Job ID = 11171256 sra ファイルのダウンロード中... Completed: 2387287K bytes transferred in 91 seconds (213663K 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 36336043 spots for /home/okishinya/chipatlas/results/dm3/SRX2982443/SRR5803102.sra Written 36336043 spots for /home/okishinya/chipatlas/results/dm3/SRX2982443/SRR5803102.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:22:44 36336043 reads; of these: 36336043 (100.00%) were paired; of these: 5037946 (13.86%) aligned concordantly 0 times 25750371 (70.87%) aligned concordantly exactly 1 time 5547726 (15.27%) aligned concordantly >1 times ---- 5037946 pairs aligned concordantly 0 times; of these: 31936 (0.63%) aligned discordantly 1 time ---- 5006010 pairs aligned 0 times concordantly or discordantly; of these: 10012020 mates make up the pairs; of these: 8591645 (85.81%) aligned 0 times 954784 (9.54%) aligned exactly 1 time 465591 (4.65%) aligned >1 times 88.18% overall alignment rate Time searching: 01:22:45 Overall time: 01:22:45 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 28 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] 15977528 / 31290438 = 0.5106 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 @ Sat, 08 Sep 2018 15:03:32: # Command line: callpeak -t SRX2982443.bam -f BAM -g dm -n SRX2982443.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2982443.10 # format = BAM # ChIP-seq file = ['SRX2982443.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 @ Sat, 08 Sep 2018 15:03:32: #1 read tag files... INFO @ Sat, 08 Sep 2018 15:03:32: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 15:03:32: # Command line: callpeak -t SRX2982443.bam -f BAM -g dm -n SRX2982443.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2982443.05 # format = BAM # ChIP-seq file = ['SRX2982443.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 @ Sat, 08 Sep 2018 15:03:32: #1 read tag files... INFO @ Sat, 08 Sep 2018 15:03:32: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 15:03:32: # Command line: callpeak -t SRX2982443.bam -f BAM -g dm -n SRX2982443.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2982443.20 # format = BAM # ChIP-seq file = ['SRX2982443.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 @ Sat, 08 Sep 2018 15:03:32: #1 read tag files... INFO @ Sat, 08 Sep 2018 15:03:32: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 15:03:39: 1000000 INFO @ Sat, 08 Sep 2018 15:03:39: 1000000 INFO @ Sat, 08 Sep 2018 15:03:39: 1000000 INFO @ Sat, 08 Sep 2018 15:03:45: 2000000 INFO @ Sat, 08 Sep 2018 15:03:45: 2000000 INFO @ Sat, 08 Sep 2018 15:03:45: 2000000 INFO @ Sat, 08 Sep 2018 15:03:51: 3000000 INFO @ Sat, 08 Sep 2018 15:03:51: 3000000 INFO @ Sat, 08 Sep 2018 15:03:51: 3000000 INFO @ Sat, 08 Sep 2018 15:03:57: 4000000 INFO @ Sat, 08 Sep 2018 15:03:57: 4000000 INFO @ Sat, 08 Sep 2018 15:03:57: 4000000 INFO @ Sat, 08 Sep 2018 15:04:03: 5000000 INFO @ Sat, 08 Sep 2018 15:04:04: 5000000 INFO @ Sat, 08 Sep 2018 15:04:04: 5000000 INFO @ Sat, 08 Sep 2018 15:04:09: 6000000 INFO @ Sat, 08 Sep 2018 15:04:10: 6000000 INFO @ Sat, 08 Sep 2018 15:04:10: 6000000 INFO @ Sat, 08 Sep 2018 15:04:16: 7000000 INFO @ Sat, 08 Sep 2018 15:04:16: 7000000 INFO @ Sat, 08 Sep 2018 15:04:16: 7000000 INFO @ Sat, 08 Sep 2018 15:04:22: 8000000 INFO @ Sat, 08 Sep 2018 15:04:22: 8000000 INFO @ Sat, 08 Sep 2018 15:04:22: 8000000 INFO @ Sat, 08 Sep 2018 15:04:28: 9000000 INFO @ Sat, 08 Sep 2018 15:04:28: 9000000 INFO @ Sat, 08 Sep 2018 15:04:28: 9000000 INFO @ Sat, 08 Sep 2018 15:04:34: 10000000 INFO @ Sat, 08 Sep 2018 15:04:34: 10000000 INFO @ Sat, 08 Sep 2018 15:04:34: 10000000 INFO @ Sat, 08 Sep 2018 15:04:40: 11000000 INFO @ Sat, 08 Sep 2018 15:04:41: 11000000 INFO @ Sat, 08 Sep 2018 15:04:41: 11000000 INFO @ Sat, 08 Sep 2018 15:04:46: 12000000 INFO @ Sat, 08 Sep 2018 15:04:47: 12000000 INFO @ Sat, 08 Sep 2018 15:04:47: 12000000 INFO @ Sat, 08 Sep 2018 15:04:52: 13000000 INFO @ Sat, 08 Sep 2018 15:04:53: 13000000 INFO @ Sat, 08 Sep 2018 15:04:53: 13000000 INFO @ Sat, 08 Sep 2018 