Job ID = 11171210 sra ファイルのダウンロード中... Completed: 833728K bytes transferred in 31 seconds (217545K 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 43476894 spots for /home/okishinya/chipatlas/results/dm3/SRX2618519/SRR5319073.sra Written 43476894 spots for /home/okishinya/chipatlas/results/dm3/SRX2618519/SRR5319073.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: 00:10:01 43476894 reads; of these: 43476894 (100.00%) were unpaired; of these: 20072179 (46.17%) aligned 0 times 19216814 (44.20%) aligned exactly 1 time 4187901 (9.63%) aligned >1 times 53.83% overall alignment rate Time searching: 00:10:01 Overall time: 00:10:01 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] 3025674 / 23404715 = 0.1293 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 13:16:12: # Command line: callpeak -t SRX2618519.bam -f BAM -g dm -n SRX2618519.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618519.10 # format = BAM # ChIP-seq file = ['SRX2618519.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 13:16:12: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:16:12: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:16:12: # Command line: callpeak -t SRX2618519.bam -f BAM -g dm -n SRX2618519.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618519.05 # format = BAM # ChIP-seq file = ['SRX2618519.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 13:16:12: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:16:12: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:16:12: # Command line: callpeak -t SRX2618519.bam -f BAM -g dm -n SRX2618519.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618519.20 # format = BAM # ChIP-seq file = ['SRX2618519.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 13:16:12: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:16:12: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:16:19: 1000000 INFO @ Sat, 08 Sep 2018 13:16:19: 1000000 INFO @ Sat, 08 Sep 2018 13:16:19: 1000000 INFO @ Sat, 08 Sep 2018 13:16:25: 2000000 INFO @ Sat, 08 Sep 2018 13:16:25: 2000000 INFO @ Sat, 08 Sep 2018 13:16:25: 2000000 INFO @ Sat, 08 Sep 2018 13:16:31: 3000000 INFO @ Sat, 08 Sep 2018 13:16:32: 3000000 INFO @ Sat, 08 Sep 2018 13:16:32: 3000000 INFO @ Sat, 08 Sep 2018 13:16:38: 4000000 INFO @ Sat, 08 Sep 2018 13:16:38: 4000000 INFO @ Sat, 08 Sep 2018 13:16:38: 4000000 INFO @ Sat, 08 Sep 2018 13:16:44: 5000000 INFO @ Sat, 08 Sep 2018 13:16:44: 5000000 INFO @ Sat, 08 Sep 2018 13:16:45: 5000000 INFO @ Sat, 08 Sep 2018 13:16:50: 6000000 INFO @ Sat, 08 Sep 2018 13:16:51: 6000000 INFO @ Sat, 08 Sep 2018 13:16:51: 6000000 INFO @ Sat, 08 Sep 2018 13:16:57: 7000000 INFO @ Sat, 08 Sep 2018 13:16:57: 7000000 INFO @ Sat, 08 Sep 2018 13:16:57: 7000000 INFO @ Sat, 08 Sep 2018 13:17:03: 8000000 INFO @ Sat, 08 Sep 2018 13:17:03: 8000000 INFO @ Sat, 08 Sep 2018 13:17:04: 8000000 INFO @ Sat, 08 Sep 2018 13:17:10: 9000000 INFO @ Sat, 08 Sep 2018 13:17:10: 9000000 INFO @ Sat, 08 Sep 2018 13:17:11: 9000000 INFO @ Sat, 08 Sep 2018 13:17:16: 10000000 INFO @ Sat, 08 Sep 2018 13:17:16: 10000000 INFO @ Sat, 08 Sep 2018 13:17:17: 10000000 INFO @ Sat, 08 Sep 2018 13:17:22: 11000000 INFO @ Sat, 08 Sep 2018 13:17:22: 11000000 INFO @ Sat, 08 Sep 2018 13:17:23: 11000000 INFO @ Sat, 08 Sep 2018 13:17:28: 12000000 INFO @ Sat, 08 Sep 2018 13:17:28: 12000000 INFO @ Sat, 08 Sep 2018 13:17:30: 12000000 INFO @ Sat, 08 Sep 2018 13:17:34: 13000000 INFO @ Sat, 08 Sep 2018 13:17:35: 13000000 INFO @ Sat, 08 Sep 2018 13:17:36: 13000000 INFO @ Sat, 08 Sep 2018 13:17:40: 14000000 INFO @ Sat, 08 Sep 2018 13:17:41: 14000000 INFO @ Sat, 08 Sep 2018 13:17:42: 14000000 INFO @ Sat, 08 Sep 2018 13:17:47: 15000000 INFO @ Sat, 08 Sep 2018 13:17:47: 15000000 INFO @ Sat, 08 Sep 2018 13:17:49: 15000000 INFO @ Sat, 08 Sep 2018 13:17:53: 16000000 INFO @ Sat, 08 Sep 2018 13:17:54: 16000000 INFO @ Sat, 08 Sep 2018 13:17:55: 16000000 INFO @ Sat, 08 Sep 2018 13:17:59: 17000000 INFO @ Sat, 08 Sep 2018 13:18:00: 17000000 INFO @ Sat, 08 Sep 2018 13:18:02: 17000000 INFO @ Sat, 08 Sep 2018 13:18:05: 18000000 INFO @ Sat, 08 Sep 2018 13:18:06: 18000000 INFO @ Sat, 08 Sep 2018 13:18:08: 18000000 INFO @ Sat, 08 Sep 2018 13:18:11: 19000000 INFO @ Sat, 08 Sep 2018 13:18:13: 19000000 INFO @ Sat, 08 Sep 2018 13:18:14: 19000000 INFO @ Sat, 08 Sep 2018 13:18:17: 20000000 INFO @ Sat, 08 Sep 2018 13:18:19: 20000000 INFO @ Sat, 08 Sep 2018 13:18:20: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:18:20: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:18:20: #1 total tags in treatment: 20379041 INFO @ Sat, 08 Sep 2018 13:18:20: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:18:20: #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 13:18:20: #1 tags after filtering in treatment: 20379041 INFO @ Sat, 08 Sep 2018 13:18:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:18:20: #1 finished! INFO @ Sat, 08 Sep 2018 