Job ID = 10714541 sra ファイルのダウンロード中... Completed: 1696402K bytes transferred in 16 seconds (848299K 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: PAIRED fastq に変換中... Read 27782531 spots for /home/okishinya/chipatlas/results/dm3/SRX1704846/SRR3383180.sra Written 27782531 spots for /home/okishinya/chipatlas/results/dm3/SRX1704846/SRR3383180.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: 00:56:35 27782531 reads; of these: 27782531 (100.00%) were paired; of these: 7795471 (28.06%) aligned concordantly 0 times 16616836 (59.81%) aligned concordantly exactly 1 time 3370224 (12.13%) aligned concordantly >1 times ---- 7795471 pairs aligned concordantly 0 times; of these: 4140639 (53.12%) aligned discordantly 1 time ---- 3654832 pairs aligned 0 times concordantly or discordantly; of these: 7309664 mates make up the pairs; of these: 3329336 (45.55%) aligned 0 times 1767913 (24.19%) aligned exactly 1 time 2212415 (30.27%) aligned >1 times 94.01% overall alignment rate Time searching: 00:56:35 Overall time: 00:56:35 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 24 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 4480788 / 24099939 = 0.1859 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 @ Sun, 03 Jun 2018 14:29:39: # Command line: callpeak -t SRX1704846.bam -f BAM -g dm -n SRX1704846.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1704846.20 # format = BAM # ChIP-seq file = ['SRX1704846.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 @ Sun, 03 Jun 2018 14:29:39: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:29:39: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:29:39: # Command line: callpeak -t SRX1704846.bam -f BAM -g dm -n SRX1704846.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1704846.10 # format = BAM # ChIP-seq file = ['SRX1704846.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 @ Sun, 03 Jun 2018 14:29:39: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:29:39: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:29:39: # Command line: callpeak -t SRX1704846.bam -f BAM -g dm -n SRX1704846.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1704846.05 # format = BAM # ChIP-seq file = ['SRX1704846.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 @ Sun, 03 Jun 2018 14:29:39: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:29:39: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:29:44: 1000000 INFO @ Sun, 03 Jun 2018 14:29:44: 1000000 INFO @ Sun, 03 Jun 2018 14:29:44: 1000000 INFO @ Sun, 03 Jun 2018 14:29:50: 2000000 INFO @ Sun, 03 Jun 2018 14:29:50: 2000000 INFO @ Sun, 03 Jun 2018 14:29:50: 2000000 INFO @ Sun, 03 Jun 2018 14:29:55: 3000000 INFO @ Sun, 03 Jun 2018 14:29:56: 3000000 INFO @ Sun, 03 Jun 2018 14:29:56: 3000000 INFO @ Sun, 03 Jun 2018 14:30:01: 4000000 INFO @ Sun, 03 Jun 2018 14:30:01: 4000000 INFO @ Sun, 03 Jun 2018 14:30:01: 4000000 INFO @ Sun, 03 Jun 2018 14:30:07: 5000000 INFO @ Sun, 03 Jun 2018 14:30:07: 5000000 INFO @ Sun, 03 Jun 2018 14:30:07: 5000000 INFO @ Sun, 03 Jun 2018 14:30:12: 6000000 INFO @ Sun, 03 Jun 2018 14:30:13: 6000000 INFO @ Sun, 03 Jun 2018 14:30:13: 6000000 INFO @ Sun, 03 Jun 2018 14:30:18: 7000000 INFO @ Sun, 03 Jun 2018 14:30:18: 7000000 INFO @ Sun, 03 Jun 2018 14:30:18: 7000000 INFO @ Sun, 03 Jun 2018 14:30:24: 8000000 INFO @ Sun, 03 Jun 2018 14:30:24: 8000000 