Job ID = 11171162 sra ファイルのダウンロード中... Completed: 1291276K bytes transferred in 70 seconds (150500K 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 35080567 spots for /home/okishinya/chipatlas/results/dm3/SRX2564136/SRR5259255.sra Written 35080567 spots for /home/okishinya/chipatlas/results/dm3/SRX2564136/SRR5259255.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: 00:14:10 35080567 reads; of these: 35080567 (100.00%) were unpaired; of these: 5793001 (16.51%) aligned 0 times 25408068 (72.43%) aligned exactly 1 time 3879498 (11.06%) aligned >1 times 83.49% overall alignment rate Time searching: 00:14:10 Overall time: 00:14:10 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 12 files... [bam_rmdupse_core] 6171756 / 29287566 = 0.2107 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 12:47:41: # Command line: callpeak -t SRX2564136.bam -f BAM -g dm -n SRX2564136.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2564136.05 # format = BAM # ChIP-seq file = ['SRX2564136.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 12:47:41: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:47:41: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:47:41: # Command line: callpeak -t SRX2564136.bam -f BAM -g dm -n SRX2564136.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2564136.20 # format = BAM # ChIP-seq file = ['SRX2564136.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 12:47:41: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:47:41: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:47:41: # Command line: callpeak -t SRX2564136.bam -f BAM -g dm -n SRX2564136.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2564136.10 # format = BAM # ChIP-seq file = ['SRX2564136.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 12:47:41: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:47:41: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:47:48: 1000000 INFO @ Sat, 08 Sep 2018 12:47:49: 1000000 INFO @ Sat, 08 Sep 2018 12:47:49: 1000000 INFO @ Sat, 08 Sep 2018 12:47:56: 2000000 INFO @ Sat, 08 Sep 2018 12:47:58: 2000000 INFO @ Sat, 08 Sep 2018 12:47:58: 2000000 INFO @ Sat, 08 Sep 2018 12:48:03: 3000000 INFO @ Sat, 08 Sep 2018 12:48:07: 3000000 INFO @ Sat, 08 Sep 2018 12:48:07: 3000000 INFO @ Sat, 08 Sep 2018 12:48:11: 4000000 INFO @ Sat, 08 Sep 2018 12:48:16: 4000000 INFO @ Sat, 08 Sep 2018 12:48:16: 4000000 INFO @ Sat, 08 Sep 2018 12:48:18: 5000000 INFO @ Sat, 08 Sep 2018 12:48:25: 5000000 INFO @ Sat, 08 Sep 2018 12:48:26: 5000000 INFO @ Sat, 08 Sep 2018 12:48:26: 6000000 INFO @ Sat, 08 Sep 2018 12:48:33: 7000000 INFO @ Sat, 08 Sep 2018 12:48:34: 6000000 INFO @ Sat, 08 Sep 2018 12:48:35: 6000000 INFO @ Sat, 08 Sep 2018 12:48:41: 8000000 INFO @ Sat, 08 Sep 2018 12:48:43: 7000000 INFO @ Sat, 08 Sep 2018 12:48:44: 7000000 INFO @ Sat, 08 Sep 2018 12:48:48: 9000000 INFO @ Sat, 08 Sep 2018 12:48:52: 8000000 INFO @ Sat, 08 Sep 2018 12:48:53: 8000000 INFO @ Sat, 08 Sep 2018 12:48:56: 10000000 INFO @ Sat, 08 Sep 2018 12:49:01: 9000000 INFO @ Sat, 08 Sep 2018 12:49:03: 9000000 INFO @ Sat, 08 Sep 2018 12:49:03: 11000000 INFO @ Sat, 08 Sep 2018 12:49:10: 10000000 INFO @ Sat, 08 Sep 2018 12:49:11: 12000000 INFO @ Sat, 08 Sep 2018 12:49:12: 10000000 INFO @ Sat, 08 Sep 2018 12:49:18: 13000000 INFO @ Sat, 08 Sep 2018 12:49:19: 11000000 INFO @ Sat, 08 Sep 2018 12:49:21: 11000000 INFO @ Sat, 08 Sep 2018 