Job ID = 10845208 sra ファイルのダウンロード中... Completed: 1060870K bytes transferred in 93 seconds (93245K 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 19805724 spots for /home/okishinya/chipatlas/results/dm3/SRX3632904/SRR6655544.sra Written 19805724 spots for /home/okishinya/chipatlas/results/dm3/SRX3632904/SRR6655544.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: 00:28:04 19805724 reads; of these: 19805724 (100.00%) were paired; of these: 1245141 (6.29%) aligned concordantly 0 times 17241733 (87.05%) aligned concordantly exactly 1 time 1318850 (6.66%) aligned concordantly >1 times ---- 1245141 pairs aligned concordantly 0 times; of these: 482202 (38.73%) aligned discordantly 1 time ---- 762939 pairs aligned 0 times concordantly or discordantly; of these: 1525878 mates make up the pairs; of these: 858942 (56.29%) aligned 0 times 523622 (34.32%) aligned exactly 1 time 143314 (9.39%) aligned >1 times 97.83% overall alignment rate Time searching: 00:28:04 Overall time: 00:28:04 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_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] 1193349 / 18988647 = 0.0628 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, 04 Jul 2018 10:09:14: # Command line: callpeak -t SRX3632904.bam -f BAM -g dm -n SRX3632904.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3632904.05 # format = BAM # ChIP-seq file = ['SRX3632904.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, 04 Jul 2018 10:09:14: #1 read tag files... INFO @ Wed, 04 Jul 2018 10:09:14: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 10:09:14: # Command line: callpeak -t SRX3632904.bam -f BAM -g dm -n SRX3632904.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3632904.20 # format = BAM # ChIP-seq file = ['SRX3632904.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, 04 Jul 2018 10:09:14: #1 read tag files... INFO @ Wed, 04 Jul 2018 10:09:14: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 10:09:14: # Command line: callpeak -t SRX3632904.bam -f BAM -g dm -n SRX3632904.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3632904.10 # format = BAM # ChIP-seq file = ['SRX3632904.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, 04 Jul 2018 10:09:14: #1 read tag files... INFO @ Wed, 04 Jul 2018 10:09:14: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 10:09:21: 1000000 INFO @ Wed, 04 Jul 2018 10:09:21: 1000000 INFO @ Wed, 04 Jul 2018 10:09:21: 1000000 INFO @ Wed, 04 Jul 2018 10:09:27: 2000000 INFO @ Wed, 04 Jul 2018 10:09:29: 2000000 INFO @ Wed, 04 Jul 2018 10:09:29: 2000000 INFO @ Wed, 04 Jul 2018 10:09:34: 3000000 INFO @ Wed, 04 Jul 2018 10:09:36: 3000000 INFO @ Wed, 04 Jul 2018 10:09:36: 3000000 INFO @ Wed, 04 Jul 2018 10:09:41: 4000000 INFO @ Wed, 04 Jul 2018 10:09:43: 4000000 INFO @ Wed, 04 Jul 2018 10:09:43: 4000000 INFO @ Wed, 04 Jul 2018 10:09:48: 5000000 INFO @ Wed, 04 Jul 2018 10:09:50: 5000000 INFO @ Wed, 04 Jul 2018 10:09:50: 5000000 INFO @ Wed, 04 Jul 2018 10:09:54: 6000000 INFO @ Wed, 04 Jul 2018 10:09:57: 6000000 INFO @ Wed, 04 Jul 2018 10:09:57: 6000000 INFO @ Wed, 