Job ID = 8696855 sra ファイルのダウンロード中... Completed: 170772K bytes transferred in 4 seconds (287537K 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 7663 0 7663 0 0 980 0 --:--:-- 0:00:07 --:--:-- 6727 100 31396 0 31396 0 0 3541 0 --:--:-- 0:00:08 --:--:-- 14368 100 31396 0 31396 0 0 3541 0 --:--:-- 0:00:08 --:--:-- 14362 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 14543262 spots for /home/okishinya/chipatlas/results/dm3/SRX110789/SRR388371.sra Written 14543262 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:29 14543262 reads; of these: 14543262 (100.00%) were unpaired; of these: 606462 (4.17%) aligned 0 times 7652454 (52.62%) aligned exactly 1 time 6284346 (43.21%) aligned >1 times 95.83% overall alignment rate Time searching: 00:11:30 Overall time: 00:11:30 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] 962205 / 13936800 = 0.0690 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 @ Fri, 10 Mar 2017 12:43:47: # Command line: callpeak -t SRX110789.bam -f BAM -g dm -n SRX110789.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110789.05 # format = BAM # ChIP-seq file = ['SRX110789.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 @ Fri, 10 Mar 2017 12:43:47: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:43:47: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:43:47: # Command line: callpeak -t SRX110789.bam -f BAM -g dm -n SRX110789.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110789.20 # format = BAM # ChIP-seq file = ['SRX110789.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 @ Fri, 10 Mar 2017 12:43:47: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:43:47: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:43:47: # Command line: callpeak -t SRX110789.bam -f BAM -g dm -n SRX110789.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110789.10 # format = BAM # ChIP-seq file = ['SRX110789.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 @ Fri, 10 Mar 2017 12:43:47: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:43:47: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:43:53: 1000000 INFO @ Fri, 10 Mar 2017 12:43:55: 1000000 INFO @ Fri, 10 Mar 2017 12:43:56: 1000000 INFO @ Fri, 10 Mar 2017 12:44:00: 2000000 INFO @ Fri, 10 Mar 2017 12:44:02: 2000000 INFO @ Fri, 10 Mar 2017 12:44:03: 2000000 INFO @ Fri, 10 Mar 2017 12:44:07: 3000000 INFO @ Fri, 10 Mar 2017 12:44:08: 3000000 INFO @ Fri, 10 Mar 2017 12:44:09: 3000000 INFO @ Fri, 10 Mar 2017 12:44:13: 4000000 INFO @ Fri, 10 Mar 2017 12:44:14: 4000000 INFO @ Fri, 10 Mar 2017 12:44:17: 4000000 INFO @ Fri, 10 Mar 2017 12:44:20: 5000000 INFO @ Fri, 10 Mar 2017 12:44:21: 5000000 INFO @ Fri, 10 Mar 2017 12:44:23: 5000000 INFO @ Fri, 10 Mar 2017 12:44:27: 6000000 INFO @ Fri, 10 Mar 2017 12:44:27: 6000000 INFO @ Fri, 10 Mar 2017 12:44:30: 6000000 INFO @ Fri, 10 Mar 2017 12:44:33: 7000000 INFO @ Fri, 10 Mar 2017 12:44:34: 7000000 INFO @ Fri, 10 Mar 2017 12:44:36: 7000000 INFO @ Fri, 10 Mar 2017 12:44:39: 8000000 INFO @ Fri, 10 Mar 2017 12:44:40: 8000000 INFO @ Fri, 10 Mar 2017 12:44:42: 8000000 INFO @ Fri, 10 Mar 2017 12:44:45: 9000000 INFO @ Fri, 10 Mar 2017 12:44:46: 9000000 INFO @ Fri, 10 Mar 2017 12:44:49: 9000000 INFO @ Fri, 10 Mar 2017 12:44:52: 10000000 INFO @ Fri, 10 Mar 2017 12:44:53: 10000000 INFO @ Fri, 10 Mar 2017 12:44:55: 10000000 INFO @ Fri, 10 Mar 2017 12:44:58: 11000000 INFO @ Fri, 10 Mar 2017 12:44:59: 11000000 INFO @ Fri, 10 Mar 2017 12:45:02: 11000000 INFO @ Fri, 10 Mar 2017 12:45:04: 12000000 INFO @ Fri, 10 Mar 2017 12:45:06: 12000000 INFO @ Fri, 10 Mar 2017 12:45:08: 12000000 INFO @ Fri, 10 Mar 2017 12:45:10: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:45:10: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:45:10: #1 total tags in treatment: 12974595 INFO @ Fri, 10 Mar 2017 12:45:10: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:45:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:45:12: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:45:12: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:45:12: #1 total tags in treatment: 12974595 INFO @ Fri, 10 Mar 2017 12:45:12: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:45:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:45:13: #1 tags after filtering in treatment: 12974595 INFO @ Fri, 10 Mar 2017 12:45:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:45:13: #1 finished! INFO @ Fri, 