INFO @ Sun, 03 Jun 2018 14:30:24: 8000000 INFO @ Sun, 03 Jun 2018 14:30:29: 9000000 INFO @ Sun, 03 Jun 2018 14:30:29: 9000000 INFO @ Sun, 03 Jun 2018 14:30:30: 9000000 INFO @ Sun, 03 Jun 2018 14:30:35: 10000000 INFO @ Sun, 03 Jun 2018 14:30:35: 10000000 INFO @ Sun, 03 Jun 2018 14:30:35: 10000000 INFO @ Sun, 03 Jun 2018 14:30:40: 11000000 INFO @ Sun, 03 Jun 2018 14:30:41: 11000000 INFO @ Sun, 03 Jun 2018 14:30:41: 11000000 INFO @ Sun, 03 Jun 2018 14:30:46: 12000000 INFO @ Sun, 03 Jun 2018 14:30:46: 12000000 INFO @ Sun, 03 Jun 2018 14:30:47: 12000000 INFO @ Sun, 03 Jun 2018 14:30:52: 13000000 INFO @ Sun, 03 Jun 2018 14:30:52: 13000000 INFO @ Sun, 03 Jun 2018 14:30:52: 13000000 INFO @ Sun, 03 Jun 2018 14:30:57: 14000000 INFO @ Sun, 03 Jun 2018 14:30:57: 14000000 INFO @ Sun, 03 Jun 2018 14:30:58: 14000000 INFO @ Sun, 03 Jun 2018 14:31:03: 15000000 INFO @ Sun, 03 Jun 2018 14:31:03: 15000000 INFO @ Sun, 03 Jun 2018 14:31:04: 15000000 INFO @ Sun, 03 Jun 2018 14:31:08: 16000000 INFO @ Sun, 03 Jun 2018 14:31:09: 16000000 INFO @ Sun, 03 Jun 2018 14:31:10: 16000000 INFO @ Sun, 03 Jun 2018 14:31:14: 17000000 INFO @ Sun, 03 Jun 2018 14:31:15: 17000000 INFO @ Sun, 03 Jun 2018 14:31:16: 17000000 INFO @ Sun, 03 Jun 2018 14:31:19: 18000000 INFO @ Sun, 03 Jun 2018 14:31:21: 18000000 INFO @ Sun, 03 Jun 2018 14:31:22: 18000000 INFO @ Sun, 03 Jun 2018 14:31:25: 19000000 INFO @ Sun, 03 Jun 2018 14:31:26: 19000000 INFO @ Sun, 03 Jun 2018 14:31:28: 19000000 INFO @ Sun, 03 Jun 2018 14:31:30: 20000000 INFO @ Sun, 03 Jun 2018 14:31:32: 20000000 INFO @ Sun, 03 Jun 2018 14:31:34: 20000000 INFO @ Sun, 03 Jun 2018 14:31:36: 21000000 INFO @ Sun, 03 Jun 2018 14:31:38: 21000000 INFO @ Sun, 03 Jun 2018 14:31:39: 21000000 INFO @ Sun, 03 Jun 2018 14:31:41: 22000000 INFO @ Sun, 03 Jun 2018 14:31:44: 22000000 INFO @ Sun, 03 Jun 2018 14:31:45: 22000000 INFO @ Sun, 03 Jun 2018 14:31:47: 23000000 INFO @ Sun, 03 Jun 2018 14:31:49: 23000000 INFO @ Sun, 03 Jun 2018 14:31:51: 23000000 INFO @ Sun, 03 Jun 2018 14:31:52: 24000000 INFO @ Sun, 03 Jun 2018 14:31:55: 24000000 INFO @ Sun, 03 Jun 2018 14:31:57: 24000000 INFO @ Sun, 03 Jun 2018 14:31:58: 25000000 INFO @ Sun, 03 Jun 2018 14:32:00: 25000000 INFO @ Sun, 03 Jun 2018 14:32:03: 25000000 INFO @ Sun, 03 Jun 2018 14:32:03: 26000000 INFO @ Sun, 03 Jun 2018 14:32:06: 26000000 INFO @ Sun, 03 Jun 2018 14:32:08: 26000000 INFO @ Sun, 03 Jun 2018 14:32:09: 27000000 INFO @ Sun, 03 Jun 2018 14:32:12: 27000000 INFO @ Sun, 03 Jun 2018 14:32:14: 28000000 INFO @ Sun, 03 Jun 2018 14:32:14: 27000000 INFO @ Sun, 03 Jun 2018 14:32:18: 28000000 INFO @ Sun, 03 Jun 2018 14:32:20: 29000000 INFO @ Sun, 03 Jun 2018 14:32:20: 28000000 INFO @ Sun, 03 Jun 2018 14:32:23: 29000000 INFO @ Sun, 03 Jun 2018 14:32:25: 30000000 INFO @ Sun, 03 Jun 2018 14:32:26: 29000000 INFO @ Sun, 03 Jun 2018 14:32:29: 30000000 INFO @ Sun, 03 Jun 2018 14:32:31: 31000000 INFO @ Sun, 03 Jun 2018 14:32:32: 30000000 INFO @ Sun, 03 Jun 2018 14:32:35: 31000000 INFO @ Sun, 03 Jun 2018 14:32:36: 32000000 INFO @ Sun, 03 Jun 2018 14:32:38: 31000000 INFO @ Sun, 03 Jun 2018 14:32:41: 32000000 INFO @ Sun, 03 Jun 2018 14:32:42: 33000000 INFO @ Sun, 03 Jun 2018 14:32:44: 32000000 INFO @ Sun, 03 Jun 2018 14:32:47: 33000000 INFO @ Sun, 03 Jun 2018 14:32:48: 34000000 INFO @ Sun, 03 Jun 2018 14:32:50: 33000000 INFO @ Sun, 03 Jun 2018 14:32:53: 