04 Jul 2018 10:10:01: 7000000 INFO @ Wed, 04 Jul 2018 10:10:04: 7000000 INFO @ Wed, 04 Jul 2018 10:10:05: 7000000 INFO @ Wed, 04 Jul 2018 10:10:09: 8000000 INFO @ Wed, 04 Jul 2018 10:10:10: 8000000 INFO @ Wed, 04 Jul 2018 10:10:13: 8000000 INFO @ Wed, 04 Jul 2018 10:10:16: 9000000 INFO @ Wed, 04 Jul 2018 10:10:17: 9000000 INFO @ Wed, 04 Jul 2018 10:10:20: 9000000 INFO @ Wed, 04 Jul 2018 10:10:23: 10000000 INFO @ Wed, 04 Jul 2018 10:10:24: 10000000 INFO @ Wed, 04 Jul 2018 10:10:27: 10000000 INFO @ Wed, 04 Jul 2018 10:10:30: 11000000 INFO @ Wed, 04 Jul 2018 10:10:31: 11000000 INFO @ Wed, 04 Jul 2018 10:10:34: 11000000 INFO @ Wed, 04 Jul 2018 10:10:37: 12000000 INFO @ Wed, 04 Jul 2018 10:10:38: 12000000 INFO @ Wed, 04 Jul 2018 10:10:42: 12000000 INFO @ Wed, 04 Jul 2018 10:10:44: 13000000 INFO @ Wed, 04 Jul 2018 10:10:46: 13000000 INFO @ Wed, 04 Jul 2018 10:10:49: 13000000 INFO @ Wed, 04 Jul 2018 10:10:51: 14000000 INFO @ Wed, 04 Jul 2018 10:10:53: 14000000 INFO @ Wed, 04 Jul 2018 10:10:57: 14000000 INFO @ Wed, 04 Jul 2018 10:10:58: 15000000 INFO @ Wed, 04 Jul 2018 10:11:00: 15000000 INFO @ Wed, 04 Jul 2018 10:11:04: 15000000 INFO @ Wed, 04 Jul 2018 10:11:05: 16000000 INFO @ Wed, 04 Jul 2018 10:11:07: 16000000 INFO @ Wed, 04 Jul 2018 10:11:12: 16000000 INFO @ Wed, 04 Jul 2018 10:11:12: 17000000 INFO @ Wed, 04 Jul 2018 10:11:14: 17000000 INFO @ Wed, 04 Jul 2018 10:11:19: 18000000 INFO @ Wed, 04 Jul 2018 10:11:19: 17000000 INFO @ Wed, 04 Jul 2018 10:11:21: 18000000 INFO @ Wed, 04 Jul 2018 10:11:26: 19000000 INFO @ Wed, 04 Jul 2018 10:11:27: 18000000 INFO @ Wed, 04 Jul 2018 10:11:28: 19000000 INFO @ Wed, 04 Jul 2018 10:11:34: 20000000 INFO @ Wed, 04 Jul 2018 10:11:35: 19000000 INFO @ Wed, 04 Jul 2018 10:11:35: 20000000 INFO @ Wed, 04 Jul 2018 10:11:40: 21000000 INFO @ Wed, 04 Jul 2018 10:11:42: 21000000 INFO @ Wed, 04 Jul 2018 10:11:42: 20000000 INFO @ Wed, 04 Jul 2018 10:11:47: 22000000 INFO @ Wed, 04 Jul 2018 10:11:49: 22000000 INFO @ Wed, 04 Jul 2018 10:11:50: 21000000 INFO @ Wed, 04 Jul 2018 10:11:55: 23000000 INFO @ Wed, 04 Jul 2018 10:11:56: 23000000 INFO @ Wed, 04 Jul 2018 10:11:57: 22000000 INFO @ Wed, 04 Jul 2018 10:12:02: 24000000 INFO @ Wed, 04 Jul 2018 10:12:03: 24000000 INFO @ Wed, 04 Jul 2018 10:12:05: 23000000 INFO @ Wed, 04 Jul 2018 10:12:08: 25000000 INFO @ Wed, 04 Jul 2018 10:12:10: 25000000 INFO @ Wed, 04 Jul 2018 10:12:12: 24000000 INFO @ Wed, 04 Jul 2018 10:12:16: 26000000 INFO @ Wed, 04 Jul 2018 10:12:17: 26000000 INFO @ Wed, 04 Jul 2018 10:12:20: 25000000 INFO @ Wed, 04 Jul 2018 10:12:23: 27000000 INFO @ Wed, 04 Jul 2018 10:12:24: 27000000 INFO @ Wed, 04 Jul 2018 10:12:28: 26000000 INFO @ Wed, 04 Jul 2018 10:12:30: 28000000 INFO @ Wed, 04 Jul 2018 10:12:31: 28000000 INFO @ Wed, 04 Jul 2018 10:12:36: 27000000 INFO @ Wed, 04 Jul 2018 10:12:37: 29000000 INFO @ Wed, 04 Jul 2018 10:12:38: 29000000 INFO @ Wed, 04 Jul 2018 10:12:43: 28000000 INFO @ Wed, 04 Jul 2018 10:12:45: 30000000 INFO @ Wed, 04 Jul 2018 10:12:45: 30000000 INFO @ Wed, 04 Jul 2018 10:12:51: 29000000 INFO @ Wed, 04 Jul 2018 10:12:52: 31000000 