Job ID = 10714548 sra ファイルのダウンロード中... Completed: 500805K bytes transferred in 10 seconds (398490K 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 21888039 spots for /home/okishinya/chipatlas/results/dm3/SRX2583182/SRR5279382.sra Written 21888039 spots for /home/okishinya/chipatlas/results/dm3/SRX2583182/SRR5279382.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: 00:07:48 21888039 reads; of these: 21888039 (100.00%) were unpaired; of these: 1097277 (5.01%) aligned 0 times 16102184 (73.57%) aligned exactly 1 time 4688578 (21.42%) aligned >1 times 94.99% overall alignment rate Time searching: 00:07:48 Overall time: 00:07:48 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] 4906650 / 20790762 = 0.2360 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 13:34:13: # Command line: callpeak -t SRX2583182.bam -f BAM -g dm -n SRX2583182.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2583182.20 # format = BAM # ChIP-seq file = ['SRX2583182.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 13:34:13: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:34:13: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:34:13: # Command line: callpeak -t SRX2583182.bam -f BAM -g dm -n SRX2583182.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2583182.10 # format = BAM # ChIP-seq file = ['SRX2583182.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 13:34:13: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:34:13: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:34:13: # Command line: callpeak -t SRX2583182.bam -f BAM -g dm -n SRX2583182.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2583182.05 # format = BAM # ChIP-seq file = ['SRX2583182.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 13:34:13: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:34:13: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:34:20: 1000000 INFO @ Sun, 03 Jun 2018 13:34:21: 1000000 INFO @ Sun, 03 Jun 2018 13:34:21: 1000000 INFO @ Sun, 03 Jun 2018 13:34:27: 2000000 INFO @ Sun, 03 Jun 2018 13:34:30: 2000000 INFO @ Sun, 03 Jun 2018 13:34:30: 2000000 INFO @ Sun, 03 Jun 2018 13:34:34: 3000000 INFO @ Sun, 03 Jun 2018 13:34:39: 3000000 INFO @ Sun, 03 Jun 2018 13:34:39: 3000000 INFO @ Sun, 03 Jun 2018 13:34:41: 4000000 INFO @ Sun, 03 Jun 2018 13:34:48: 5000000 INFO @ Sun, 03 Jun 2018 13:34:48: 4000000 INFO @ Sun, 03 Jun 2018 13:34:48: 4000000 INFO @ Sun, 03 Jun 2018 13:34:55: 6000000 INFO @ Sun, 03 Jun 2018 13:34:57: 5000000 INFO @ Sun, 03 Jun 2018 13:34:57: 5000000 INFO @ Sun, 03 Jun 2018 13:35:02: 7000000 INFO @ Sun, 03 Jun 2018 13:35:06: 6000000 INFO @ Sun, 03 Jun 2018 13:35:06: 6000000 INFO @ Sun, 03 Jun 2018 13:35:09: 8000000 INFO @ Sun, 03 Jun 2018 13:35:15: 7000000 INFO @ Sun, 03 Jun 2018 13:35:15: 7000000 INFO @ Sun, 03 Jun 2018 13:35:16: 9000000 INFO @ Sun, 03 Jun 2018 13:35:23: 10000000 INFO @ Sun, 03 Jun 2018 13:35:24: 8000000 INFO @ Sun, 03 Jun 2018 13:35:24: 8000000 INFO @ Sun, 03 Jun 2018 13:35:29: 11000000 INFO @ Sun, 03 Jun 2018 13:35:32: 9000000 INFO @ Sun, 03 Jun 2018 13:35:32: 9000000 INFO @ Sun, 03 Jun 2018 13:35:37: 12000000 INFO @ Sun, 03 Jun 2018 13:35:40: 10000000 INFO @ Sun, 03 Jun 2018 13:35:41: 10000000 INFO @ Sun, 03 Jun 2018 13:35:44: 13000000 INFO @ Sun, 03 Jun 2018 13:35:48: 11000000 INFO @ Sun, 03 Jun 2018 13:35:49: 11000000 INFO @ Sun, 03 Jun 2018 13:35:51: 14000000 INFO @ Sun, 03 Jun 2018 13:35:56: 12000000 INFO @ Sun, 03 Jun 2018 13:35:57: 12000000 INFO @ Sun, 03 Jun 2018 13:35:59: 15000000 INFO @ Sun, 03 Jun 2018 13:36:04: 13000000 INFO @ Sun, 03 Jun 2018 13:36:05: 13000000 INFO @ Sun, 03 Jun 2018 13:36:06: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:36:06: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:36:06: #1 total tags in treatment: 15884112 INFO @ Sun, 03 Jun 2018 13:36:06: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:36:06: #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 13:36:06: #1 tags after filtering in treatment: 15884112 INFO @ Sun, 03 Jun 2018 13:36:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:36:06: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:06: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:07: #2 number of paired peaks: 778 WARNING @ Sun, 03 Jun 2018 13:36:07: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Sun, 03 Jun 2018 13:36:07: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:07: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:07: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:07: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:07: #2 predicted fragment length is 50 bps INFO @ Sun, 03 Jun 2018 13:36:07: #2 alternative fragment length(s) may be 3,50 bps INFO @ Sun, 03 Jun 2018 13:36:07: #2.2 Generate R script for model : SRX2583182.20_model.r WARNING @ Sun, 03 Jun 2018 