Job ID = 9029476 sra ファイルのダウンロード中... Completed: 259093K bytes transferred in 4 seconds (435628K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 7663 0 7663 0 0 1070 0 --:--:-- 0:00:07 --:--:-- 10482 100 38318 0 38318 0 0 4697 0 --:--:-- 0:00:08 --:--:-- 22200 100 51656 0 51656 0 0 6206 0 --:--:-- 0:00:08 --:--:-- 27287 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 10164975 spots for /home/okishinya/chipatlas/results/dm3/SRX1794227/SRR3575264.sra Written 10164975 spots total 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: 00:03:56 10164975 reads; of these: 10164975 (100.00%) were unpaired; of these: 299799 (2.95%) aligned 0 times 7281795 (71.64%) aligned exactly 1 time 2583381 (25.41%) aligned >1 times 97.05% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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 8 files... [bam_rmdupse_core] 377751 / 9865176 = 0.0383 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, 03 Jun 2017 13:58:53: # Command line: callpeak -t SRX1794227.bam -f BAM -g dm -n SRX1794227.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794227.20 # format = BAM # ChIP-seq file = ['SRX1794227.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 INFO @ Sat, 03 Jun 2017 13:58:53: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:58:53: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:58:53: # Command line: callpeak -t SRX1794227.bam -f BAM -g dm -n SRX1794227.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794227.10 # format = BAM # ChIP-seq file = ['SRX1794227.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 INFO @ Sat, 03 Jun 2017 13:58:53: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:58:53: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:58:53: # Command line: callpeak -t SRX1794227.bam -f BAM -g dm -n SRX1794227.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794227.05 # format = BAM # ChIP-seq file = ['SRX1794227.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 INFO @ Sat, 03 Jun 2017 13:58:53: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:58:53: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:58:59: 1000000 INFO @ Sat, 03 Jun 2017 13:58:59: 1000000 INFO @ Sat, 03 Jun 2017 13:58:59: 1000000 INFO @ Sat, 03 Jun 2017 13:59:04: 2000000 INFO @ Sat, 03 Jun 2017 13:59:05: 2000000 INFO @ Sat, 03 Jun 2017 13:59:05: 2000000 INFO @ Sat, 03 Jun 2017 13:59:10: 3000000 INFO @ Sat, 03 Jun 2017 13:59:10: 3000000 INFO @ Sat, 03 Jun 2017 13:59:12: 3000000 INFO @ Sat, 03 Jun 2017 13:59:15: 4000000 INFO @ Sat, 03 Jun 2017 13:59:16: 4000000 INFO @ Sat, 03 Jun 2017 13:59:18: 4000000 INFO @ Sat, 03 Jun 2017 13:59:21: 5000000 INFO @ Sat, 03 Jun 2017 13:59:22: 5000000 INFO @ Sat, 03 Jun 2017 13:59:24: 5000000 INFO @ Sat, 03 Jun 2017 13:59:26: 6000000 INFO @ Sat, 03 Jun 2017 13:59:28: 6000000 INFO @ Sat, 03 Jun 2017 13:59:31: 6000000 INFO @ Sat, 03 Jun 2017 13:59:31: 7000000 INFO @ Sat, 03 Jun 2017 13:59:33: 7000000 INFO @ Sat, 03 Jun 2017 13:59:37: 8000000 INFO @ Sat, 03 Jun 2017 13:59:37: 7000000 INFO @ Sat, 03 Jun 2017 13:59:39: 8000000 INFO @ Sat, 03 Jun 2017 13:59:42: 9000000 INFO @ Sat, 03 Jun 2017 13:59:43: 8000000 INFO @ Sat, 03 Jun 2017 13:59:45: 9000000 INFO @ Sat, 03 Jun 2017 13:59:45: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:59:45: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:59:45: #1 total tags in treatment: 9487425 INFO @ Sat, 03 Jun 2017 13:59:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:59:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:59:47: #1 tags after filtering in treatment: 9486394 INFO @ Sat, 03 Jun 2017 13:59:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:59:47: #1 finished! INFO @ Sat, 03 Jun 2017 13:59:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:59:48: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:59:48: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:59:48: #1 total tags in treatment: 9487425 INFO @ Sat, 03 Jun 2017 13:59:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:59:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:59:49: #2 number of paired peaks: 482 WARNING @ Sat, 03 Jun 2017 13:59:49: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Sat, 03 Jun 2017 13:59:49: start model_add_line... INFO @ Sat, 03 Jun 2017 13:59:50: #1 tags after filtering in treatment: 9486394 INFO @ Sat, 03 Jun 2017 13:59:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:59:50: #1 finished! INFO @ Sat, 03 Jun 2017 