10 Mar 2017 12:45:13: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:45:15: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:45:15: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:45:15: #1 total tags in treatment: 12974595 INFO @ Fri, 10 Mar 2017 12:45:15: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:45:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:45:15: #1 tags after filtering in treatment: 12974595 INFO @ Fri, 10 Mar 2017 12:45:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:45:15: #1 finished! INFO @ Fri, 10 Mar 2017 12:45:15: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:45:16: #2 number of paired peaks: 157 WARNING @ Fri, 10 Mar 2017 12:45:16: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Fri, 10 Mar 2017 12:45:16: start model_add_line... INFO @ Fri, 10 Mar 2017 12:45:18: #1 tags after filtering in treatment: 12974595 INFO @ Fri, 10 Mar 2017 12:45:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:45:18: #1 finished! INFO @ Fri, 10 Mar 2017 12:45:18: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:45:18: #2 number of paired peaks: 157 WARNING @ Fri, 10 Mar 2017 12:45:18: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Fri, 10 Mar 2017 12:45:18: start model_add_line... INFO @ Fri, 10 Mar 2017 12:45:19: start X-correlation... INFO @ Fri, 10 Mar 2017 12:45:19: end of X-cor INFO @ Fri, 10 Mar 2017 12:45:19: #2 finished! INFO @ Fri, 10 Mar 2017 12:45:19: #2 predicted fragment length is 87 bps INFO @ Fri, 10 Mar 2017 12:45:19: #2 alternative fragment length(s) may be 87 bps INFO @ Fri, 10 Mar 2017 12:45:19: #2.2 Generate R script for model : SRX110789.05_model.r INFO @ Fri, 10 Mar 2017 12:45:19: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:45:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:45:20: #2 number of paired peaks: 157 WARNING @ Fri, 10 Mar 2017 12:45:20: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Fri, 10 Mar 2017 12:45:20: start model_add_line... INFO @ Fri, 10 Mar 2017 12:45:21: start X-correlation... INFO @ Fri, 10 Mar 2017 12:45:21: end of X-cor INFO @ Fri, 10 Mar 2017 12:45:21: #2 finished! INFO @ Fri, 10 Mar 2017 12:45:21: #2 predicted fragment length is 87 bps INFO @ Fri, 10 Mar 2017 12:45:21: #2 alternative fragment length(s) may be 87 bps INFO @ Fri, 10 Mar 2017 12:45:21: #2.2 Generate R script for model : SRX110789.20_model.r INFO @ Fri, 10 Mar 2017 12:45:21: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:45:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:45:23: start X-correlation... INFO @ Fri, 10 Mar 2017 12:45:23: end of X-cor INFO @ Fri, 10 Mar 2017 12:45:23: #2 finished! INFO @ Fri, 10 Mar 2017 12:45:23: #2 predicted fragment length is 87 bps INFO @ Fri, 10 Mar 2017 12:45:23: #2 alternative fragment length(s) may be 87 bps INFO @ Fri, 10 Mar 2017 12:45:23: #2.2 Generate R script for model : SRX110789.10_model.r INFO @ Fri, 10 Mar 2017 12:45:23: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:46:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:46:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:46:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:47:42: #4 Write output xls file... SRX110789.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:47:42: #4 Write peak in narrowPeak format file... SRX110789.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:47:42: #4 Write summits bed file... SRX110789.20_summits.bed INFO @ Fri, 10 Mar 2017 12:47:42: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (398 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:47:43: #4 Write output xls file... SRX110789.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:47:43: #4 Write peak in narrowPeak format file... SRX110789.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:47:43: #4 Write summits bed file... SRX110789.10_summits.bed INFO @ Fri, 10 Mar 2017 12:47:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2108 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:47:52: #4 Write output xls file... SRX110789.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:47:52: #4 Write peak in narrowPeak format file... SRX110789.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:47:53: #4 Write summits bed file... SRX110789.05_summits.bed INFO @ Fri, 10 Mar 2017 12:47:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6104 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。