13:36:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:36:07: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Sun, 03 Jun 2018 13:36:07: #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 13:36:07: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:12: 14000000 INFO @ Sun, 03 Jun 2018 13:36:13: 14000000 INFO @ Sun, 03 Jun 2018 13:36:20: 15000000 INFO @ Sun, 03 Jun 2018 13:36:21: 15000000 INFO @ Sun, 03 Jun 2018 13:36:28: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:36:28: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:36:28: #1 total tags in treatment: 15884112 INFO @ Sun, 03 Jun 2018 13:36:28: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:36:28: #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 13:36:28: #1 tags after filtering in treatment: 15884112 INFO @ Sun, 03 Jun 2018 13:36:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:36:28: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:28: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:28: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:36:28: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:36:28: #1 total tags in treatment: 15884112 INFO @ Sun, 03 Jun 2018 13:36:28: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:36:28: #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 13:36:28: #1 tags after filtering in treatment: 15884112 INFO @ Sun, 03 Jun 2018 13:36:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:36:28: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:28: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:29: #2 number of paired peaks: 778 WARNING @ Sun, 03 Jun 2018 13:36:29: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Sun, 03 Jun 2018 13:36:29: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:29: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:29: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:29: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:29: #2 predicted fragment length is 50 bps INFO @ Sun, 03 Jun 2018 13:36:29: #2 alternative fragment length(s) may be 3,50 bps INFO @ Sun, 03 Jun 2018 13:36:29: #2.2 Generate R script for model : SRX2583182.10_model.r WARNING @ Sun, 03 Jun 2018 13:36:29: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:36:29: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Sun, 03 Jun 2018 13:36:29: #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 13:36:29: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:29: #2 number of paired peaks: 778 WARNING @ Sun, 03 Jun 2018 13:36:29: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Sun, 03 Jun 2018 13:36:29: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:30: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:30: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:30: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:30: #2 predicted fragment length is 50 bps INFO @ Sun, 03 Jun 2018 13:36:30: #2 alternative fragment length(s) may be 3,50 bps INFO @ Sun, 03 Jun 2018 13:36:30: #2.2 Generate R script for model : SRX2583182.05_model.r WARNING @ Sun, 03 Jun 2018 13:36:30: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:36:30: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Sun, 03 Jun 2018 13:36:30: #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 13:36:30: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:41: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:36:59: #4 Write output xls file... SRX2583182.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:36:59: #4 Write peak in narrowPeak format file... SRX2583182.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:36:59: #4 Write summits bed file... SRX2583182.20_summits.bed INFO @ Sun, 03 Jun 2018 13:36:59: Done! pass1 - making usageList (12 chroms): 11 millis pass2 - checking and writing primary data (1236 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:37:02: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:03: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:20: #4 Write output xls file... SRX2583182.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:20: #4 Write peak in narrowPeak format file... SRX2583182.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:20: #4 Write summits bed file... SRX2583182.05_summits.bed INFO @ Sun, 03 Jun 2018 13:37:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4122 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:37:22: #4 Write output xls file... SRX2583182.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:22: #4 Write peak in narrowPeak format file... SRX2583182.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:22: #4 Write summits bed file... SRX2583182.10_summits.bed INFO @ Sun, 03 Jun 2018 13:37:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2596 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。