Job ID = 9029760 sra ファイルのダウンロード中... Completed: 450414K bytes transferred in 7 seconds (485436K 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 1053 0 --:--:-- 0:00:07 --:--:-- 11170 100 38318 0 38318 0 0 4635 0 --:--:-- 0:00:08 --:--:-- 22794 100 52667 0 52667 0 0 6125 0 --:--:-- 0:00:08 --:--:-- 26176 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 21130231 spots for /home/okishinya/chipatlas/results/dm3/SRX2055944/SRR4069176.sra Written 21130231 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: 00:14:11 21130231 reads; of these: 21130231 (100.00%) were unpaired; of these: 593781 (2.81%) aligned 0 times 9516116 (45.04%) aligned exactly 1 time 11020334 (52.15%) aligned >1 times 97.19% overall alignment rate Time searching: 00:14:12 Overall time: 00:14:12 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 12 files... [bam_rmdupse_core] 3704533 / 20536450 = 0.1804 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 15:23:59: # Command line: callpeak -t SRX2055944.bam -f BAM -g dm -n SRX2055944.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055944.05 # format = BAM # ChIP-seq file = ['SRX2055944.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 15:23:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:23:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:23:59: # Command line: callpeak -t SRX2055944.bam -f BAM -g dm -n SRX2055944.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055944.10 # format = BAM # ChIP-seq file = ['SRX2055944.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 15:23:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:23:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:23:59: # Command line: callpeak -t SRX2055944.bam -f BAM -g dm -n SRX2055944.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055944.20 # format = BAM # ChIP-seq file = ['SRX2055944.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 15:23:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:23:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:24:04: 1000000 INFO @ Sat, 03 Jun 2017 15:24:04: 1000000 INFO @ Sat, 03 Jun 2017 15:24:04: 1000000 INFO @ Sat, 03 Jun 2017 15:24:09: 2000000 INFO @ Sat, 03 Jun 2017 15:24:10: 2000000 INFO @ Sat, 03 Jun 2017 15:24:10: 2000000 INFO @ Sat, 03 Jun 2017 15:24:14: 3000000 INFO @ Sat, 03 Jun 2017 15:24:15: 3000000 INFO @ Sat, 03 Jun 2017 15:24:15: 3000000 INFO @ Sat, 03 Jun 2017 15:24:19: 4000000 INFO @ Sat, 03 Jun 2017 15:24:20: 4000000 INFO @ Sat, 03 Jun 2017 15:24:21: 4000000 INFO @ Sat, 03 Jun 2017 15:24:24: 5000000 INFO @ Sat, 03 Jun 2017 15:24:26: 5000000 INFO @ Sat, 03 Jun 2017 15:24:26: 5000000 INFO @ Sat, 03 Jun 2017 15:24:29: 6000000 INFO @ Sat, 03 Jun 2017 15:24:31: 6000000 INFO @ Sat, 03 Jun 2017 15:24:32: 6000000 INFO @ Sat, 03 Jun 2017 15:24:34: 7000000 INFO @ Sat, 03 Jun 2017 15:24:37: 7000000 INFO @ Sat, 03 Jun 2017 15:24:38: 7000000 INFO @ Sat, 03 Jun 2017 15:24:39: 8000000 INFO @ Sat, 03 Jun 2017 15:24:43: 8000000 INFO @ Sat, 03 Jun 2017 15:24:43: 8000000 INFO @ Sat, 03 Jun 2017 15:24:45: 9000000 INFO @ Sat, 03 Jun 2017 15:24:48: 9000000 INFO @ Sat, 03 Jun 2017 15:24:49: 9000000 INFO @ Sat, 03 Jun 2017 15:24:50: 10000000 INFO @ Sat, 03 Jun 2017 15:24:54: 10000000 INFO @ Sat, 03 Jun 2017 15:24:55: 11000000 INFO @ Sat, 03 Jun 2017 15:24:55: 10000000 INFO @ Sat, 03 Jun 2017 15:25:00: 11000000 INFO @ Sat, 03 Jun 2017 15:25:00: 12000000 INFO @ Sat, 03 Jun 2017 15:25:01: 11000000 INFO @ Sat, 03 Jun 2017 15:25:05: 13000000 INFO @ Sat, 03 Jun 2017 15:25:05: 12000000 INFO @ Sat, 03 Jun 2017 15:25:06: 12000000 INFO @ Sat, 03 Jun 2017 15:25:10: 14000000 INFO @ Sat, 03 Jun 2017 15:25:11: 13000000 INFO @ Sat, 03 Jun 2017 15:25:12: 13000000 INFO @ Sat, 03 Jun 2017 15:25:15: 15000000 INFO @ Sat, 03 Jun 2017 15:25:17: 14000000 INFO @ Sat, 03 Jun 2017 15:25:18: 14000000 INFO @ Sat, 03 Jun 2017 15:25:20: 16000000 INFO @ Sat, 03 Jun 2017 15:25:22: 15000000 INFO @ Sat, 03 Jun 2017 15:25:24: 15000000 INFO @ Sat, 03 Jun 2017 15:25:24: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:25:24: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:25:24: #1 total tags in treatment: 16831917 INFO @ Sat, 03 Jun 2017 15:25:24: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:25:24: #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 15:25:27: #1 tags after filtering in treatment: 16827794 INFO @ Sat, 03 Jun 2017 15:25:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:25:27: #1 finished! INFO @ Sat, 03 Jun 2017 15:25:27: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:25:28: 16000000 INFO @ Sat, 03 Jun 2017 15:25:29: 16000000 INFO @ Sat, 03 Jun 2017 15:25:31: #2 number of paired peaks: 898 WARNING @ Sat, 03 Jun 2017 15:25:31: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Sat, 03 Jun 2017 15:25:31: start model_add_line... INFO @ Sat, 03 Jun 2017 15:25:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:25:33: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:25:33: #1 total tags in