Job ID = 10450993 sra ファイルのダウンロード中... Completed: 557907K bytes transferred in 12 seconds (354113K 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... Written 29502913 spots for /home/okishinya/chipatlas/results/dm3/SRX3404046/SRR6303523.sra Written 29502913 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:22:14 29502913 reads; of these: 29502913 (100.00%) were unpaired; of these: 964457 (3.27%) aligned 0 times 20126751 (68.22%) aligned exactly 1 time 8411705 (28.51%) aligned >1 times 96.73% overall alignment rate Time searching: 00:22:14 Overall time: 00:22:14 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] 3004166 / 28538456 = 0.1053 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 @ Wed, 07 Feb 2018 14:58:38: # Command line: callpeak -t SRX3404046.bam -f BAM -g dm -n SRX3404046.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404046.10 # format = BAM # ChIP-seq file = ['SRX3404046.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 @ Wed, 07 Feb 2018 14:58:38: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:58:38: # Command line: callpeak -t SRX3404046.bam -f BAM -g dm -n SRX3404046.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404046.20 # format = BAM # ChIP-seq file = ['SRX3404046.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 @ Wed, 07 Feb 2018 14:58:38: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:58:38: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:58:38: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:58:38: # Command line: callpeak -t SRX3404046.bam -f BAM -g dm -n SRX3404046.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404046.05 # format = BAM # ChIP-seq file = ['SRX3404046.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 @ Wed, 07 Feb 2018 14:58:38: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:58:38: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:58:46: 1000000 INFO @ Wed, 07 Feb 2018 14:58:47: 1000000 INFO @ Wed, 07 Feb 2018 14:58:47: 1000000 INFO @ Wed, 07 Feb 2018 14:58:55: 2000000 INFO @ Wed, 07 Feb 2018 14:58:56: 2000000 INFO @ Wed, 07 Feb 2018 14:58:57: 2000000 INFO @ Wed, 07 Feb 2018 14:59:03: 3000000 INFO @ Wed, 07 Feb 2018 14:59:05: 3000000 INFO @ Wed, 07 Feb 2018 14:59:05: 3000000 INFO @ Wed, 07 Feb 2018 14:59:11: 4000000 INFO @ Wed, 07 Feb 2018 14:59:14: 4000000 INFO @ Wed, 07 Feb 2018 14:59:14: 4000000 INFO @ Wed, 07 Feb 2018 14:59:20: 5000000 INFO @ Wed, 07 Feb 2018 14:59:23: 5000000 INFO @ Wed, 07 Feb 2018 14:59:23: 5000000 INFO @ Wed, 07 Feb 2018 14:59:28: 6000000 INFO @ Wed, 07 Feb 2018 14:59:32: 6000000 INFO @ Wed, 07 Feb 2018 14:59:33: 6000000 INFO @ Wed, 07 Feb 2018 14:59:37: 7000000 INFO @ Wed, 07 Feb 2018 14:59:41: 7000000 INFO @ Wed, 07 Feb 2018 14:59:42: 7000000 INFO @ Wed, 07 Feb 2018 14:59:45: 8000000 INFO @ Wed, 07 Feb 2018 14:59:49: 8000000 INFO @ Wed, 07 Feb 2018 14:59:51: 8000000 INFO @ Wed, 07 Feb 2018 14:59:53: 9000000 INFO @ Wed, 07 Feb 2018 14:59:58: 9000000 INFO @ Wed, 07 Feb 2018 15:00:00: 9000000 INFO @ Wed, 07 Feb 2018 15:00:02: 10000000 INFO @ Wed, 07 Feb 2018 15:00:07: 10000000 INFO @ Wed, 07 Feb 2018 15:00:08: 10000000 INFO @ Wed, 07 Feb 2018 15:00:10: 11000000 INFO @ Wed, 07 Feb 2018 15:00:16: 11000000 INFO @ Wed, 07 Feb 2018 15:00:18: 11000000 INFO @ Wed, 07 Feb 2018 15:00:18: 12000000 INFO @ Wed, 07 Feb 2018 15:00:24: 12000000 INFO @ Wed, 07 Feb 2018 15:00:27: 12000000 INFO @ Wed, 07 Feb 2018 15:00:27: 13000000 