Job ID = 11240719 sra ファイルのダウンロード中... Completed: 808368K bytes transferred in 45 seconds (144355K 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: SINGLE fastq に変換中... Read 39277236 spots for /home/okishinya/chipatlas/results/dm3/SRX3630328/SRR6652850.sra Written 39277236 spots for /home/okishinya/chipatlas/results/dm3/SRX3630328/SRR6652850.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:22:17 39277236 reads; of these: 39277236 (100.00%) were unpaired; of these: 1462771 (3.72%) aligned 0 times 14380357 (36.61%) aligned exactly 1 time 23434108 (59.66%) aligned >1 times 96.28% overall alignment rate Time searching: 00:22:18 Overall time: 00:22:18 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_rmdupse_core] 22359541 / 37814465 = 0.5913 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 @ Sun, 07 Oct 2018 21:01:24: # Command line: callpeak -t SRX3630328.bam -f BAM -g dm -n SRX3630328.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3630328.20 # format = BAM # ChIP-seq file = ['SRX3630328.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 @ Sun, 07 Oct 2018 21:01:24: # Command line: callpeak -t SRX3630328.bam -f BAM -g dm -n SRX3630328.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3630328.05 # format = BAM # ChIP-seq file = ['SRX3630328.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 @ Sun, 07 Oct 2018 21:01:24: # Command line: callpeak -t SRX3630328.bam -f BAM -g dm -n SRX3630328.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3630328.10 # format = BAM # ChIP-seq file = ['SRX3630328.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 @ Sun, 07 Oct 2018 21:01:24: #1 read tag files... INFO @ Sun, 07 Oct 2018 21:01:24: #1 read tag files... INFO @ Sun, 07 Oct 2018 21:01:24: #1 read tag files... INFO @ Sun, 07 Oct 2018 21:01:24: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 21:01:24: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 21:01:24: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 21:01:31: 1000000 INFO @ Sun, 07 Oct 2018 21:01:31: 1000000 INFO @ Sun, 07 Oct 2018 21:01:31: 1000000 INFO @ Sun, 07 Oct 2018 21:01:38: 2000000 INFO @ Sun, 07 Oct 2018 21:01:38: 2000000 INFO @ Sun, 07 Oct 2018 21:01:38: 2000000 INFO @ Sun, 07 Oct 2018 21:01:44: 3000000 INFO @ Sun, 07 Oct 2018 21:01:45: 3000000 INFO @ Sun, 07 Oct 2018 21:01:45: 3000000 INFO @ Sun, 07 Oct 2018 21:01:51: 4000000 INFO @ Sun, 07 Oct 2018 21:01:52: 4000000 INFO @ Sun, 07 Oct 2018 21:01:52: 4000000 INFO @ Sun, 07 Oct 2018 21:01:58: 5000000 INFO @ Sun, 07 Oct 2018 21:01:59: 5000000 INFO @ Sun, 07 Oct 2018 21:01:59: 5000000 INFO @ Sun, 07 Oct 2018 21:02:05: 6000000 INFO @ Sun, 07 Oct 2018 21:02:06: 6000000 INFO @ Sun, 07 Oct 2018 21:02:06: 6000000 INFO @ Sun, 07 Oct 2018 21:02:12: 7000000 INFO @ Sun, 07 Oct 2018 21:02:13: 7000000 INFO @ Sun, 07 Oct 2018 21:02:13: 7000000 INFO @ Sun, 07 Oct 2018 21:02:19: 8000000 INFO @ Sun, 07 Oct 2018 21:02:20: 8000000 INFO @ Sun, 07 Oct 2018 21:02:20: 8000000 INFO @ Sun, 07 Oct 2018 21:02:26: 9000000 INFO @ Sun, 07 Oct 2018 21:02:27: 9000000 INFO @ Sun, 07 Oct 2018 21:02:27: 9000000 INFO @ Sun, 07 Oct 2018 21:02:33: 10000000 INFO @ Sun, 07 Oct 2018 21:02:34: 10000000 INFO @ Sun, 07 Oct 2018 21:02:34: 10000000 INFO @ Sun, 07 Oct 2018 21:02:40: 11000000 INFO @ Sun, 07 Oct 2018 21:02:41: 11000000 INFO @ Sun, 07 Oct 2018 21:02:41: 11000000 INFO @ Sun, 07 Oct 2018 21:02:46: 12000000 INFO @ Sun, 07 Oct 2018 21:02:48: 12000000 INFO @ Sun, 07 Oct 2018 21:02:48: 12000000 INFO @ Sun, 07 Oct 2018 21:02:54: 13000000 INFO @ Sun, 07 Oct 2018 21:02:54: 13000000 INFO @ Sun, 07 Oct 2018 21:02:55: 13000000 INFO @ Sun, 07 Oct 2018 21:03:01: 14000000 INFO @ Sun, 07 Oct 2018 21:03:01: 14000000 INFO @ Sun, 07 Oct 2018 21:03:02: 14000000 INFO @ Sun, 07 Oct 2018 21:03:08: 15000000 INFO @ Sun, 07 Oct 2018 21:03:08: 15000000 INFO @ Sun, 07 Oct 2018 21:03:09: 15000000 INFO @ Sun, 07 Oct 2018 21:03:11: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 21:03:11: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 21:03:11: #1 total tags in treatment: 15454924 INFO @ Sun, 07 Oct 2018 21:03:11: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:03:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 21:03:11: #1 tags after filtering in treatment: 15454924 INFO @ Sun, 07 Oct 2018 21:03:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:03:11: #1 finished! INFO @ Sun, 07 Oct 2018 21:03:11: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:03:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:03:11: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 21:03:11: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 21:03:11: #1 total tags in treatment: 15454924 INFO @ Sun, 07 Oct 2018 21:03:11: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:03:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 21:03:12: #1 tags after filtering in