Job ID = 9371917 sra ファイルのダウンロード中... Completed: 698938K bytes transferred in 26 seconds (216498K bits/sec), in 1 file, 2 directories. 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 31912281 spots for /home/okishinya/chipatlas/results/dm3/SRX2520641/SRR5206760.sra Written 31912281 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: 00:11:40 31912281 reads; of these: 31912281 (100.00%) were unpaired; of these: 841451 (2.64%) aligned 0 times 24785390 (77.67%) aligned exactly 1 time 6285440 (19.70%) aligned >1 times 97.36% overall alignment rate Time searching: 00:11:40 Overall time: 00:11:40 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 16 files... [bam_rmdupse_core] 8106808 / 31070830 = 0.2609 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, 04 Aug 2017 15:09:23: # Command line: callpeak -t SRX2520641.bam -f BAM -g dm -n SRX2520641.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520641.10 # format = BAM # ChIP-seq file = ['SRX2520641.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 @ Fri, 04 Aug 2017 15:09:23: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:09:23: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:09:23: # Command line: callpeak -t SRX2520641.bam -f BAM -g dm -n SRX2520641.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520641.05 # format = BAM # ChIP-seq file = ['SRX2520641.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 @ Fri, 04 Aug 2017 15:09:23: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:09:23: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:09:23: # Command line: callpeak -t SRX2520641.bam -f BAM -g dm -n SRX2520641.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520641.20 # format = BAM # ChIP-seq file = ['SRX2520641.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 @ Fri, 04 Aug 2017 15:09:23: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:09:23: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:09:31: 1000000 INFO @ Fri, 04 Aug 2017 15:09:31: 1000000 INFO @ Fri, 04 Aug 2017 15:09:31: 1000000 INFO @ Fri, 04 Aug 2017 15:09:38: 2000000 INFO @ Fri, 04 Aug 2017 15:09:38: 2000000 INFO @ Fri, 04 Aug 2017 15:09:39: 2000000 INFO @ Fri, 04 Aug 2017 15:09:46: 3000000 INFO @ Fri, 04 Aug 2017 15:09:46: 3000000 INFO @ Fri, 04 Aug 2017 15:09:46: 3000000 INFO @ Fri, 04 Aug 2017 15:09:53: 4000000 INFO @ Fri, 04 Aug 2017 15:09:53: 4000000 INFO @ Fri, 04 Aug 2017 15:09:54: 4000000 INFO @ Fri, 04 Aug 2017 15:10:01: 5000000 INFO @ Fri, 04 Aug 2017 15:10:01: 5000000 INFO @ Fri, 04 Aug 2017 15:10:02: 5000000 INFO @ Fri, 04 Aug 2017 15:10:08: 6000000 INFO @ Fri, 04 Aug 2017 15:10:08: 6000000 INFO @ Fri, 04 Aug 2017 15:10:09: 6000000 INFO @ Fri, 04 Aug 2017 15:10:15: 7000000 INFO @ Fri, 04 Aug 2017 15:10:15: 7000000 INFO @ Fri, 04 Aug 2017 15:10:17: 7000000 INFO @ Fri, 04 Aug 2017 15:10:23: 8000000 INFO @ Fri, 04 Aug 2017 15:10:23: 8000000 INFO @ Fri, 04 Aug 2017 15:10:25: 8000000 INFO @ Fri, 04 Aug 2017 15:10:30: 9000000 INFO @ Fri, 04 Aug 2017 15:10:30: 9000000 INFO @ Fri, 04 Aug 2017 15:10:33: 9000000 INFO @ Fri, 04 Aug 2017 15:10:37: 10000000 INFO @ Fri, 04 Aug 2017 15:10:37: 10000000 INFO @ Fri, 04 Aug 2017 15:10:41: 10000000 INFO @ Fri, 04 Aug 2017 15:10:45: 11000000 INFO @ Fri, 04 Aug 2017 15:10:45: 11000000 INFO @ Fri, 04 Aug 2017 15:10:48: 11000000 INFO @ Fri, 04 Aug 2017 15:10:52: 12000000 INFO @ Fri, 04 Aug 2017 15:10:52: 12000000 INFO @ Fri, 04 Aug 2017 15:10:56: 12000000 INFO @ Fri, 04 Aug 2017 15:10:59: 13000000 INFO @ Fri, 04 Aug 2017 15:10:59: 13000000 INFO @ Fri, 04 Aug 2017 15:11:04: 13000000 INFO @ Fri, 04 Aug 2017 15:11:07: 14000000 INFO @ Fri, 04 Aug 2017 15:11:07: 14000000 INFO @ Fri, 04 Aug 2017 15:11:12: 14000000 INFO @ Fri, 04 Aug 2017 15:11:14: 15000000 INFO @ Fri, 04 Aug 2017 15:11:14: 15000000 INFO @ Fri, 04 Aug 2017 15:11:20: 15000000 INFO @ Fri, 04 Aug 2017 15:11:21: 16000000 INFO @ Fri, 04 Aug 2017 15:11:21: 16000000 INFO @ Fri, 04 Aug 2017 15:11:28: 16000000 INFO @ Fri, 04 Aug 2017 15:11:29: 17000000 INFO @ Fri, 04 Aug 2017 15:11:29: 17000000 INFO @ Fri, 04 Aug 2017 15:11:35: 17000000 INFO @ Fri, 04 Aug 2017 15:11:36: 18000000 INFO @ Fri, 04 Aug 2017 15:11:36: 18000000 INFO @ Fri, 04 Aug 2017 15:11:43: 18000000 INFO @ Fri, 04 Aug 2017 15:11:44: 19000000 INFO @ Fri, 04 Aug 2017 15:11:44: 19000000 INFO @ Fri, 04 Aug 2017 15:11:51: 20000000 INFO @ Fri, 04 Aug 2017 15:11:51: 20000000 INFO @ Fri, 04 Aug 2017 15:11:51: 19000000 INFO @ Fri, 04 Aug 2017 15:11:59: 21000000 INFO @ Fri, 04 Aug 2017 15:11:59: 21000000 INFO @ Fri, 04 Aug 2017 15:11:59: 20000000 INFO @ Fri, 04 Aug 2017 15:12:06: 22000000 INFO @ Fri, 04 Aug 2017 15:12:06: 22000000 INFO @ Fri, 04 Aug 2017 15:12:06: 21000000 INFO @ Fri, 04 Aug 2017 15:12:13: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:12:13: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:12:13: #1 total tags in treatment: 22964022 INFO @ Fri, 04 Aug 2017 