Job ID = 11171160 sra ファイルのダウンロード中... Completed: 1288915K bytes transferred in 33 seconds (315096K bits/sec), in 1 file. 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... Read 44733354 spots for /home/okishinya/chipatlas/results/dm3/SRX2564134/SRR5259253.sra Written 44733354 spots for /home/okishinya/chipatlas/results/dm3/SRX2564134/SRR5259253.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:20:02 44733354 reads; of these: 44733354 (100.00%) were unpaired; of these: 1816965 (4.06%) aligned 0 times 35385429 (79.10%) aligned exactly 1 time 7530960 (16.84%) aligned >1 times 95.94% overall alignment rate Time searching: 00:20:02 Overall time: 00:20:02 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 20 files... [bam_rmdupse_core] 13729008 / 42916389 = 0.3199 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, 08 Sep 2018 12:49:41: # Command line: callpeak -t SRX2564134.bam -f BAM -g dm -n SRX2564134.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2564134.20 # format = BAM # ChIP-seq file = ['SRX2564134.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 12:49:41: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:49:41: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:49:41: # Command line: callpeak -t SRX2564134.bam -f BAM -g dm -n SRX2564134.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2564134.05 # format = BAM # ChIP-seq file = ['SRX2564134.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 12:49:41: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:49:41: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:49:41: # Command line: callpeak -t SRX2564134.bam -f BAM -g dm -n SRX2564134.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2564134.10 # format = BAM # ChIP-seq file = ['SRX2564134.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 12:49:41: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:49:41: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:49:49: 1000000 INFO @ Sat, 08 Sep 2018 12:49:49: 1000000 INFO @ Sat, 08 Sep 2018 12:49:49: 1000000 INFO @ Sat, 08 Sep 2018 12:49:56: 2000000 INFO @ Sat, 08 Sep 2018 12:49:57: 2000000 INFO @ Sat, 08 Sep 2018 12:49:57: 2000000 INFO @ Sat, 08 Sep 2018 12:50:03: 3000000 INFO @ Sat, 08 Sep 2018 12:50:05: 3000000 INFO @ Sat, 08 Sep 2018 12:50:05: 3000000 INFO @ Sat, 08 Sep 2018 12:50:10: 4000000 INFO @ Sat, 08 Sep 2018 12:50:13: 4000000 INFO @ Sat, 08 Sep 2018 12:50:13: 4000000 INFO @ Sat, 08 Sep 2018 12:50:17: 5000000 INFO @ Sat, 08 Sep 2018 12:50:21: 5000000 INFO @ Sat, 08 Sep 2018 12:50:21: 5000000 INFO @ Sat, 08 Sep 2018 12:50:24: 6000000 INFO @ Sat, 08 Sep 2018 12:50:29: 6000000 INFO @ Sat, 08 Sep 2018 12:50:29: 6000000 INFO @ Sat, 08 Sep 2018 12:50:31: 7000000 INFO @ Sat, 08 Sep 2018 12:50:37: 7000000 INFO @ Sat, 08 Sep 2018 12:50:37: 7000000 INFO @ Sat, 08 Sep 2018 12:50:38: 8000000 INFO @ Sat, 08 Sep 2018 12:50:45: 8000000 INFO @ Sat, 08 Sep 2018 12:50:45: 8000000 INFO @ Sat, 08 Sep 2018 12:50:45: 9000000 INFO @ Sat, 08 Sep 2018 12:50:52: 10000000 INFO @ Sat, 08 Sep 2018 12:50:53: 9000000 INFO @ Sat, 08 Sep 2018 12:50:53: 9000000 INFO @ Sat, 08 Sep 2018 12:51:00: 11000000 INFO @ Sat, 08 Sep 2018 12:51:01: 10000000 INFO @ Sat, 08 Sep 2018 12:51:01: 10000000 INFO @ Sat, 08 Sep 2018 12:51:07: 12000000 INFO @ Sat, 08 Sep 2018 12:51:09: 11000000 INFO @ Sat, 08 Sep 2018 12:51:09: 11000000 INFO @ Sat, 08 Sep 2018 12:51:14: 13000000 INFO @ Sat, 08 Sep 2018 12:51:17: 12000000 INFO @ Sat, 08 Sep 2018 12:51:18: 12000000 INFO @ Sat, 08 Sep 2018 12:51:21: 14000000 INFO @ Sat, 08 Sep 2018 12:51:25: 13000000 INFO @ Sat, 08 Sep 2018 12:51:26: 13000000 INFO @ Sat, 08 Sep 2018 12:51:28: 