12:49:26: 14000000 INFO @ Sat, 08 Sep 2018 12:49:29: 12000000 INFO @ Sat, 08 Sep 2018 12:49:30: 12000000 INFO @ Sat, 08 Sep 2018 12:49:33: 15000000 INFO @ Sat, 08 Sep 2018 12:49:38: 13000000 INFO @ Sat, 08 Sep 2018 12:49:40: 13000000 INFO @ Sat, 08 Sep 2018 12:49:41: 16000000 INFO @ Sat, 08 Sep 2018 12:49:47: 14000000 INFO @ Sat, 08 Sep 2018 12:49:48: 17000000 INFO @ Sat, 08 Sep 2018 12:49:49: 14000000 INFO @ Sat, 08 Sep 2018 12:49:56: 18000000 INFO @ Sat, 08 Sep 2018 12:49:56: 15000000 INFO @ Sat, 08 Sep 2018 12:49:58: 15000000 INFO @ Sat, 08 Sep 2018 12:50:03: 19000000 INFO @ Sat, 08 Sep 2018 12:50:05: 16000000 INFO @ Sat, 08 Sep 2018 12:50:07: 16000000 INFO @ Sat, 08 Sep 2018 12:50:11: 20000000 INFO @ Sat, 08 Sep 2018 12:50:14: 17000000 INFO @ Sat, 08 Sep 2018 12:50:16: 17000000 INFO @ Sat, 08 Sep 2018 12:50:18: 21000000 INFO @ Sat, 08 Sep 2018 12:50:23: 18000000 INFO @ Sat, 08 Sep 2018 12:50:25: 18000000 INFO @ Sat, 08 Sep 2018 12:50:26: 22000000 INFO @ Sat, 08 Sep 2018 12:50:33: 19000000 INFO @ Sat, 08 Sep 2018 12:50:33: 23000000 INFO @ Sat, 08 Sep 2018 12:50:34: 19000000 INFO @ Sat, 08 Sep 2018 12:50:34: #1 tag size is determined as 66 bps INFO @ Sat, 08 Sep 2018 12:50:34: #1 tag size = 66 INFO @ Sat, 08 Sep 2018 12:50:34: #1 total tags in treatment: 23115810 INFO @ Sat, 08 Sep 2018 12:50:34: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:50:34: #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 12:50:35: #1 tags after filtering in treatment: 23115810 INFO @ Sat, 08 Sep 2018 12:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:50:35: #1 finished! INFO @ Sat, 08 Sep 2018 12:50:35: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:50:36: #2 number of paired peaks: 657 WARNING @ Sat, 08 Sep 2018 12:50:36: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sat, 08 Sep 2018 12:50:36: start model_add_line... INFO @ Sat, 08 Sep 2018 12:50:37: start X-correlation... INFO @ Sat, 08 Sep 2018 12:50:37: end of X-cor INFO @ Sat, 08 Sep 2018 12:50:37: #2 finished! INFO @ Sat, 08 Sep 2018 12:50:37: #2 predicted fragment length is 162 bps INFO @ Sat, 08 Sep 2018 12:50:37: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 08 Sep 2018 12:50:37: #2.2 Generate R script for model : SRX2564136.05_model.r INFO @ Sat, 08 Sep 2018 12:50:37: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:50:42: 20000000 INFO @ Sat, 08 Sep 2018 12:50:43: 20000000 INFO @ Sat, 08 Sep 2018 12:50:51: 21000000 INFO @ Sat, 08 Sep 2018 12:50:52: 21000000 INFO @ Sat, 08 Sep 2018 12:51:00: 22000000 INFO @ Sat, 08 Sep 2018 12:51:01: 22000000 INFO @ Sat, 08 Sep 2018 12:51:09: 23000000 INFO @ Sat, 08 Sep 2018 12:51:09: 23000000 INFO @ Sat, 08 Sep 2018 12:51:10: #1 tag size is determined as 66 bps INFO @ Sat, 08 Sep 2018 12:51:10: #1 tag size = 66 INFO @ Sat, 08 Sep 2018 12:51:10: #1 total tags in treatment: 23115810 INFO @ Sat, 08 Sep 2018 12:51:10: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:51:10: #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 12:51:11: #1 tag size is determined as 66 bps INFO @ Sat, 08 Sep 2018 12:51:11: #1 tag size = 66 INFO @ Sat, 08 Sep 2018 12:51:11: #1 total tags in treatment: 23115810 INFO @ Sat, 08 Sep 2018 12:51:11: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:51:11: #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 12:51:11: #1 tags after filtering in treatment: 23115810 INFO @ Sat, 