Job ID = 9371920 sra ファイルのダウンロード中... Completed: 498443K bytes transferred in 16 seconds (243091K 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 22861352 spots for /home/okishinya/chipatlas/results/dm3/SRX2520643/SRR5206762.sra Written 22861352 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:41 22861352 reads; of these: 22861352 (100.00%) were unpaired; of these: 1459288 (6.38%) aligned 0 times 16784356 (73.42%) aligned exactly 1 time 4617708 (20.20%) aligned >1 times 93.62% overall alignment rate Time searching: 00:08:42 Overall time: 00:08:42 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] 2243433 / 21402064 = 0.1048 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 15:03:56: # Command line: callpeak -t SRX2520643.bam -f BAM -g dm -n SRX2520643.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520643.05 # format = BAM # ChIP-seq file = ['SRX2520643.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 15:03:56: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:03:56: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:03:56: # Command line: callpeak -t SRX2520643.bam -f BAM -g dm -n SRX2520643.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520643.20 # format = BAM # ChIP-seq file = ['SRX2520643.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 15:03:56: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:03:56: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:03:56: # Command line: callpeak -t SRX2520643.bam -f BAM -g dm -n SRX2520643.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520643.10 # format = BAM # ChIP-seq file = ['SRX2520643.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 15:03:56: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:03:56: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:04:03: 1000000 INFO @ Fri, 04 Aug 2017 15:04:03: 1000000 INFO @ Fri, 04 Aug 2017 15:04:04: 1000000 INFO @ Fri, 04 Aug 2017 15:04:10: 2000000 INFO @ Fri, 04 Aug 2017 15:04:11: 2000000 INFO @ Fri, 04 Aug 2017 15:04:12: 2000000 INFO @ Fri, 04 Aug 2017 15:04:18: 3000000 INFO @ Fri, 04 Aug 2017 15:04:18: 3000000 INFO @ Fri, 04 Aug 2017 15:04:20: 3000000 INFO @ Fri, 04 Aug 2017 15:04:25: 4000000 INFO @ Fri, 04 Aug 2017 15:04:26: 4000000 INFO @ Fri, 04 Aug 2017 15:04:28: 4000000 INFO @ Fri, 04 Aug 2017 15:04:33: 5000000 INFO @ Fri, 04 Aug 2017 15:04:34: 5000000 INFO @ Fri, 04 Aug 2017 15:04:38: 5000000 INFO @ Fri, 04 Aug 2017 15:04:42: 6000000 INFO @ Fri, 04 Aug 2017 15:04:43: 6000000 INFO @ Fri, 04 Aug 2017 15:04:47: 6000000 INFO @ Fri, 04 Aug 2017 15:04:50: 7000000 INFO @ Fri, 04 Aug 2017 15:04:52: 7000000 INFO @ Fri, 04 Aug 2017 15:04:57: 7000000 INFO @ Fri, 04 Aug 2017 15:04:58: 8000000 INFO @ Fri, 04 Aug 2017 15:05:00: 8000000 INFO @ Fri, 04 Aug 2017 15:05:07: 8000000 INFO @ Fri, 04 Aug 2017 15:05:07: 9000000 INFO @ Fri, 04 Aug 2017 15:05:09: 9000000 INFO @ Fri, 04 Aug 2017 15:05:16: 10000000 INFO @ Fri, 04 Aug 2017 15:05:17: 9000000 INFO @ Fri, 04 Aug 2017 15:05:18: 10000000 INFO @ Fri, 04 Aug 2017 15:05:24: 11000000 INFO @ Fri, 04 Aug 2017 15:05:27: 10000000 INFO @ Fri, 04 Aug 2017 15:05:27: 11000000 INFO @ Fri, 04 Aug 2017 15:05:33: 12000000 INFO @ Fri, 04 Aug 2017 15:05:36: 12000000 INFO @ Fri, 04 Aug 2017 15:05:37: 11000000 INFO @ Fri, 04 Aug 2017 15:05:42: 13000000 INFO @ Fri, 04 Aug 2017 15:05:45: 13000000 INFO @ Fri, 04 Aug 2017 15:05:47: 12000000 INFO @ Fri, 04 Aug 2017 15:05:50: 14000000 INFO @ Fri, 04 Aug 2017 15:05:54: 14000000 INFO @ Fri, 04 Aug 2017 15:05:57: 13000000 INFO @ Fri, 04 Aug 2017 15:05:59: 15000000 INFO @ Fri, 04 Aug 2017 15:06:03: 15000000 INFO @ Fri, 04 Aug 2017 15:06:07: 14000000 INFO @ Fri, 04 Aug 2017 15:06:08: 16000000 INFO @ Fri, 04 Aug 2017 15:06:13: 16000000 INFO @ Fri, 04 Aug 2017 15:06:16: 17000000 INFO @ Fri, 04 Aug 2017 15:06:16: 15000000 INFO @ Fri, 04 Aug 2017 15:06:24: 18000000 INFO @ Fri, 04 Aug 2017 15:06:24: 17000000 INFO @ Fri, 04 Aug 2017 15:06:25: 16000000 INFO @ Fri, 04 Aug 2017 15:06:32: 19000000 INFO @ Fri, 04 Aug 2017 15:06:33: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:06:33: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:06:33: #1 total tags in treatment: 19158631 INFO @ Fri, 04 Aug 2017 15:06:33: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:06:33: #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 15:06:33: #1 tags after filtering in treatment: 19158631 INFO @ Fri, 04 Aug 2017 15:06:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:06:33: #1 finished! INFO @ Fri, 04 Aug 2017 15:06:33: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:06:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:06:34: 17000000 INFO @ Fri, 04 Aug 2017 15:06:35: #2 number of paired peaks: 472 WARNING @ Fri, 04 Aug 2017 15:06:35: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Fri, 