Job ID = 10845205 sra ファイルのダウンロード中... Completed: 914327K bytes transferred in 76 seconds (97657K 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 17083675 spots for /home/okishinya/chipatlas/results/dm3/SRX3632901/SRR6655541.sra Written 17083675 spots for /home/okishinya/chipatlas/results/dm3/SRX3632901/SRR6655541.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: 00:28:37 17083675 reads; of these: 17083675 (100.00%) were paired; of these: 1092114 (6.39%) aligned concordantly 0 times 14400085 (84.29%) aligned concordantly exactly 1 time 1591476 (9.32%) aligned concordantly >1 times ---- 1092114 pairs aligned concordantly 0 times; of these: 410722 (37.61%) aligned discordantly 1 time ---- 681392 pairs aligned 0 times concordantly or discordantly; of these: 1362784 mates make up the pairs; of these: 759005 (55.70%) aligned 0 times 452415 (33.20%) aligned exactly 1 time 151364 (11.11%) aligned >1 times 97.78% overall alignment rate Time searching: 00:28:37 Overall time: 00:28:37 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] 890532 / 16353266 = 0.0545 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 10:08:11: # Command line: callpeak -t SRX3632901.bam -f BAM -g dm -n SRX3632901.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3632901.10 # format = BAM # ChIP-seq file = ['SRX3632901.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 10:08:11: # Command line: callpeak -t SRX3632901.bam -f BAM -g dm -n SRX3632901.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3632901.20 # format = BAM # ChIP-seq file = ['SRX3632901.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 10:08:11: # Command line: callpeak -t SRX3632901.bam -f BAM -g dm -n SRX3632901.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3632901.05 # format = BAM # ChIP-seq file = ['SRX3632901.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 10:08:11: #1 read tag files... INFO @ Wed, 04 Jul 2018 10:08:11: #1 read tag files... INFO @ Wed, 04 Jul 2018 10:08:11: #1 read tag files... INFO @ Wed, 04 Jul 2018 10:08:11: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 10:08:11: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 10:08:11: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 10:08:17: 1000000 INFO @ Wed, 04 Jul 2018 10:08:17: 1000000 INFO @ Wed, 04 Jul 2018 10:08:17: 1000000 INFO @ Wed, 04 Jul 2018 10:08:23: 2000000 INFO @ Wed, 04 Jul 2018 10:08:23: 2000000 INFO @ Wed, 04 Jul 2018 10:08:23: 2000000 INFO @ Wed, 04 Jul 2018 10:08:29: 3000000 INFO @ Wed, 04 Jul 2018 10:08:29: 3000000 INFO @ Wed, 04 Jul 2018 10:08:29: 3000000 INFO @ Wed, 04 Jul 2018 10:08:35: 4000000 INFO @ Wed, 04 Jul 2018 10:08:35: 4000000 INFO @ Wed, 04 Jul 2018 10:08:36: 4000000 INFO @ Wed, 04 Jul 2018 10:08:41: 5000000 INFO @ Wed, 04 Jul 2018 10:08:42: 5000000 INFO @ Wed, 04 Jul 2018 10:08:42: 5000000 INFO @ Wed, 04 Jul 2018 10:08:47: 6000000 INFO @ Wed, 04 Jul 2018 10:08:48: 6000000 INFO @ Wed, 04 Jul 2018 10:08:48: 6000000 INFO @ Wed, 04 Jul 2018 10:08:52: 7000000 INFO @ Wed, 04 Jul 2018 10:08:54: 7000000 INFO @ Wed, 04 Jul 2018 10:08:55: 7000000 INFO @ Wed, 04 Jul 2018 10:08:58: 8000000 INFO @ Wed, 04 Jul 2018 10:09:00: 8000000 INFO @ Wed, 04 Jul 2018 10:09:01: 8000000 INFO @ Wed, 04 Jul 2018 10:09:04: 9000000 INFO @ Wed, 04 Jul 2018 10:09:06: 9000000 INFO @ Wed, 04 Jul 2018 10:09:08: 9000000 INFO @ Wed, 04 Jul 2018 10:09:10: 10000000 INFO @ Wed, 04 Jul 2018 10:09:13: 10000000 INFO @ Wed, 04 Jul 2018 10:09:14: 10000000 INFO @ Wed, 04 Jul 2018 10:09:16: 11000000 INFO @ Wed, 04 Jul 2018 10:09:19: 11000000 INFO @ Wed, 04 Jul 2018 10:09:21: 11000000 INFO @ Wed, 04 Jul 2018 10:09:22: 12000000 INFO @ Wed, 04 Jul 2018 10:09:25: 12000000 INFO @ Wed, 04 Jul 2018 10:09:27: 12000000 INFO @ Wed, 04 Jul 2018 10:09:28: 13000000 INFO @ Wed, 04 Jul 2018 10:09:32: 13000000 INFO @ Wed, 04 Jul 2018 10:09:33: 13000000 INFO @ Wed, 04 Jul 2018 