragment length is 238 bps INFO @ Sat, 03 Jun 2017 15:50:46: #2 alternative fragment length(s) may be 238 bps INFO @ Sat, 03 Jun 2017 15:50:46: #2.2 Generate R script for model : SRX2551009.10_model.r INFO @ Sat, 03 Jun 2017 15:50:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:50:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:50:54: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 15:50:54: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 15:50:54: #1 total tags in treatment: 5738845 INFO @ Sat, 03 Jun 2017 15:50:54: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:50:54: #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 15:50:55: #1 tags after filtering in treatment: 5735838 INFO @ Sat, 03 Jun 2017 15:50:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:50:55: #1 finished! INFO @ Sat, 03 Jun 2017 15:50:55: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:50:56: #2 number of paired peaks: 496 WARNING @ Sat, 03 Jun 2017 15:50:56: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Sat, 03 Jun 2017 15:50:56: start model_add_line... INFO @ Sat, 03 Jun 2017 15:50:58: start X-correlation... INFO @ Sat, 03 Jun 2017 15:50:58: end of X-cor INFO @ Sat, 03 Jun 2017 15:50:58: #2 finished! INFO @ Sat, 03 Jun 2017 15:50:58: #2 predicted fragment length is 238 bps INFO @ Sat, 03 Jun 2017 15:50:58: #2 alternative fragment length(s) may be 238 bps INFO @ Sat, 03 Jun 2017 15:50:58: #2.2 Generate R script for model : SRX2551009.05_model.r INFO @ Sat, 03 Jun 2017 15:50:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:50:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:51:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:51:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:51:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:51:47: #4 Write output xls file... SRX2551009.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:51:47: #4 Write peak in narrowPeak format file... SRX2551009.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:51:47: #4 Write summits bed file... SRX2551009.20_summits.bed INFO @ Sat, 03 Jun 2017 15:51:47: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (795 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:51:51: #4 Write output xls file... SRX2551009.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:51:51: #4 Write peak in narrowPeak format file... SRX2551009.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:51:51: #4 Write summits bed file... SRX2551009.10_summits.bed INFO @ Sat, 03 Jun 2017 15:51:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1565 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:52:02: #4 Write output xls file... SRX2551009.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:52:02: #4 Write peak in narrowPeak format file... SRX2551009.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:52:03: #4 Write summits bed file... SRX2551009.05_summits.bed INFO @ Sat, 03 Jun 2017 15:52:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2897 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。