15:04:58: 14000000 INFO @ Sat, 08 Sep 2018 15:04:59: 14000000 INFO @ Sat, 08 Sep 2018 15:04:59: 14000000 INFO @ Sat, 08 Sep 2018 15:05:04: 15000000 INFO @ Sat, 08 Sep 2018 15:05:05: 15000000 INFO @ Sat, 08 Sep 2018 15:05:05: 15000000 INFO @ Sat, 08 Sep 2018 15:05:10: 16000000 INFO @ Sat, 08 Sep 2018 15:05:11: 16000000 INFO @ Sat, 08 Sep 2018 15:05:12: 16000000 INFO @ Sat, 08 Sep 2018 15:05:16: 17000000 INFO @ Sat, 08 Sep 2018 15:05:18: 17000000 INFO @ Sat, 08 Sep 2018 15:05:18: 17000000 INFO @ Sat, 08 Sep 2018 15:05:22: 18000000 INFO @ Sat, 08 Sep 2018 15:05:24: 18000000 INFO @ Sat, 08 Sep 2018 15:05:24: 18000000 INFO @ Sat, 08 Sep 2018 15:05:28: 19000000 INFO @ Sat, 08 Sep 2018 15:05:30: 19000000 INFO @ Sat, 08 Sep 2018 15:05:30: 19000000 INFO @ Sat, 08 Sep 2018 15:05:34: 20000000 INFO @ Sat, 08 Sep 2018 15:05:36: 20000000 INFO @ Sat, 08 Sep 2018 15:05:37: 20000000 INFO @ Sat, 08 Sep 2018 15:05:40: 21000000 INFO @ Sat, 08 Sep 2018 15:05:43: 21000000 INFO @ Sat, 08 Sep 2018 15:05:43: 21000000 INFO @ Sat, 08 Sep 2018 15:05:46: 22000000 INFO @ Sat, 08 Sep 2018 15:05:49: 22000000 INFO @ Sat, 08 Sep 2018 15:05:50: 22000000 INFO @ Sat, 08 Sep 2018 15:05:52: 23000000 INFO @ Sat, 08 Sep 2018 15:05:55: 23000000 INFO @ Sat, 08 Sep 2018 15:05:56: 23000000 INFO @ Sat, 08 Sep 2018 15:05:59: 24000000 INFO @ Sat, 08 Sep 2018 15:06:02: 24000000 INFO @ Sat, 08 Sep 2018 15:06:02: 24000000 INFO @ Sat, 08 Sep 2018 15:06:05: 25000000 INFO @ Sat, 08 Sep 2018 15:06:08: 25000000 INFO @ Sat, 08 Sep 2018 15:06:09: 25000000 INFO @ Sat, 08 Sep 2018 15:06:11: 26000000 INFO @ Sat, 08 Sep 2018 15:06:14: 26000000 INFO @ Sat, 08 Sep 2018 15:06:15: 26000000 INFO @ Sat, 08 Sep 2018 15:06:17: 27000000 INFO @ Sat, 08 Sep 2018 15:06:21: 27000000 INFO @ Sat, 08 Sep 2018 15:06:22: 27000000 INFO @ Sat, 08 Sep 2018 15:06:23: 28000000 INFO @ Sat, 08 Sep 2018 15:06:27: 28000000 INFO @ Sat, 08 Sep 2018 15:06:28: 28000000 INFO @ Sat, 08 Sep 2018 15:06:29: 29000000 INFO @ Sat, 08 Sep 2018 15:06:33: 29000000 INFO @ Sat, 08 Sep 2018 15:06:34: 29000000 INFO @ Sat, 08 Sep 2018 15:06:35: 30000000 INFO @ Sat, 08 Sep 2018 15:06:39: 30000000 INFO @ Sat, 08 Sep 2018 15:06:40: 30000000 INFO @ Sat, 08 Sep 2018 15:06:41: 31000000 INFO @ Sat, 08 Sep 2018 15:06:45: 31000000 INFO @ Sat, 08 Sep 2018 15:06:47: 31000000 INFO @ Sat, 08 Sep 2018 15:06:48: 32000000 INFO @ Sat, 08 Sep 2018 15:06:48: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 15:06:48: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 15:06:48: #1 total tags in treatment: 15330649 INFO @ Sat, 08 Sep 2018 15:06:48: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 15:06:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 15:06:49: #1 tags after filtering in treatment: 14451366 INFO @ Sat, 08 Sep 2018 15:06:49: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Sep 2018 15:06:49: #1 finished! INFO @ Sat, 08 Sep 2018 15:06:49: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 15:06:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 15:06:50: #2 number of paired peaks: 209 WARNING @ Sat, 08 Sep 2018 15:06:50: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sat, 08 Sep 2018 15:06:50: start model_add_line... INFO @ Sat, 08 Sep 2018 15:06:50: start X-correlation... INFO @ Sat, 08 Sep 2018 15:06:50: end of X-cor INFO @ Sat, 08 Sep 2018 15:06:50: #2 finished! INFO @ Sat, 08 Sep 2018 15:06:50: #2 predicted fragment length is 189 bps INFO @ Sat, 08 Sep 2018 15:06:50: #2 alternative fragment length(s) may be 2,170,189 bps INFO @ Sat, 08 Sep 2018 15:06:50: #2.2 Generate R script for model : SRX2982443.20_model.r INFO @ Sat, 08 Sep 2018 15:06:50: #3 Call peaks... INFO @ Sat, 08 Sep 2018 15:06:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 15:06:52: 32000000 INFO @ Sat, 08 Sep 2018 15:06:53: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 15:06:53: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 15:06:53: #1 total tags in treatment: 15330649 INFO @ Sat, 08 Sep 2018 15:06:53: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 