Job ID = 10714551 sra ファイルのダウンロード中... Completed: 509532K bytes transferred in 24 seconds (169078K 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 22211482 spots for /home/okishinya/chipatlas/results/dm3/SRX2583185/SRR5279385.sra Written 22211482 spots for /home/okishinya/chipatlas/results/dm3/SRX2583185/SRR5279385.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: 00:09:07 22211482 reads; of these: 22211482 (100.00%) were unpaired; of these: 571025 (2.57%) aligned 0 times 15510502 (69.83%) aligned exactly 1 time 6129955 (27.60%) aligned >1 times 97.43% overall alignment rate Time searching: 00:09:07 Overall time: 00:09:07 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] 2898096 / 21640457 = 0.1339 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, 03 Jun 2018 13:37:41: # Command line: callpeak -t SRX2583185.bam -f BAM -g dm -n SRX2583185.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2583185.20 # format = BAM # ChIP-seq file = ['SRX2583185.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, 03 Jun 2018 13:37:41: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:37:41: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:37:41: # Command line: callpeak -t SRX2583185.bam -f BAM -g dm -n SRX2583185.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2583185.10 # format = BAM # ChIP-seq file = ['SRX2583185.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, 03 Jun 2018 13:37:41: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:37:41: # Command line: callpeak -t SRX2583185.bam -f BAM -g dm -n SRX2583185.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2583185.05 # format = BAM # ChIP-seq file = ['SRX2583185.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, 03 Jun 2018 13:37:41: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:37:41: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:37:41: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:37:47: 1000000 INFO @ Sun, 03 Jun 2018 13:37:47: 1000000 INFO @ Sun, 03 Jun 2018 13:37:47: 1000000 INFO @ Sun, 03 Jun 2018 13:37:53: 2000000 INFO @ Sun, 03 Jun 2018 13:37:53: 2000000 INFO @ Sun, 03 Jun 2018 13:37:53: 2000000 INFO @ Sun, 03 Jun 2018 13:37:59: 3000000 INFO @ Sun, 03 Jun 2018 13:37:59: 3000000 INFO @ Sun, 03 Jun 2018 13:37:59: 3000000 INFO @ Sun, 03 Jun 2018 13:38:05: 4000000 INFO @ Sun, 03 Jun 2018 13:38:05: 4000000 INFO @ Sun, 03 Jun 2018 13:38:05: 4000000 INFO @ Sun, 03 Jun 2018 13:38:11: 5000000 INFO @ Sun, 03 Jun 2018 13:38:11: 5000000 INFO @ Sun, 03 Jun 2018 13:38:11: 5000000 INFO @ Sun, 03 Jun 2018 13:38:17: 6000000 INFO @ Sun, 03 Jun 2018 13:38:17: 6000000 INFO @ Sun, 03 Jun 2018 13:38:17: 6000000 INFO @ Sun, 03 Jun 2018 13:38:23: 7000000 INFO @ Sun, 03 Jun 2018 13:38:23: 7000000 INFO @ Sun, 03 Jun 2018 13:38:23: 7000000 INFO @ Sun, 03 Jun 2018 13:38:29: 8000000 INFO @ Sun, 03 Jun 2018 13:38:29: 8000000 INFO @ Sun, 03 Jun 2018 13:38:29: 8000000 INFO @ Sun, 03 Jun 2018 13:38:35: 9000000 INFO @ Sun, 03 Jun 2018 13:38:35: 9000000 INFO @ Sun, 03 Jun 2018 13:38:35: 9000000 INFO @ Sun, 03 Jun 2018 13:38:41: 10000000 INFO @ Sun, 03 Jun 2018 13:38:41: 10000000 INFO @ Sun, 03 Jun 2018 13:38:41: 10000000 INFO @ Sun, 03 Jun 2018 13:38:47: 11000000 INFO @ Sun, 03 Jun 2018 13:38:47: 11000000 INFO @ Sun, 03 Jun 2018 13:38:47: 11000000 INFO @ Sun, 03 Jun 2018 13:38:53: 12000000 INFO @ Sun, 03 Jun 2018 13:38:53: 12000000 INFO @ Sun, 03 Jun 2018 13:38:53: 12000000 INFO @ Sun, 03 Jun 2018 13:38:59: 13000000 INFO @ Sun, 03 Jun 2018 13:38:59: 13000000 INFO @ Sun, 03 Jun 2018 13:38:59: 13000000 INFO @ Sun, 03 Jun 2018 13:39:05: 14000000 INFO @ Sun, 03 Jun 2018 13:39:05: 14000000 INFO @ Sun, 03 Jun 2018 13:39:06: 14000000 INFO @ Sun, 03 Jun 2018 13:39:11: 15000000 INFO @ Sun, 03 Jun 2018 13:39:11: 15000000 INFO @ Sun, 03 Jun 2018 13:39:12: 15000000 INFO @ Sun, 03 Jun 2018 13:39:17: 16000000 INFO @ Sun, 03 Jun 2018 13:39:17: 16000000 INFO @ Sun, 03 Jun 2018 13:39:18: 16000000 INFO @ Sun, 03 Jun 2018 13:39:23: 17000000 INFO @ Sun, 03 Jun 2018 13:39:23: 17000000 INFO @ Sun, 03 Jun 2018 13:39:24: 17000000 INFO @ Sun, 03 Jun 2018 13:39:29: 18000000 INFO @ Sun, 03 Jun 2018 13:39:29: 18000000 INFO @ Sun, 03 Jun 2018 13:39:30: 18000000 INFO @ Sun, 03 Jun 2018 13:39:34: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:39:34: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:39:34: #1 total tags in treatment: 18742361 INFO @ Sun, 03 Jun 2018 13:39:34: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:39:34: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:39:34: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:39:34: #1 total tags in treatment: 18742361 INFO @ Sun, 03 Jun 2018 13:39:34: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:39:34: #1 tags after filtering in treatment: 18742361 INFO @ Sun, 03 Jun 2018 