15:12:13: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:12:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:12:13: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:12:13: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:12:13: #1 total tags in treatment: 22964022 INFO @ Fri, 04 Aug 2017 15:12:13: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:12:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:12:14: #1 tags after filtering in treatment: 22964022 INFO @ Fri, 04 Aug 2017 15:12:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:12:14: #1 finished! INFO @ Fri, 04 Aug 2017 15:12:14: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:12:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:12:14: #1 tags after filtering in treatment: 22964022 INFO @ Fri, 04 Aug 2017 15:12:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:12:14: #1 finished! INFO @ Fri, 04 Aug 2017 15:12:14: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:12:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:12:14: 22000000 INFO @ Fri, 04 Aug 2017 15:12:15: #2 number of paired peaks: 341 WARNING @ Fri, 04 Aug 2017 15:12:15: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Fri, 04 Aug 2017 15:12:15: start model_add_line... INFO @ Fri, 04 Aug 2017 15:12:15: #2 number of paired peaks: 341 WARNING @ Fri, 04 Aug 2017 15:12:15: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Fri, 04 Aug 2017 15:12:15: start model_add_line... INFO @ Fri, 04 Aug 2017 15:12:16: start X-correlation... INFO @ Fri, 04 Aug 2017 15:12:16: end of X-cor INFO @ Fri, 04 Aug 2017 15:12:16: #2 finished! INFO @ Fri, 04 Aug 2017 15:12:16: #2 predicted fragment length is 147 bps INFO @ Fri, 04 Aug 2017 15:12:16: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 04 Aug 2017 15:12:16: #2.2 Generate R script for model : SRX2520641.05_model.r INFO @ Fri, 04 Aug 2017 15:12:16: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:12:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:12:16: start X-correlation... INFO @ Fri, 04 Aug 2017 15:12:16: end of X-cor INFO @ Fri, 04 Aug 2017 15:12:16: #2 finished! INFO @ Fri, 04 Aug 2017 15:12:16: #2 predicted fragment length is 147 bps INFO @ Fri, 04 Aug 2017 15:12:16: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 04 Aug 2017 15:12:16: #2.2 Generate R script for model : SRX2520641.10_model.r INFO @ Fri, 04 Aug 2017 15:12:16: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:12:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:12:21: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:12:21: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:12:21: #1 total tags in treatment: 22964022 INFO @ Fri, 04 Aug 2017 15:12:21: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:12:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:12:22: #1 tags after filtering in treatment: 22964022 INFO @ Fri, 04 Aug 2017 15:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:12:22: #1 finished! INFO @ Fri, 04 Aug 2017 15:12:22: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:12:24: #2 number of paired peaks: 341 WARNING @ Fri, 04 Aug 2017 15:12:24: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Fri, 04 Aug 2017 15:12:24: start model_add_line... INFO @ Fri, 04 Aug 2017 15:12:24: start X-correlation... INFO @ Fri, 04 Aug 2017 15:12:24: end of X-cor INFO @ Fri, 04 Aug 2017 15:12:24: #2 finished! INFO @ Fri, 04 Aug 2017 15:12:24: #2 predicted fragment length is 147 bps INFO @ Fri, 04 Aug 2017 15:12:24: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 04 Aug 2017 15:12:24: #2.2 Generate R script for model : SRX2520641.20_model.r INFO @ Fri, 04 Aug 2017 15:12:24: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:13:07: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:13:10: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:13:15: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:13:35: #4 Write output xls file... SRX2520641.05_peaks.xls INFO @ Fri, 04 Aug 2017 15:13:35: #4 Write peak in narrowPeak format file... SRX2520641.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:13:35: #4 Write summits bed file... SRX2520641.05_summits.bed INFO @ Fri, 04 Aug 2017 15:13:35: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8698 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:13:40: #4 Write output xls file... SRX2520641.10_peaks.xls INFO @ Fri, 04 Aug 2017 15:13:40: #4 Write peak in narrowPeak format file... SRX2520641.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:13:40: #4 Write summits bed file... SRX2520641.10_summits.bed INFO @ Fri, 04 Aug 2017 15:13:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5022 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:13:41: #4 Write output xls file... SRX2520641.20_peaks.xls INFO @ Fri, 04 Aug 2017 15:13:41: #4 Write peak in narrowPeak format file... SRX2520641.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:13:41: #4 Write summits bed file... SRX2520641.20_summits.bed INFO @ Fri, 04 Aug 2017 15:13:41: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2108 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。