10:09:34: 14000000 INFO @ Wed, 04 Jul 2018 10:09:38: 14000000 INFO @ Wed, 04 Jul 2018 10:09:40: 15000000 INFO @ Wed, 04 Jul 2018 10:09:40: 14000000 INFO @ Wed, 04 Jul 2018 10:09:44: 15000000 INFO @ Wed, 04 Jul 2018 10:09:46: 16000000 INFO @ Wed, 04 Jul 2018 10:09:46: 15000000 INFO @ Wed, 04 Jul 2018 10:09:50: 16000000 INFO @ Wed, 04 Jul 2018 10:09:52: 17000000 INFO @ Wed, 04 Jul 2018 10:09:53: 16000000 INFO @ Wed, 04 Jul 2018 10:09:56: 17000000 INFO @ Wed, 04 Jul 2018 10:09:57: 18000000 INFO @ Wed, 04 Jul 2018 10:09:59: 17000000 INFO @ Wed, 04 Jul 2018 10:10:02: 18000000 INFO @ Wed, 04 Jul 2018 10:10:03: 19000000 INFO @ Wed, 04 Jul 2018 10:10:05: 18000000 INFO @ Wed, 04 Jul 2018 10:10:09: 19000000 INFO @ Wed, 04 Jul 2018 10:10:09: 20000000 INFO @ Wed, 04 Jul 2018 10:10:11: 19000000 INFO @ Wed, 04 Jul 2018 10:10:15: 20000000 INFO @ Wed, 04 Jul 2018 10:10:15: 21000000 INFO @ Wed, 04 Jul 2018 10:10:18: 20000000 INFO @ Wed, 04 Jul 2018 10:10:21: 21000000 INFO @ Wed, 04 Jul 2018 10:10:21: 22000000 INFO @ Wed, 04 Jul 2018 10:10:24: 21000000 INFO @ Wed, 04 Jul 2018 10:10:27: 22000000 INFO @ Wed, 04 Jul 2018 10:10:27: 23000000 INFO @ Wed, 04 Jul 2018 10:10:30: 22000000 INFO @ Wed, 04 Jul 2018 10:10:33: 23000000 INFO @ Wed, 04 Jul 2018 10:10:33: 24000000 INFO @ Wed, 04 Jul 2018 10:10:36: 23000000 INFO @ Wed, 04 Jul 2018 10:10:39: 24000000 INFO @ Wed, 04 Jul 2018 10:10:39: 25000000 INFO @ Wed, 04 Jul 2018 10:10:43: 24000000 INFO @ Wed, 04 Jul 2018 10:10:45: 26000000 INFO @ Wed, 04 Jul 2018 10:10:45: 25000000 INFO @ Wed, 04 Jul 2018 10:10:50: 25000000 INFO @ Wed, 04 Jul 2018 10:10:51: 27000000 INFO @ Wed, 04 Jul 2018 10:10:52: 26000000 INFO @ Wed, 04 Jul 2018 10:10:57: 26000000 INFO @ Wed, 04 Jul 2018 10:10:57: 28000000 INFO @ Wed, 04 Jul 2018 10:10:58: 27000000 INFO @ Wed, 04 Jul 2018 10:11:02: 29000000 INFO @ Wed, 04 Jul 2018 10:11:03: 27000000 INFO @ Wed, 04 Jul 2018 10:11:05: 28000000 INFO @ Wed, 04 Jul 2018 10:11:08: 30000000 INFO @ Wed, 04 Jul 2018 10:11:10: 28000000 INFO @ Wed, 04 Jul 2018 10:11:12: 29000000 INFO @ Wed, 04 Jul 2018 10:11:14: 31000000 INFO @ Wed, 04 Jul 2018 10:11:17: 29000000 INFO @ Wed, 04 Jul 2018 10:11:18: #1 tag size is determined as 75 bps INFO @ Wed, 04 Jul 2018 10:11:18: #1 tag size = 75 INFO @ Wed, 04 Jul 2018 10:11:18: #1 total tags in treatment: 15116877 INFO @ Wed, 04 Jul 2018 10:11:18: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:11:18: #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 10:11:18: 30000000 INFO @ Wed, 04 Jul 2018 10:11:18: #1 tags after filtering in treatment: 12939038 INFO @ Wed, 04 Jul 2018 10:11:18: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 04 Jul 2018 10:11:18: #1 finished! INFO @ Wed, 04 Jul 2018 10:11:18: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:11:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:11:19: #2 number of paired peaks: 100 WARNING @ Wed, 04 Jul 2018 10:11:19: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Wed, 04 Jul 2018 10:11:19: start model_add_line... INFO @ Wed, 04 Jul 2018 10:11:19: start X-correlation... INFO @ Wed, 04 Jul 2018 10:11:19: end of X-cor INFO @ Wed, 04 Jul 2018 10:11:19: #2 finished! INFO @ Wed, 04 Jul 2018 10:11:19: #2 predicted fragment length is 188 bps INFO @ Wed, 04 Jul 2018 10:11:19: #2 alternative fragment length(s) may be 188 bps INFO @ Wed, 04 Jul 2018 10:11:19: #2.2 Generate R script for model : SRX3632901.05_model.r INFO @ Wed, 04 Jul 2018 10:11:19: #3 Call peaks... INFO @ Wed, 04 Jul 2018 10:11:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 10:11:23: 30000000 INFO @ Wed, 04 Jul 2018 10:11:25: 31000000 INFO @ Wed, 04 Jul 2018 10:11:29: #1 tag size is determined as 75 bps INFO @ Wed, 04 Jul 2018 10:11:29: #1 tag size = 75 INFO @ Wed, 04 Jul 2018 10:11:29: #1 total tags in treatment: 15116877 INFO @ Wed, 04 Jul 2018 10:11:29: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:11:29: #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 10:11:29: #1 tags after filtering in treatment: 12939038 INFO @ Wed, 04 Jul 2018 10:11:29: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 04 Jul 2018 10:11:29: #1 finished! INFO @ Wed, 04 Jul 2018 10:11:29: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:11:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:11:30: 31000000 INFO @ Wed, 04 Jul 2018 10:11:30: #2 number of paired peaks: 100 WARNING @ Wed, 04 Jul 2018 10:11:30: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Wed, 04 Jul 2018 10:11:30: start model_add_line... INFO @ Wed, 04 Jul 2018 10:11:30: start X-correlation... INFO @ Wed, 04 Jul 2018 10:11:30: end of X-cor INFO @ Wed, 04 Jul 2018 10:11:30: #2 finished! INFO @ Wed, 04 Jul 2018 10:11:30: #2 predicted fragment length is 188 bps INFO @ Wed, 04 Jul 2018 10:11:30: #2 alternative fragment length(s) may be 188 bps INFO @ Wed, 04 Jul 2018 10:11:30: #2.2 Generate R script for model : SRX3632901.10_model.r INFO @ Wed, 04 Jul 2018 10:11:30: #3 Call peaks... INFO @ Wed, 04 Jul 2018 10:11:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 10:11:34: #1 tag size is determined as 75 bps INFO @ Wed, 04 Jul 2018 10:11:34: #1 tag size = 75 INFO @ Wed, 04 Jul 2018 10:11:34: #1 total tags in treatment: 15116877 INFO @ Wed, 04 Jul 2018 10:11:34: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:11:34: #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 10:11:34: #1 tags after filtering in treatment: 12939038 INFO @ Wed, 04 Jul 2018 10:11:34: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 04 Jul 2018 10:11:34: #1 finished! INFO @ Wed, 04 Jul 2018 10:11:34: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:11:35: #2 number of paired peaks: 100 WARNING @ Wed, 04 Jul 2018 10:11:35: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Wed, 04 Jul 2018 10:11:35: start model_add_line... INFO @ Wed, 04 Jul 2018 10:11:35: start X-correlation... INFO @ Wed, 04 Jul 2018 10:11:35: end of X-cor INFO @ Wed, 04 Jul 2018 10:11:35: #2 finished! INFO @ Wed, 04 Jul 2018 10:11:35: #2 predicted fragment length is 188 bps INFO @ Wed, 04 Jul 2018 10:11:35: #2 alternative fragment length(s) may be 188 bps INFO @ Wed, 04 Jul 2018 10:11:35: #2.2 Generate R script for model : SRX3632901.20_model.r INFO @ Wed, 04 Jul 2018 10:11:35: #3 Call peaks... INFO @ Wed, 04 Jul 2018 10:11:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 10:11:48: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 10:12:02: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 10:12:05: #4 Write output xls file... SRX3632901.05_peaks.xls INFO @ Wed, 04 Jul 2018 10:12:05: #4 Write peak in narrowPeak format file... SRX3632901.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 10:12:05: #4 Write summits bed file... SRX3632901.05_summits.bed INFO @ Wed, 04 Jul 2018 10:12:05: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4958 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 10:12:06: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 10:12:18: #4 Write output xls file... SRX3632901.10_peaks.xls INFO @ Wed, 04 Jul 2018 10:12:18: #4 Write peak in narrowPeak format file... SRX3632901.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 10:12:18: #4 Write summits bed file... SRX3632901.10_summits.bed INFO @ Wed, 04 Jul 2018 10:12:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2361 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 10:12:23: #4 Write output xls file... SRX3632901.20_peaks.xls INFO @ Wed, 04 Jul 2018 10:12:23: #4 Write peak in narrowPeak format file... SRX3632901.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 10:12:23: #4 Write summits bed file... SRX3632901.20_summits.bed INFO @ Wed, 04 Jul 2018 10:12:23: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (565 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。