treatment: 16831917 INFO @ Sat, 03 Jun 2017 15:25:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:25:33: #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 15:25:34: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:25:34: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:25:34: #1 total tags in treatment: 16831917 INFO @ Sat, 03 Jun 2017 15:25:34: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:25:34: #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 15:25:36: #1 tags after filtering in treatment: 16827794 INFO @ Sat, 03 Jun 2017 15:25:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:25:36: #1 finished! INFO @ Sat, 03 Jun 2017 15:25:36: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:25:37: #1 tags after filtering in treatment: 16827794 INFO @ Sat, 03 Jun 2017 15:25:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:25:37: #1 finished! INFO @ Sat, 03 Jun 2017 15:25:37: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:25:39: #2 number of paired peaks: 898 WARNING @ Sat, 03 Jun 2017 15:25:39: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Sat, 03 Jun 2017 15:25:39: start model_add_line... INFO @ Sat, 03 Jun 2017 15:25:40: start X-correlation... INFO @ Sat, 03 Jun 2017 15:25:40: end of X-cor INFO @ Sat, 03 Jun 2017 15:25:40: #2 finished! INFO @ Sat, 03 Jun 2017 15:25:40: #2 predicted fragment length is 44 bps INFO @ Sat, 03 Jun 2017 15:25:40: #2 alternative fragment length(s) may be 44 bps INFO @ Sat, 03 Jun 2017 15:25:40: #2.2 Generate R script for model : SRX2055944.20_model.r WARNING @ Sat, 03 Jun 2017 15:25:40: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:25:40: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sat, 03 Jun 2017 15:25:40: #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 15:25:40: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:25:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:25:40: #2 number of paired peaks: 898 WARNING @ Sat, 03 Jun 2017 15:25:40: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Sat, 03 Jun 2017 15:25:40: start model_add_line... INFO @ Sat, 03 Jun 2017 15:25:49: start X-correlation... INFO @ Sat, 03 Jun 2017 15:25:49: end of X-cor INFO @ Sat, 03 Jun 2017 15:25:49: #2 finished! INFO @ Sat, 03 Jun 2017 15:25:49: #2 predicted fragment length is 44 bps INFO @ Sat, 03 Jun 2017 15:25:49: #2 alternative fragment length(s) may be 44 bps INFO @ Sat, 03 Jun 2017 15:25:49: #2.2 Generate R script for model : SRX2055944.05_model.r WARNING @ Sat, 03 Jun 2017 15:25:49: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:25:49: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sat, 03 Jun 2017 15:25:49: #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 15:25:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:25:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:25:50: start X-correlation... INFO @ Sat, 03 Jun 2017 15:25:50: end of X-cor INFO @ Sat, 03 Jun 2017 15:25:50: #2 finished! INFO @ Sat, 03 Jun 2017 15:25:50: #2 predicted fragment length is 44 bps INFO @ Sat, 03 Jun 2017 15:25:50: #2 alternative fragment length(s) may be 44 bps INFO @ Sat, 03 Jun 2017 15:25:50: #2.2 Generate R script for model : SRX2055944.10_model.r WARNING @ Sat, 03 Jun 2017 15:25:50: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:25:50: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sat, 03 Jun 2017 15:25:50: #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 15:25:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:25:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:27:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:27:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:27:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:28:08: #4 Write output xls file... SRX2055944.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:28:08: #4 Write peak in narrowPeak format file... SRX2055944.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:28:08: #4 Write summits bed file... SRX2055944.20_summits.bed INFO @ Sat, 03 Jun 2017 15:28:08: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1372 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:28:14: #4 Write output xls file... SRX2055944.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:28:14: #4 Write peak in narrowPeak format file... SRX2055944.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:28:14: #4 Write summits bed file... SRX2055944.05_summits.bed INFO @ Sat, 03 Jun 2017 15:28:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4527 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:28:21: #4 Write output xls file... SRX2055944.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:28:21: #4 Write peak in narrowPeak format file... SRX2055944.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:28:21: #4 Write summits bed file... SRX2055944.10_summits.bed INFO @ Sat, 03 Jun 2017 15:28:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2600 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。