treatment: 15454924 INFO @ Sun, 07 Oct 2018 21:03:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:03:12: #1 finished! INFO @ Sun, 07 Oct 2018 21:03:12: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:03:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:03:12: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 21:03:12: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 21:03:12: #1 total tags in treatment: 15454924 INFO @ Sun, 07 Oct 2018 21:03:12: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:03:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 21:03:12: #1 tags after filtering in treatment: 15454924 INFO @ Sun, 07 Oct 2018 21:03:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:03:12: #1 finished! INFO @ Sun, 07 Oct 2018 21:03:12: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:03:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:03:13: #2 number of paired peaks: 5309 INFO @ Sun, 07 Oct 2018 21:03:13: start model_add_line... INFO @ Sun, 07 Oct 2018 21:03:13: start X-correlation... INFO @ Sun, 07 Oct 2018 21:03:14: #2 number of paired peaks: 5309 INFO @ Sun, 07 Oct 2018 21:03:14: start model_add_line... INFO @ Sun, 07 Oct 2018 21:03:14: end of X-cor INFO @ Sun, 07 Oct 2018 21:03:14: #2 finished! INFO @ Sun, 07 Oct 2018 21:03:14: #2 predicted fragment length is 43 bps INFO @ Sun, 07 Oct 2018 21:03:14: #2 alternative fragment length(s) may be 43 bps INFO @ Sun, 07 Oct 2018 21:03:14: #2.2 Generate R script for model : SRX3630328.20_model.r WARNING @ Sun, 07 Oct 2018 21:03:14: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 21:03:14: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Sun, 07 Oct 2018 21:03:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 21:03:14: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:03:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:03:14: start X-correlation... INFO @ Sun, 07 Oct 2018 21:03:14: end of X-cor INFO @ Sun, 07 Oct 2018 21:03:14: #2 finished! INFO @ Sun, 07 Oct 2018 21:03:14: #2 predicted fragment length is 43 bps INFO @ Sun, 07 Oct 2018 21:03:14: #2 alternative fragment length(s) may be 43 bps INFO @ Sun, 07 Oct 2018 21:03:14: #2.2 Generate R script for model : SRX3630328.10_model.r WARNING @ Sun, 07 Oct 2018 21:03:14: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 21:03:14: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Sun, 07 Oct 2018 21:03:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 21:03:14: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:03:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:03:14: #2 number of paired peaks: 5309 INFO @ Sun, 07 Oct 2018 21:03:14: start model_add_line... INFO @ Sun, 07 Oct 2018 21:03:14: start X-correlation... INFO @ Sun, 07 Oct 2018 21:03:14: end of X-cor INFO @ Sun, 07 Oct 2018 21:03:14: #2 finished! INFO @ Sun, 07 Oct 2018 21:03:14: #2 predicted fragment length is 43 bps INFO @ Sun, 07 Oct 2018 21:03:14: #2 alternative fragment length(s) may be 43 bps INFO @ Sun, 07 Oct 2018 21:03:14: #2.2 Generate R script for model : SRX3630328.05_model.r WARNING @ Sun, 07 Oct 2018 21:03:14: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 21:03:14: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Sun, 07 Oct 2018 21:03:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 21:03:14: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:03:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:03:43: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:03:44: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:03:44: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:03:59: #4 Write output xls file... SRX3630328.20_peaks.xls INFO @ Sun, 07 Oct 2018 21:04:00: #4 Write peak in narrowPeak format file... SRX3630328.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:04:00: #4 Write summits bed file... SRX3630328.20_summits.bed INFO @ Sun, 07 Oct 2018 21:04:00: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (4343 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 21:04:00: #4 Write output xls file... SRX3630328.10_peaks.xls INFO @ Sun, 07 Oct 2018 21:04:00: #4 Write peak in narrowPeak format file... SRX3630328.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:04:01: #4 Write summits bed file... SRX3630328.10_summits.bed INFO @ Sun, 07 Oct 2018 21:04:01: Done! INFO @ Sun, 07 Oct 2018 21:04:01: #4 Write output xls file... SRX3630328.05_peaks.xls pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12362 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 21:04:01: #4 Write peak in narrowPeak format file... SRX3630328.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:04:01: #4 Write summits bed file... SRX3630328.05_summits.bed INFO @ Sun, 07 Oct 2018 21:04:02: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (22148 records, 4 fields): 37 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。