13:18:20: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:18:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:18:21: 20000000 INFO @ Sat, 08 Sep 2018 13:18:22: #2 number of paired peaks: 225 WARNING @ Sat, 08 Sep 2018 13:18:22: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Sat, 08 Sep 2018 13:18:22: start model_add_line... INFO @ Sat, 08 Sep 2018 13:18:22: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:18:22: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:18:22: #1 total tags in treatment: 20379041 INFO @ Sat, 08 Sep 2018 13:18:22: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:18:22: #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 13:18:22: start X-correlation... INFO @ Sat, 08 Sep 2018 13:18:22: end of X-cor INFO @ Sat, 08 Sep 2018 13:18:22: #2 finished! INFO @ Sat, 08 Sep 2018 13:18:22: #2 predicted fragment length is 161 bps INFO @ Sat, 08 Sep 2018 13:18:22: #2 alternative fragment length(s) may be 161 bps INFO @ Sat, 08 Sep 2018 13:18:22: #2.2 Generate R script for model : SRX2618519.10_model.r INFO @ Sat, 08 Sep 2018 13:18:22: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:18:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:18:22: #1 tags after filtering in treatment: 20379041 INFO @ Sat, 08 Sep 2018 13:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:18:22: #1 finished! INFO @ Sat, 08 Sep 2018 13:18:22: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:18:23: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:18:23: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:18:23: #1 total tags in treatment: 20379041 INFO @ Sat, 08 Sep 2018 13:18:23: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:18:23: #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 13:18:23: #2 number of paired peaks: 225 WARNING @ Sat, 08 Sep 2018 13:18:23: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Sat, 08 Sep 2018 13:18:23: start model_add_line... INFO @ Sat, 08 Sep 2018 13:18:24: #1 tags after filtering in treatment: 20379041 INFO @ Sat, 08 Sep 2018 13:18:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:18:24: #1 finished! INFO @ Sat, 08 Sep 2018 13:18:24: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:18:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:18:24: start X-correlation... INFO @ Sat, 08 Sep 2018 13:18:24: end of X-cor INFO @ Sat, 08 Sep 2018 13:18:24: #2 finished! INFO @ Sat, 08 Sep 2018 13:18:24: #2 predicted fragment length is 161 bps INFO @ Sat, 08 Sep 2018 13:18:24: #2 alternative fragment length(s) may be 161 bps INFO @ Sat, 08 Sep 2018 13:18:24: #2.2 Generate R script for model : SRX2618519.20_model.r INFO @ Sat, 08 Sep 2018 13:18:24: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:18:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:18:25: #2 number of paired peaks: 225 WARNING @ Sat, 08 Sep 2018 13:18:25: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Sat, 08 Sep 2018 13:18:25: start model_add_line... INFO @ Sat, 08 Sep 2018 13:18:25: start X-correlation... INFO @ Sat, 08 Sep 2018 13:18:25: end of X-cor INFO @ Sat, 08 Sep 2018 13:18:25: #2 finished! INFO @ Sat, 08 Sep 2018 13:18:25: #2 predicted fragment length is 161 bps INFO @ Sat, 08 Sep 2018 13:18:25: #2 alternative fragment length(s) may be 161 bps INFO @ Sat, 08 Sep 2018 13:18:25: #2.2 Generate R script for model : SRX2618519.05_model.r INFO @ Sat, 08 Sep 2018 13:18:25: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:18:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:19:03: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:19:07: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:19:11: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:19:27: #4 Write output xls file... SRX2618519.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:19:27: #4 Write peak in narrowPeak format file... SRX2618519.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:19:27: #4 Write summits bed file... SRX2618519.10_summits.bed INFO @ Sat, 08 Sep 2018 13:19:27: Done! pass1 - making usageList (14 chroms): 50 millis pass2 - checking and writing primary data (6252 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:19:30: #4 Write output xls file... SRX2618519.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:19:30: #4 Write peak in narrowPeak format file... SRX2618519.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:19:30: #4 Write summits bed file... SRX2618519.20_summits.bed INFO @ Sat, 08 Sep 2018 13:19:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4155 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:19:35: #4 Write output xls file... SRX2618519.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:19:35: #4 Write peak in narrowPeak format file... SRX2618519.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:19:35: #4 Write summits bed file... SRX2618519.05_summits.bed INFO @ Sat, 08 Sep 2018 13:19:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7361 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。