INFO @ Wed, 04 Jul 2018 10:12:52: 31000000 INFO @ Wed, 04 Jul 2018 10:12:58: 32000000 INFO @ Wed, 04 Jul 2018 10:12:59: 30000000 INFO @ Wed, 04 Jul 2018 10:13:00: 32000000 INFO @ Wed, 04 Jul 2018 10:13:05: 33000000 INFO @ Wed, 04 Jul 2018 10:13:07: 31000000 INFO @ Wed, 04 Jul 2018 10:13:07: 33000000 INFO @ Wed, 04 Jul 2018 10:13:12: 34000000 INFO @ Wed, 04 Jul 2018 10:13:15: 34000000 INFO @ Wed, 04 Jul 2018 10:13:15: 32000000 INFO @ Wed, 04 Jul 2018 10:13:19: 35000000 INFO @ Wed, 04 Jul 2018 10:13:22: 35000000 INFO @ Wed, 04 Jul 2018 10:13:22: 33000000 INFO @ Wed, 04 Jul 2018 10:13:26: 36000000 INFO @ Wed, 04 Jul 2018 10:13:28: #1 tag size is determined as 75 bps INFO @ Wed, 04 Jul 2018 10:13:28: #1 tag size = 75 INFO @ Wed, 04 Jul 2018 10:13:28: #1 total tags in treatment: 17386780 INFO @ Wed, 04 Jul 2018 10:13:28: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:13:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 10:13:29: 36000000 INFO @ Wed, 04 Jul 2018 10:13:29: #1 tags after filtering in treatment: 13627212 INFO @ Wed, 04 Jul 2018 10:13:29: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 04 Jul 2018 10:13:29: #1 finished! INFO @ Wed, 04 Jul 2018 10:13:29: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:13:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:13:29: 34000000 INFO @ Wed, 04 Jul 2018 10:13:30: #2 number of paired peaks: 598 WARNING @ Wed, 04 Jul 2018 10:13:30: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Wed, 04 Jul 2018 10:13:30: start model_add_line... INFO @ Wed, 04 Jul 2018 10:13:30: start X-correlation... INFO @ Wed, 04 Jul 2018 10:13:30: end of X-cor INFO @ Wed, 04 Jul 2018 10:13:30: #2 finished! INFO @ Wed, 04 Jul 2018 10:13:30: #2 predicted fragment length is 196 bps INFO @ Wed, 04 Jul 2018 10:13:30: #2 alternative fragment length(s) may be 196 bps INFO @ Wed, 04 Jul 2018 10:13:30: #2.2 Generate R script for model : SRX3632904.20_model.r INFO @ Wed, 04 Jul 2018 10:13:30: #3 Call peaks... INFO @ Wed, 04 Jul 2018 10:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 10:13:31: #1 tag size is determined as 75 bps INFO @ Wed, 04 Jul 2018 10:13:31: #1 tag size = 75 INFO @ Wed, 04 Jul 2018 10:13:31: #1 total tags in treatment: 17386780 INFO @ Wed, 04 Jul 2018 10:13:31: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:13:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 10:13:32: #1 tags after filtering in treatment: 13627212 INFO @ Wed, 04 Jul 2018 10:13:32: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 04 Jul 2018 10:13:32: #1 finished! INFO @ Wed, 04 Jul 2018 10:13:32: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:13:33: #2 number of paired peaks: 598 WARNING @ Wed, 04 Jul 2018 10:13:33: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Wed, 04 Jul 2018 10:13:33: start model_add_line... INFO @ Wed, 04 Jul 2018 10:13:33: start X-correlation... INFO @ Wed, 04 Jul 2018 10:13:33: end of X-cor INFO @ Wed, 04 Jul 2018 10:13:33: #2 finished! INFO @ Wed, 04 Jul 2018 10:13:33: #2 predicted fragment length is 196 bps INFO @ Wed, 04 Jul 2018 10:13:33: #2 alternative fragment length(s) may be 196 bps INFO @ Wed, 04 Jul 2018 10:13:33: #2.2 Generate R script for model : SRX3632904.10_model.r INFO @ Wed, 04 Jul 2018 10:13:33: #3 Call peaks... INFO @ Wed, 04 Jul 2018 10:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 10:13:36: 35000000 INFO @ Wed, 04 Jul 2018 10:13:42: 36000000 INFO @ Wed, 04 Jul 2018 10:13:45: #1 tag size is determined as 75 bps INFO @ Wed, 04 Jul 2018 10:13:45: #1 tag size = 75 INFO @ Wed, 04 Jul 2018 10:13:45: #1 total tags in treatment: 17386780 INFO @ Wed, 04 Jul 2018 10:13:45: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:13:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 10:13:45: #1 tags after filtering in treatment: 13627212 INFO @ Wed, 04 Jul 2018 10:13:45: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 04 Jul 2018 10:13:45: #1 finished! INFO @ Wed, 04 Jul 2018 10:13:45: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:13:46: #2 number of paired peaks: 598 WARNING @ Wed, 04 Jul 2018 10:13:46: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Wed, 04 Jul 2018 10:13:46: start model_add_line... INFO @ Wed, 04 Jul 2018 10:13:46: start X-correlation... INFO @ Wed, 04 Jul 2018 10:13:46: end of X-cor INFO @ Wed, 04 Jul 2018 10:13:46: #2 finished! INFO @ Wed, 04 Jul 2018 10:13:46: #2 predicted fragment length is 196 bps INFO @ Wed, 04 Jul 2018 10:13:46: #2 alternative fragment length(s) may be 196 bps INFO @ Wed, 04 Jul 2018 10:13:46: #2.2 Generate R script for model : SRX3632904.05_model.r INFO @ Wed, 04 Jul 2018 10:13:46: #3 Call peaks... INFO @ Wed, 04 Jul 2018 10:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 10:14:01: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 10:14:07: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 10:14:21: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 10:14:23: #4 Write output xls file... SRX3632904.20_peaks.xls INFO @ Wed, 04 Jul 2018 10:14:23: #4 Write peak in narrowPeak format file... SRX3632904.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 10:14:23: #4 Write summits bed file... SRX3632904.20_summits.bed INFO @ Wed, 04 Jul 2018 10:14:23: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1948 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 10:14:25: #4 Write output xls file... SRX3632904.10_peaks.xls INFO @ Wed, 04 Jul 2018 10:14:25: #4 Write peak in narrowPeak format file... SRX3632904.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 10:14:25: #4 Write summits bed file... SRX3632904.10_summits.bed INFO @ Wed, 04 Jul 2018 10:14:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4617 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 10:14:41: #4 Write output xls file... SRX3632904.05_peaks.xls INFO @ Wed, 04 Jul 2018 10:14:41: #4 Write peak in narrowPeak format file... SRX3632904.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 10:14:41: #4 Write summits bed file... SRX3632904.05_summits.bed INFO @ Wed, 04 Jul 2018 10:14:41: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8253 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。