15:06:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 15:06:53: #1 tags after filtering in treatment: 14451366 INFO @ Sat, 08 Sep 2018 15:06:53: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Sep 2018 15:06:53: #1 finished! INFO @ Sat, 08 Sep 2018 15:06:53: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 15:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 15:06:53: 32000000 INFO @ Sat, 08 Sep 2018 15:06:54: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 15:06:54: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 15:06:54: #1 total tags in treatment: 15330649 INFO @ Sat, 08 Sep 2018 15:06:54: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 15:06:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 15:06:54: #2 number of paired peaks: 209 WARNING @ Sat, 08 Sep 2018 15:06:54: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sat, 08 Sep 2018 15:06:54: start model_add_line... INFO @ Sat, 08 Sep 2018 15:06:54: #1 tags after filtering in treatment: 14451366 INFO @ Sat, 08 Sep 2018 15:06:54: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Sep 2018 15:06:54: #1 finished! INFO @ Sat, 08 Sep 2018 15:06:54: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 15:06:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 15:06:54: start X-correlation... INFO @ Sat, 08 Sep 2018 15:06:54: end of X-cor INFO @ Sat, 08 Sep 2018 15:06:54: #2 finished! INFO @ Sat, 08 Sep 2018 15:06:54: #2 predicted fragment length is 189 bps INFO @ Sat, 08 Sep 2018 15:06:54: #2 alternative fragment length(s) may be 2,170,189 bps INFO @ Sat, 08 Sep 2018 15:06:54: #2.2 Generate R script for model : SRX2982443.10_model.r INFO @ Sat, 08 Sep 2018 15:06:54: #3 Call peaks... INFO @ Sat, 08 Sep 2018 15:06:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 15:06:55: #2 number of paired peaks: 209 WARNING @ Sat, 08 Sep 2018 15:06:55: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sat, 08 Sep 2018 15:06:55: start model_add_line... INFO @ Sat, 08 Sep 2018 15:06:55: start X-correlation... INFO @ Sat, 08 Sep 2018 15:06:55: end of X-cor INFO @ Sat, 08 Sep 2018 15:06:55: #2 finished! INFO @ Sat, 08 Sep 2018 15:06:55: #2 predicted fragment length is 189 bps INFO @ Sat, 08 Sep 2018 15:06:55: #2 alternative fragment length(s) may be 2,170,189 bps INFO @ Sat, 08 Sep 2018 15:06:55: #2.2 Generate R script for model : SRX2982443.05_model.r INFO @ Sat, 08 Sep 2018 15:06:55: #3 Call peaks... INFO @ Sat, 08 Sep 2018 15:06:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 15:07:25: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 15:07:26: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 15:07:26: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 15:07:42: #4 Write output xls file... SRX2982443.20_peaks.xls INFO @ Sat, 08 Sep 2018 15:07:42: #4 Write peak in narrowPeak format file... SRX2982443.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 15:07:42: #4 Write summits bed file... SRX2982443.20_summits.bed INFO @ Sat, 08 Sep 2018 15:07:42: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 2 millis INFO @ Sat, 08 Sep 2018 15:07:42: #4 Write output xls file... SRX2982443.10_peaks.xls CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 15:07:42: #4 Write peak in narrowPeak format file... SRX2982443.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 15:07:42: #4 Write summits bed file... SRX2982443.10_summits.bed INFO @ Sat, 08 Sep 2018 15:07:42: Done! INFO @ Sat, 08 Sep 2018 15:07:43: #4 Write output xls file... SRX2982443.05_peaks.xls pass1 - making usageList (14 chroms): 95 millis pass2 - checking and writing primary data (1803 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 15:07:43: #4 Write peak in narrowPeak format file... SRX2982443.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 15:07:43: #4 Write summits bed file... SRX2982443.05_summits.bed INFO @ Sat, 08 Sep 2018 15:07:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3781 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。