04 Aug 2017 15:06:35: start model_add_line... INFO @ Fri, 04 Aug 2017 15:06:35: 18000000 INFO @ Fri, 04 Aug 2017 15:06:35: start X-correlation... INFO @ Fri, 04 Aug 2017 15:06:35: end of X-cor INFO @ Fri, 04 Aug 2017 15:06:35: #2 finished! INFO @ Fri, 04 Aug 2017 15:06:35: #2 predicted fragment length is 128 bps INFO @ Fri, 04 Aug 2017 15:06:35: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 04 Aug 2017 15:06:35: #2.2 Generate R script for model : SRX2520643.05_model.r INFO @ Fri, 04 Aug 2017 15:06:35: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:06:41: 18000000 INFO @ Fri, 04 Aug 2017 15:06:46: 19000000 INFO @ Fri, 04 Aug 2017 15:06:47: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:06:47: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:06:47: #1 total tags in treatment: 19158631 INFO @ Fri, 04 Aug 2017 15:06:47: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:06:47: #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 15:06:48: #1 tags after filtering in treatment: 19158631 INFO @ Fri, 04 Aug 2017 15:06:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:06:48: #1 finished! INFO @ Fri, 04 Aug 2017 15:06:48: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:06:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:06:49: #2 number of paired peaks: 472 WARNING @ Fri, 04 Aug 2017 15:06:49: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Fri, 04 Aug 2017 15:06:49: start model_add_line... INFO @ Fri, 04 Aug 2017 15:06:49: 19000000 INFO @ Fri, 04 Aug 2017 15:06:49: start X-correlation... INFO @ Fri, 04 Aug 2017 15:06:49: end of X-cor INFO @ Fri, 04 Aug 2017 15:06:49: #2 finished! INFO @ Fri, 04 Aug 2017 15:06:49: #2 predicted fragment length is 128 bps INFO @ Fri, 04 Aug 2017 15:06:49: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 04 Aug 2017 15:06:49: #2.2 Generate R script for model : SRX2520643.10_model.r INFO @ Fri, 04 Aug 2017 15:06:49: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:06:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:06:50: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:06:50: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:06:50: #1 total tags in treatment: 19158631 INFO @ Fri, 04 Aug 2017 15:06:50: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:06:50: #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 15:06:51: #1 tags after filtering in treatment: 19158631 INFO @ Fri, 04 Aug 2017 15:06:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:06:51: #1 finished! INFO @ Fri, 04 Aug 2017 15:06:51: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:06:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:06:52: #2 number of paired peaks: 472 WARNING @ Fri, 04 Aug 2017 15:06:52: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Fri, 04 Aug 2017 15:06:52: start model_add_line... INFO @ Fri, 04 Aug 2017 15:06:52: start X-correlation... INFO @ Fri, 04 Aug 2017 15:06:52: end of X-cor INFO @ Fri, 04 Aug 2017 15:06:52: #2 finished! INFO @ Fri, 04 Aug 2017 15:06:52: #2 predicted fragment length is 128 bps INFO @ Fri, 04 Aug 2017 15:06:52: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 04 Aug 2017 15:06:52: #2.2 Generate R script for model : SRX2520643.20_model.r INFO @ Fri, 04 Aug 2017 15:06:52: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:06:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:07:17: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:07:35: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:07:37: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:07:40: #4 Write output xls file... SRX2520643.05_peaks.xls INFO @ Fri, 04 Aug 2017 15:07:40: #4 Write peak in narrowPeak format file... SRX2520643.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:07:41: #4 Write summits bed file... SRX2520643.05_summits.bed INFO @ Fri, 04 Aug 2017 15:07:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6768 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:07:59: #4 Write output xls file... SRX2520643.20_peaks.xls INFO @ Fri, 04 Aug 2017 15:07:59: #4 Write peak in narrowPeak format file... SRX2520643.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:07:59: #4 Write summits bed file... SRX2520643.20_summits.bed INFO @ Fri, 04 Aug 2017 15:07:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1431 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:08:02: #4 Write output xls file... SRX2520643.10_peaks.xls INFO @ Fri, 04 Aug 2017 15:08:02: #4 Write peak in narrowPeak format file... SRX2520643.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:08:02: #4 Write summits bed file... SRX2520643.10_summits.bed INFO @ Fri, 04 Aug 2017 15:08:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3588 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。