13:39:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:39:34: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:34: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:34: #1 tags after filtering in treatment: 18742361 INFO @ Sun, 03 Jun 2018 13:39:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:39:34: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:34: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:34: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:39:34: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:39:34: #1 total tags in treatment: 18742361 INFO @ Sun, 03 Jun 2018 13:39:34: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:39:35: #1 tags after filtering in treatment: 18742361 INFO @ Sun, 03 Jun 2018 13:39:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:39:35: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:35: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:35: #2 number of paired peaks: 255 WARNING @ Sun, 03 Jun 2018 13:39:35: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Sun, 03 Jun 2018 13:39:35: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:35: #2 number of paired peaks: 255 WARNING @ Sun, 03 Jun 2018 13:39:35: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Sun, 03 Jun 2018 13:39:35: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:35: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:35: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:35: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:35: #2 predicted fragment length is 45 bps INFO @ Sun, 03 Jun 2018 13:39:35: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 03 Jun 2018 13:39:35: #2.2 Generate R script for model : SRX2583185.20_model.r WARNING @ Sun, 03 Jun 2018 13:39:35: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:39:35: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 03 Jun 2018 13:39:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:39:35: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:36: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:36: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:36: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:36: #2 predicted fragment length is 45 bps INFO @ Sun, 03 Jun 2018 13:39:36: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 03 Jun 2018 13:39:36: #2.2 Generate R script for model : SRX2583185.10_model.r WARNING @ Sun, 03 Jun 2018 13:39:36: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:39:36: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 03 Jun 2018 13:39:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:39:36: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:36: #2 number of paired peaks: 255 WARNING @ Sun, 03 Jun 2018 13:39:36: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Sun, 03 Jun 2018 13:39:36: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:36: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:36: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:36: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:36: #2 predicted fragment length is 45 bps INFO @ Sun, 03 Jun 2018 13:39:36: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 03 Jun 2018 13:39:36: #2.2 Generate R script for model : SRX2583185.05_model.r WARNING @ Sun, 03 Jun 2018 13:39:36: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:39:36: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 03 Jun 2018 13:39:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:39:36: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:40:11: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:40:13: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:40:14: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:40:30: #4 Write output xls file... SRX2583185.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:30: #4 Write peak in narrowPeak format file... SRX2583185.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:30: #4 Write summits bed file... SRX2583185.20_summits.bed INFO @ Sun, 03 Jun 2018 13:40:30: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1183 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:40:33: #4 Write output xls file... SRX2583185.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:33: #4 Write peak in narrowPeak format file... SRX2583185.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:33: #4 Write summits bed file... SRX2583185.10_summits.bed INFO @ Sun, 03 Jun 2018 13:40:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2079 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:40:34: #4 Write output xls file... SRX2583185.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:34: #4 Write peak in narrowPeak format file... SRX2583185.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:34: #4 Write summits bed file... SRX2583185.05_summits.bed INFO @ Sun, 03 Jun 2018 13:40:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3297 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。