15000000 INFO @ Sat, 08 Sep 2018 12:51:33: 14000000 INFO @ Sat, 08 Sep 2018 12:51:34: 14000000 INFO @ Sat, 08 Sep 2018 12:51:35: 16000000 INFO @ Sat, 08 Sep 2018 12:51:42: 15000000 INFO @ Sat, 08 Sep 2018 12:51:43: 15000000 INFO @ Sat, 08 Sep 2018 12:51:44: 17000000 INFO @ Sat, 08 Sep 2018 12:51:51: 16000000 INFO @ Sat, 08 Sep 2018 12:51:52: 16000000 INFO @ Sat, 08 Sep 2018 12:51:54: 18000000 INFO @ Sat, 08 Sep 2018 12:52:00: 17000000 INFO @ Sat, 08 Sep 2018 12:52:00: 17000000 INFO @ Sat, 08 Sep 2018 12:52:03: 19000000 INFO @ Sat, 08 Sep 2018 12:52:09: 18000000 INFO @ Sat, 08 Sep 2018 12:52:09: 18000000 INFO @ Sat, 08 Sep 2018 12:52:12: 20000000 INFO @ Sat, 08 Sep 2018 12:52:18: 19000000 INFO @ Sat, 08 Sep 2018 12:52:18: 19000000 INFO @ Sat, 08 Sep 2018 12:52:22: 21000000 INFO @ Sat, 08 Sep 2018 12:52:27: 20000000 INFO @ Sat, 08 Sep 2018 12:52:27: 20000000 INFO @ Sat, 08 Sep 2018 12:52:31: 22000000 INFO @ Sat, 08 Sep 2018 12:52:36: 21000000 INFO @ Sat, 08 Sep 2018 12:52:36: 21000000 INFO @ Sat, 08 Sep 2018 12:52:40: 23000000 INFO @ Sat, 08 Sep 2018 12:52:45: 22000000 INFO @ Sat, 08 Sep 2018 12:52:45: 22000000 INFO @ Sat, 08 Sep 2018 12:52:50: 24000000 INFO @ Sat, 08 Sep 2018 12:52:54: 23000000 INFO @ Sat, 08 Sep 2018 12:52:54: 23000000 INFO @ Sat, 08 Sep 2018 12:52:59: 25000000 INFO @ Sat, 08 Sep 2018 12:53:03: 24000000 INFO @ Sat, 08 Sep 2018 12:53:03: 24000000 INFO @ Sat, 08 Sep 2018 12:53:09: 26000000 INFO @ Sat, 08 Sep 2018 12:53:12: 25000000 INFO @ Sat, 08 Sep 2018 12:53:12: 25000000 INFO @ Sat, 08 Sep 2018 12:53:18: 27000000 INFO @ Sat, 08 Sep 2018 12:53:21: 26000000 INFO @ Sat, 08 Sep 2018 12:53:21: 26000000 INFO @ Sat, 08 Sep 2018 12:53:27: 28000000 INFO @ Sat, 08 Sep 2018 12:53:30: 27000000 INFO @ Sat, 08 Sep 2018 12:53:30: 27000000 INFO @ Sat, 08 Sep 2018 12:53:36: 29000000 INFO @ Sat, 08 Sep 2018 12:53:38: #1 tag size is determined as 71 bps INFO @ Sat, 08 Sep 2018 12:53:38: #1 tag size = 71 INFO @ Sat, 08 Sep 2018 12:53:38: #1 total tags in treatment: 29187381 INFO @ Sat, 08 Sep 2018 12:53:38: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:53:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 12:53:38: 28000000 INFO @ Sat, 08 Sep 2018 12:53:39: 28000000 INFO @ Sat, 08 Sep 2018 12:53:39: #1 tags after filtering in treatment: 29187381 INFO @ Sat, 08 Sep 2018 12:53:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:53:39: #1 finished! INFO @ Sat, 08 Sep 2018 12:53:39: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:53:41: #2 number of paired peaks: 301 WARNING @ Sat, 08 Sep 2018 12:53:41: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Sat, 08 Sep 2018 12:53:41: start model_add_line... INFO @ Sat, 08 Sep 2018 12:53:41: start X-correlation... INFO @ Sat, 08 Sep 2018 12:53:41: end of X-cor INFO @ Sat, 08 Sep 2018 12:53:41: #2 finished! INFO @ Sat, 08 Sep 2018 12:53:41: #2 predicted fragment length is 144 bps INFO @ Sat, 08 Sep 2018 12:53:41: #2 alternative fragment length(s) may be 144 bps INFO @ Sat, 08 Sep 2018 12:53:41: #2.2 Generate R script for model : SRX2564134.20_model.r INFO @ Sat, 08 Sep 2018 12:53:41: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:53:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:53:47: 29000000 INFO @ Sat, 08 Sep 2018 12:53:47: 29000000 INFO @ Sat, 08 Sep 2018 12:53:48: #1 tag size is determined as 71 bps INFO @ Sat, 08 Sep 2018 12:53:48: #1 tag size = 71 INFO @ Sat, 08 Sep 2018 12:53:48: #1 total tags in treatment: 29187381 INFO @ Sat, 08 Sep 2018 12:53:48: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:53:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 12:53:48: #1 tag size is determined