13:59:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:59:50: 9000000 INFO @ Sat, 03 Jun 2017 13:59:52: #2 number of paired peaks: 482 WARNING @ Sat, 03 Jun 2017 13:59:52: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Sat, 03 Jun 2017 13:59:52: start model_add_line... INFO @ Sat, 03 Jun 2017 13:59:53: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:59:53: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:59:53: #1 total tags in treatment: 9487425 INFO @ Sat, 03 Jun 2017 13:59:53: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:59:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:59:53: start X-correlation... INFO @ Sat, 03 Jun 2017 13:59:53: end of X-cor INFO @ Sat, 03 Jun 2017 13:59:53: #2 finished! INFO @ Sat, 03 Jun 2017 13:59:53: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 13:59:53: #2 alternative fragment length(s) may be 3,48,591 bps INFO @ Sat, 03 Jun 2017 13:59:53: #2.2 Generate R script for model : SRX1794227.05_model.r WARNING @ Sat, 03 Jun 2017 13:59:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:59:53: #2 You may need to consider one of the other alternative d(s): 3,48,591 WARNING @ Sat, 03 Jun 2017 13:59:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:59:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:59:54: #1 tags after filtering in treatment: 9486394 INFO @ Sat, 03 Jun 2017 13:59:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:59:54: #1 finished! INFO @ Sat, 03 Jun 2017 13:59:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:59:55: start X-correlation... INFO @ Sat, 03 Jun 2017 13:59:55: end of X-cor INFO @ Sat, 03 Jun 2017 13:59:55: #2 finished! INFO @ Sat, 03 Jun 2017 13:59:55: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 13:59:55: #2 alternative fragment length(s) may be 3,48,591 bps INFO @ Sat, 03 Jun 2017 13:59:55: #2.2 Generate R script for model : SRX1794227.10_model.r WARNING @ Sat, 03 Jun 2017 13:59:55: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:59:55: #2 You may need to consider one of the other alternative d(s): 3,48,591 WARNING @ Sat, 03 Jun 2017 13:59:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:59:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:59:56: #2 number of paired peaks: 482 WARNING @ Sat, 03 Jun 2017 13:59:56: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Sat, 03 Jun 2017 13:59:56: start model_add_line... INFO @ Sat, 03 Jun 2017 14:00:00: start X-correlation... INFO @ Sat, 03 Jun 2017 14:00:00: end of X-cor INFO @ Sat, 03 Jun 2017 14:00:00: #2 finished! INFO @ Sat, 03 Jun 2017 14:00:00: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 14:00:00: #2 alternative fragment length(s) may be 3,48,591 bps INFO @ Sat, 03 Jun 2017 14:00:00: #2.2 Generate R script for model : SRX1794227.20_model.r WARNING @ Sat, 03 Jun 2017 14:00:00: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:00:00: #2 You may need to consider one of the other alternative d(s): 3,48,591 WARNING @ Sat, 03 Jun 2017 14:00:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:00:00: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:00:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:00:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:00:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:00:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:01:27: #4 Write output xls file... SRX1794227.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:01:27: #4 Write peak in narrowPeak format file... SRX1794227.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:01:27: #4 Write summits bed file... SRX1794227.10_summits.bed INFO @ Sat, 03 Jun 2017 14:01:27: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:01:28: #4 Write output xls file... SRX1794227.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:01:28: #4 Write peak in narrowPeak format file... SRX1794227.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:01:28: #4 Write summits bed file... SRX1794227.05_summits.bed INFO @ Sat, 03 Jun 2017 14:01:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1433 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:01:33: #4 Write output xls file... SRX1794227.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:01:33: #4 Write peak in narrowPeak format file... SRX1794227.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:01:33: #4 Write summits bed file... SRX1794227.20_summits.bed INFO @ Sat, 03 Jun 2017 14:01:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。