INFO @ Wed, 07 Feb 2018 15:00:34: 13000000 INFO @ Wed, 07 Feb 2018 15:00:35: 14000000 INFO @ Wed, 07 Feb 2018 15:00:36: 13000000 INFO @ Wed, 07 Feb 2018 15:00:43: 14000000 INFO @ Wed, 07 Feb 2018 15:00:44: 15000000 INFO @ Wed, 07 Feb 2018 15:00:45: 14000000 INFO @ Wed, 07 Feb 2018 15:00:52: 16000000 INFO @ Wed, 07 Feb 2018 15:00:52: 15000000 INFO @ Wed, 07 Feb 2018 15:00:54: 15000000 INFO @ Wed, 07 Feb 2018 15:01:00: 17000000 INFO @ Wed, 07 Feb 2018 15:01:01: 16000000 INFO @ Wed, 07 Feb 2018 15:01:03: 16000000 INFO @ Wed, 07 Feb 2018 15:01:09: 18000000 INFO @ Wed, 07 Feb 2018 15:01:10: 17000000 INFO @ Wed, 07 Feb 2018 15:01:12: 17000000 INFO @ Wed, 07 Feb 2018 15:01:17: 19000000 INFO @ Wed, 07 Feb 2018 15:01:20: 18000000 INFO @ Wed, 07 Feb 2018 15:01:22: 18000000 INFO @ Wed, 07 Feb 2018 15:01:26: 20000000 INFO @ Wed, 07 Feb 2018 15:01:29: 19000000 INFO @ Wed, 07 Feb 2018 15:01:31: 19000000 INFO @ Wed, 07 Feb 2018 15:01:34: 21000000 INFO @ Wed, 07 Feb 2018 15:01:38: 20000000 INFO @ Wed, 07 Feb 2018 15:01:40: 20000000 INFO @ Wed, 07 Feb 2018 15:01:43: 22000000 INFO @ Wed, 07 Feb 2018 15:01:47: 21000000 INFO @ Wed, 07 Feb 2018 15:01:49: 21000000 INFO @ Wed, 07 Feb 2018 15:01:51: 23000000 INFO @ Wed, 07 Feb 2018 15:01:55: 22000000 INFO @ Wed, 07 Feb 2018 15:01:58: 22000000 INFO @ Wed, 07 Feb 2018 15:01:59: 24000000 INFO @ Wed, 07 Feb 2018 15:02:04: 23000000 INFO @ Wed, 07 Feb 2018 15:02:06: 23000000 INFO @ Wed, 07 Feb 2018 15:02:08: 25000000 INFO @ Wed, 07 Feb 2018 15:02:12: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:02:12: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:02:12: #1 total tags in treatment: 25534290 INFO @ Wed, 07 Feb 2018 15:02:12: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:02:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:02:13: #1 tags after filtering in treatment: 25534290 INFO @ Wed, 07 Feb 2018 15:02:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:02:13: #1 finished! INFO @ Wed, 07 Feb 2018 15:02:13: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:02:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:02:13: 24000000 INFO @ Wed, 07 Feb 2018 15:02:15: 24000000 INFO @ Wed, 07 Feb 2018 15:02:16: #2 number of paired peaks: 194 WARNING @ Wed, 07 Feb 2018 15:02:16: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Wed, 07 Feb 2018 15:02:16: start model_add_line... INFO @ Wed, 07 Feb 2018 15:02:16: start X-correlation... INFO @ Wed, 07 Feb 2018 15:02:16: end of X-cor INFO @ Wed, 07 Feb 2018 15:02:16: #2 finished! INFO @ Wed, 07 Feb 2018 15:02:16: #2 predicted fragment length is 112 bps INFO @ Wed, 07 Feb 2018 15:02:16: #2 alternative fragment length(s) may be 4,112 bps INFO @ Wed, 07 Feb 2018 15:02:16: #2.2 Generate R script for model : SRX3404046.10_model.r INFO @ Wed, 07 Feb 2018 15:02:16: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:02:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:02:22: 25000000 INFO @ Wed, 07 Feb 2018 15:02:24: 25000000 INFO @ Wed, 07 Feb 2018 15:02:27: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:02:27: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:02:27: #1 total tags in treatment: 25534290 INFO @ Wed, 07 Feb 2018 15:02:27: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:02:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:02:28: #1 tags after filtering in treatment: 25534290 INFO @ Wed, 07 Feb 2018 15:02:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:02:28: #1 finished! INFO @ Wed, 07 Feb 2018 15:02:28: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:02:29: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:02:29: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:02:29: #1 total tags in treatment: 25534290 INFO @ Wed, 07 Feb 2018 15:02:29: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:02:30: #1 tags after filtering in treatment: 25534290 INFO @ Wed, 07 Feb 2018 15:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:02:30: #1 finished! INFO @ Wed, 07 Feb 2018 15:02:30: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:02:30: #2 number of paired peaks: 194 WARNING @ Wed, 07 Feb 2018 15:02:30: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Wed, 07 Feb 2018 15:02:30: start model_add_line... INFO @ Wed, 07 Feb 2018 15:02:31: start X-correlation... INFO @ Wed, 07 Feb 2018 15:02:31: end of X-cor INFO @ Wed, 07 Feb 2018 15:02:31: #2 finished! INFO @ Wed, 07 Feb 2018 15:02:31: #2 predicted fragment length is 112 bps INFO @ Wed, 07 Feb 2018 15:02:31: #2 alternative fragment length(s) may be 4,112 bps INFO @ Wed, 07 Feb 2018 15:02:31: #2.2 Generate R script for model : SRX3404046.20_model.r INFO @ Wed, 07 Feb 2018 15:02:31: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:02:32: #2 number of paired peaks: 194 WARNING @ Wed, 07 Feb 2018 15:02:32: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Wed, 07 Feb 2018 15:02:32: start model_add_line... INFO @ Wed, 07 Feb 2018 15:02:32: start X-correlation... INFO @ Wed, 07 Feb 2018 15:02:32: end of X-cor INFO @ Wed, 07 Feb 2018 15:02:32: #2 finished! INFO @ Wed, 07 Feb 2018 15:02:32: #2 predicted fragment length is 112 bps INFO @ Wed, 07 Feb 2018 15:02:32: #2 alternative fragment length(s) may be 4,112 bps INFO @ Wed, 07 Feb 2018 15:02:32: #2.2 Generate R script for model : SRX3404046.05_model.r INFO @ Wed, 07 Feb 2018 15:02:32: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:02:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:03:20: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:03:34: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:03:37: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:03:53: #4 Write output xls file... SRX3404046.10_peaks.xls INFO @ Wed, 07 Feb 2018 15:03:53: #4 Write peak in narrowPeak format file... SRX3404046.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:03:53: #4 Write summits bed file... SRX3404046.10_summits.bed INFO @ Wed, 07 Feb 2018 15:03:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2790 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 15:04:06: #4 Write output xls file... SRX3404046.20_peaks.xls INFO @ Wed, 07 Feb 2018 15:04:06: #4 Write peak in narrowPeak format file... SRX3404046.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:04:06: #4 Write summits bed file... SRX3404046.20_summits.bed INFO @ Wed, 07 Feb 2018 15:04:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1555 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 15:04:11: #4 Write output xls file... SRX3404046.05_peaks.xls INFO @ Wed, 07 Feb 2018 15:04:11: #4 Write peak in narrowPeak format file... SRX3404046.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:04:11: #4 Write summits bed file... SRX3404046.05_summits.bed INFO @ Wed, 07 Feb 2018 15:04:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4251 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。