as 71 bps INFO @ Sat, 08 Sep 2018 12:53:48: #1 tag size = 71 INFO @ Sat, 08 Sep 2018 12:53:48: #1 total tags in treatment: 29187381 INFO @ Sat, 08 Sep 2018 12:53:48: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:53:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 12:53:49: #1 tags after filtering in treatment: 29187381 INFO @ Sat, 08 Sep 2018 12:53:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:53:49: #1 finished! INFO @ Sat, 08 Sep 2018 12:53:49: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:53:49: #1 tags after filtering in treatment: 29187381 INFO @ Sat, 08 Sep 2018 12:53:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:53:49: #1 finished! INFO @ Sat, 08 Sep 2018 12:53:49: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:53:51: #2 number of paired peaks: 301 WARNING @ Sat, 08 Sep 2018 12:53:51: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Sat, 08 Sep 2018 12:53:51: start model_add_line... INFO @ Sat, 08 Sep 2018 12:53:51: #2 number of paired peaks: 301 WARNING @ Sat, 08 Sep 2018 12:53:51: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Sat, 08 Sep 2018 12:53:51: start model_add_line... INFO @ Sat, 08 Sep 2018 12:53:51: start X-correlation... INFO @ Sat, 08 Sep 2018 12:53:51: end of X-cor INFO @ Sat, 08 Sep 2018 12:53:51: #2 finished! INFO @ Sat, 08 Sep 2018 12:53:51: #2 predicted fragment length is 144 bps INFO @ Sat, 08 Sep 2018 12:53:51: #2 alternative fragment length(s) may be 144 bps INFO @ Sat, 08 Sep 2018 12:53:51: #2.2 Generate R script for model : SRX2564134.10_model.r INFO @ Sat, 08 Sep 2018 12:53:51: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:53:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:53:51: start X-correlation... INFO @ Sat, 08 Sep 2018 12:53:51: end of X-cor INFO @ Sat, 08 Sep 2018 12:53:51: #2 finished! INFO @ Sat, 08 Sep 2018 12:53:51: #2 predicted fragment length is 144 bps INFO @ Sat, 08 Sep 2018 12:53:51: #2 alternative fragment length(s) may be 144 bps INFO @ Sat, 08 Sep 2018 12:53:51: #2.2 Generate R script for model : SRX2564134.05_model.r INFO @ Sat, 08 Sep 2018 12:53:51: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:53:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:54:38: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:54:50: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:54:52: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:55:13: #4 Write output xls file... SRX2564134.20_peaks.xls INFO @ Sat, 08 Sep 2018 12:55:13: #4 Write peak in narrowPeak format file... SRX2564134.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:55:14: #4 Write summits bed file... SRX2564134.20_summits.bed INFO @ Sat, 08 Sep 2018 12:55:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7731 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:55:23: #4 Write output xls file... SRX2564134.05_peaks.xls INFO @ Sat, 08 Sep 2018 12:55:23: #4 Write peak in narrowPeak format file... SRX2564134.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:55:23: #4 Write summits bed file... SRX2564134.05_summits.bed INFO @ Sat, 08 Sep 2018 12:55:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11835 records, 4 fields): 16 millis INFO @ Sat, 08 Sep 2018 12:55:23: #4 Write output xls file... SRX2564134.10_peaks.xls CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:55:24: #4 Write peak in narrowPeak format file... SRX2564134.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:55:24: #4 Write summits bed file... SRX2564134.10_summits.bed INFO @ Sat, 08 Sep 2018 12:55:24: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9815 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。