08 Sep 2018 12:51:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:51:11: #1 finished! INFO @ Sat, 08 Sep 2018 12:51:11: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:51:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:51:11: #1 tags after filtering in treatment: 23115810 INFO @ Sat, 08 Sep 2018 12:51:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:51:11: #1 finished! INFO @ Sat, 08 Sep 2018 12:51:11: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:51:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:51:12: #2 number of paired peaks: 657 WARNING @ Sat, 08 Sep 2018 12:51:12: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sat, 08 Sep 2018 12:51:12: start model_add_line... INFO @ Sat, 08 Sep 2018 12:51:13: start X-correlation... INFO @ Sat, 08 Sep 2018 12:51:13: end of X-cor INFO @ Sat, 08 Sep 2018 12:51:13: #2 finished! INFO @ Sat, 08 Sep 2018 12:51:13: #2 predicted fragment length is 162 bps INFO @ Sat, 08 Sep 2018 12:51:13: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 08 Sep 2018 12:51:13: #2.2 Generate R script for model : SRX2564136.10_model.r INFO @ Sat, 08 Sep 2018 12:51:13: #2 number of paired peaks: 657 WARNING @ Sat, 08 Sep 2018 12:51:13: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sat, 08 Sep 2018 12:51:13: start model_add_line... INFO @ Sat, 08 Sep 2018 12:51:13: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:51:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:51:13: start X-correlation... INFO @ Sat, 08 Sep 2018 12:51:13: end of X-cor INFO @ Sat, 08 Sep 2018 12:51:13: #2 finished! INFO @ Sat, 08 Sep 2018 12:51:13: #2 predicted fragment length is 162 bps INFO @ Sat, 08 Sep 2018 12:51:13: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 08 Sep 2018 12:51:13: #2.2 Generate R script for model : SRX2564136.20_model.r INFO @ Sat, 08 Sep 2018 12:51:13: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:51:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:51:34: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:52:01: #4 Write output xls file... SRX2564136.05_peaks.xls INFO @ Sat, 08 Sep 2018 12:52:01: #4 Write peak in narrowPeak format file... SRX2564136.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:52:01: #4 Write summits bed file... SRX2564136.05_summits.bed INFO @ Sat, 08 Sep 2018 12:52:01: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9726 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:52:07: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:52:10: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:52:37: #4 Write output xls file... SRX2564136.10_peaks.xls INFO @ Sat, 08 Sep 2018 12:52:37: #4 Write peak in narrowPeak format file... SRX2564136.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:52:37: #4 Write summits bed file... SRX2564136.10_summits.bed INFO @ Sat, 08 Sep 2018 12:52:37: Done! INFO @ Sat, 08 Sep 2018 12:52:37: #4 Write output xls file... SRX2564136.20_peaks.xls pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7193 records, 4 fields): 10 millis INFO @ Sat, 08 Sep 2018 12:52:37: #4 Write peak in narrowPeak format file... SRX2564136.20_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:52:37: #4 Write summits bed file... SRX2564136.20_summits.bed INFO @ Sat, 08 Sep 2018 12:52:37: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4447 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。