34000000 INFO @ Sun, 03 Jun 2018 14:32:53: 35000000 INFO @ Sun, 03 Jun 2018 14:32:56: 34000000 INFO @ Sun, 03 Jun 2018 14:32:58: 35000000 INFO @ Sun, 03 Jun 2018 14:32:59: 36000000 INFO @ Sun, 03 Jun 2018 14:33:01: 35000000 INFO @ Sun, 03 Jun 2018 14:33:04: 36000000 INFO @ Sun, 03 Jun 2018 14:33:05: 37000000 INFO @ Sun, 03 Jun 2018 14:33:07: 36000000 INFO @ Sun, 03 Jun 2018 14:33:10: 37000000 INFO @ Sun, 03 Jun 2018 14:33:10: 38000000 INFO @ Sun, 03 Jun 2018 14:33:13: 37000000 INFO @ Sun, 03 Jun 2018 14:33:16: 39000000 INFO @ Sun, 03 Jun 2018 14:33:16: 38000000 INFO @ Sun, 03 Jun 2018 14:33:19: 38000000 INFO @ Sun, 03 Jun 2018 14:33:21: 40000000 INFO @ Sun, 03 Jun 2018 14:33:21: 39000000 INFO @ Sun, 03 Jun 2018 14:33:25: 39000000 INFO @ Sun, 03 Jun 2018 14:33:27: 41000000 INFO @ Sun, 03 Jun 2018 14:33:27: 40000000 INFO @ Sun, 03 Jun 2018 14:33:30: 40000000 INFO @ Sun, 03 Jun 2018 14:33:32: 41000000 INFO @ Sun, 03 Jun 2018 14:33:32: 42000000 INFO @ Sun, 03 Jun 2018 14:33:36: 41000000 INFO @ Sun, 03 Jun 2018 14:33:38: 43000000 INFO @ Sun, 03 Jun 2018 14:33:38: 42000000 INFO @ Sun, 03 Jun 2018 14:33:40: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:33:40: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:33:40: #1 total tags in treatment: 15927327 INFO @ Sun, 03 Jun 2018 14:33:40: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:33:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 14:33:40: #1 tags after filtering in treatment: 12407467 INFO @ Sun, 03 Jun 2018 14:33:40: #1 Redundant rate of treatment: 0.22 INFO @ Sun, 03 Jun 2018 14:33:40: #1 finished! INFO @ Sun, 03 Jun 2018 14:33:40: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:33:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:33:41: #2 number of paired peaks: 219 WARNING @ Sun, 03 Jun 2018 14:33:41: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sun, 03 Jun 2018 14:33:41: start model_add_line... INFO @ Sun, 03 Jun 2018 14:33:41: start X-correlation... INFO @ Sun, 03 Jun 2018 14:33:41: end of X-cor INFO @ Sun, 03 Jun 2018 14:33:41: #2 finished! INFO @ Sun, 03 Jun 2018 14:33:41: #2 predicted fragment length is 239 bps INFO @ Sun, 03 Jun 2018 14:33:41: #2 alternative fragment length(s) may be 239 bps INFO @ Sun, 03 Jun 2018 14:33:41: #2.2 Generate R script for model : SRX1704846.10_model.r INFO @ Sun, 03 Jun 2018 14:33:41: #3 Call peaks... INFO @ Sun, 03 Jun 2018 14:33:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 14:33:42: 42000000 INFO @ Sun, 03 Jun 2018 14:33:44: 43000000 INFO @ Sun, 03 Jun 2018 14:33:45: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:33:45: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:33:45: #1 total tags in treatment: 15927327 INFO @ Sun, 03 Jun 2018 14:33:45: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:33:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 14:33:46: #1 tags after filtering in treatment: 12407467 INFO @ Sun, 03 Jun 2018 14:33:46: #1 Redundant rate of treatment: 0.22 INFO @ Sun, 03 Jun 2018 14:33:46: #1 finished! INFO @ Sun, 03 Jun 2018 14:33:46: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:33:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:33:47: #2 number of paired peaks: 219 WARNING @ Sun, 03 Jun 2018 14:33:47: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sun, 03 Jun 2018 14:33:47: start model_add_line... INFO @ Sun, 03 Jun 2018 14:33:47: start X-correlation... INFO @ Sun, 03 Jun 2018 14:33:47: end of X-cor INFO @ Sun, 03 Jun 2018 14:33:47: #2 finished! INFO @ Sun, 03 Jun 2018 14:33:47: #2 predicted fragment length is 239 bps INFO @ Sun, 03 Jun 2018 14:33:47: #2 alternative fragment length(s) may be 239 bps INFO @ Sun, 03 Jun 2018 14:33:47: #2.2 Generate R script for model : SRX1704846.05_model.r INFO @ Sun, 03 Jun 2018 14:33:47: #3 Call peaks... INFO @ Sun, 03 Jun 2018 14:33:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 14:33:48: 43000000 INFO @ Sun, 03 Jun 2018 14:33:49: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:33:49: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:33:49: #1 total tags in treatment: 15927327 INFO @ Sun, 03 Jun 2018 14:33:49: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:33:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 14:33:50: #1 tags after filtering in treatment: 12407467 INFO @ Sun, 03 Jun 2018 14:33:50: #1 Redundant rate of treatment: 0.22 INFO @ Sun, 03 Jun 2018 14:33:50: #1 finished! INFO @ Sun, 03 Jun 2018 14:33:50: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:33:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:33:51: #2 number of paired peaks: 219 WARNING @ Sun, 03 Jun 2018 14:33:51: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sun, 03 Jun 2018 14:33:51: start model_add_line... INFO @ Sun, 03 Jun 2018 14:33:51: start X-correlation... INFO @ Sun, 03 Jun 2018 14:33:51: end of X-cor INFO @ Sun, 03 Jun 2018 14:33:51: #2 finished! INFO @ Sun, 03 Jun 2018 14:33:51: #2 predicted fragment length is 239 bps INFO @ Sun, 03 Jun 2018 14:33:51: #2 alternative fragment length(s) may be 239 bps INFO @ Sun, 03 Jun 2018 14:33:51: #2.2 Generate R script for model : SRX1704846.20_model.r INFO @ Sun, 03 Jun 2018 14:33:51: #3 Call peaks... INFO @ Sun, 03 Jun 2018 14:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 14:34:11: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 14:34:14: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 14:34:19: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 14:34:26: #4 Write output xls file... SRX1704846.10_peaks.xls INFO @ Sun, 03 Jun 2018 14:34:26: #4 Write peak in narrowPeak format file... SRX1704846.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 14:34:26: #4 Write summits bed file... SRX1704846.10_summits.bed INFO @ Sun, 03 Jun 2018 14:34:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1129 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 14:34:29: #4 Write output xls file... SRX1704846.05_peaks.xls INFO @ Sun, 03 Jun 2018 14:34:29: #4 Write peak in narrowPeak format file... SRX1704846.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 14:34:29: #4 Write summits bed file... SRX1704846.05_summits.bed INFO @ Sun, 03 Jun 2018 14:34:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3035 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 14:34:34: #4 Write output xls file... SRX1704846.20_peaks.xls INFO @ Sun, 03 Jun 2018 14:34:34: #4 Write peak in narrowPeak format file... SRX1704846.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 14:34:34: #4 Write summits bed file... SRX1704846.20_summits.bed INFO @ Sun, 03 Jun 2018 14:34:34: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (598 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。