Job ID = 10175231 sra ファイルのダウンロード中... Completed: 614219K bytes transferred in 10 seconds (495249K 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... Written 20075401 spots for /home/okishinya/chipatlas/results/dm3/SRX2458934/SRR5140283.sra Written 20075401 spots total 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: 00:06:51 20075401 reads; of these: 20075401 (100.00%) were unpaired; of these: 2181517 (10.87%) aligned 0 times 12502561 (62.28%) aligned exactly 1 time 5391323 (26.86%) aligned >1 times 89.13% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 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] 6293623 / 17893884 = 0.3517 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 @ Mon, 06 Nov 2017 11:53:53: # Command line: callpeak -t SRX2458934.bam -f BAM -g dm -n SRX2458934.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2458934.05 # format = BAM # ChIP-seq file = ['SRX2458934.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 @ Mon, 06 Nov 2017 11:53:53: # Command line: callpeak -t SRX2458934.bam -f BAM -g dm -n SRX2458934.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2458934.20 # format = BAM # ChIP-seq file = ['SRX2458934.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 @ Mon, 06 Nov 2017 11:53:53: # Command line: callpeak -t SRX2458934.bam -f BAM -g dm -n SRX2458934.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2458934.10 # format = BAM # ChIP-seq file = ['SRX2458934.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 @ Mon, 06 Nov 2017 11:53:53: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:53:53: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:53:53: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:53:53: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:53:53: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:53:53: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:54:01: 1000000 INFO @ Mon, 06 Nov 2017 11:54:01: 1000000 INFO @ Mon, 06 Nov 2017 11:54:01: 1000000 INFO @ Mon, 06 Nov 2017 11:54:08: 2000000 INFO @ Mon, 06 Nov 2017 11:54:09: 2000000 INFO @ Mon, 06 Nov 2017 11:54:09: 2000000 INFO @ Mon, 06 Nov 2017 11:54:16: 3000000 INFO @ Mon, 06 Nov 2017 11:54:17: 3000000 INFO @ Mon, 06 Nov 2017 11:54:17: 3000000 INFO @ Mon, 06 Nov 2017 11:54:24: 4000000 INFO @ Mon, 06 Nov 2017 11:54:26: 4000000 INFO @ Mon, 06 Nov 2017 11:54:26: 4000000 INFO @ Mon, 06 Nov 2017 11:54:32: 5000000 INFO @ Mon, 06 Nov 2017 11:54:34: 5000000 INFO @ Mon, 06 Nov 2017 11:54:34: 5000000 INFO @ Mon, 06 Nov 2017 11:54:39: 6000000 INFO @ Mon, 06 Nov 2017 11:54:42: 6000000 INFO @ Mon, 06 Nov 2017 11:54:42: 6000000 INFO @ Mon, 06 Nov 2017 11:54:46: 7000000 INFO @ Mon, 06 Nov 2017 11:54:50: 7000000 INFO @ Mon, 06 Nov 2017 11:54:50: 7000000 INFO @ Mon, 06 Nov 2017 11:54:53: 8000000 INFO @ Mon, 06 Nov 2017 11:54:58: 8000000 INFO @ Mon, 06 Nov 2017 11:54:58: 8000000 INFO @ Mon, 06 Nov 2017 11:55:01: 9000000 INFO @ Mon, 06 Nov 2017 11:55:07: 9000000 INFO @ Mon, 06 Nov 2017 11:55:07: 9000000 INFO @ Mon, 06 Nov 2017 11:55:09: 10000000 INFO @ Mon, 06 Nov 2017 11:55:15: 10000000 INFO @ Mon, 06 Nov 2017 11:55:15: 10000000 INFO @ Mon, 06 Nov 2017 11:55:17: 11000000 INFO @ Mon, 06 Nov 2017 11:55:22: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:55:22: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:55:22: #1 total tags in treatment: 11600261 INFO @ Mon, 06 Nov 2017 11:55:22: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:55:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:55:22: #1 tags after filtering in treatment: 11600261 INFO @ Mon, 06 Nov 2017 11:55:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:55:22: #1 finished! INFO @ Mon, 06 Nov 2017 11:55:22: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:55:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:55:23: #2 number of paired peaks: 932 WARNING @ Mon, 06 Nov 2017 11:55:23: Fewer paired peaks (932) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 932 pairs to build model! INFO @ Mon, 06 Nov 2017 11:55:23: start model_add_line... INFO @ Mon, 06 Nov 2017 11:55:23: start X-correlation... INFO @ Mon, 06 Nov 2017 11:55:24: end of X-cor INFO @ Mon, 06 Nov 2017 11:55:24: #2 finished! INFO @ Mon, 06 Nov 2017 11:55:24: #2 predicted fragment length is 46 bps INFO @ Mon, 06 Nov 2017 11:55:24: #2 alternative fragment length(s) may be 2,46 bps INFO @ Mon, 06 Nov 2017 11:55:24: #2.2 Generate R script for model : SRX2458934.10_model.r WARNING @ Mon, 06 Nov 2017 11:55:24: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:55:24: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Mon, 06 Nov 2017 11:55:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:55:24: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:55:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:55:24: 11000000 INFO @ Mon, 06 Nov 2017 11:55:24: 11000000 INFO @ Mon, 06 Nov 2017 11:55:29: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:55:29: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:55:29: #1 total tags in treatment: 11600261 INFO @ Mon, 06 Nov 2017 11:55:29: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:55:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:55:29: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:55:29: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:55:29: #1 total tags in treatment: 11600261 INFO @ Mon, 06 Nov 2017 11:55:29: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:55:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:55:29: #1 tags after filtering in treatment: 11600261 INFO @ Mon, 06 Nov 2017 11:55:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:55:29: #1 finished! INFO @ Mon, 06 Nov 2017 11:55:29: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:55:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:55:29: #1 tags after filtering in treatment: 11600261 INFO @ Mon, 06 Nov 2017 11:55:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:55:29: #1 finished! INFO @ Mon, 06 Nov 2017 11:55:29: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:55:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:55:30: #2 number of paired peaks: 932 WARNING @ Mon, 06 Nov 2017 11:55:30: Fewer paired peaks (932) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 932 pairs to build model! INFO @ Mon, 06 Nov 2017 11:55:30: start model_add_line... INFO @ Mon, 06 Nov 2017 11:55:30: #2 number of paired peaks: 932 WARNING @ Mon, 06 Nov 2017 11:55:30: Fewer paired peaks (932) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 932 pairs to build model! INFO @ Mon, 06 Nov 2017 11:55:30: start model_add_line... INFO @ Mon, 06 Nov 2017 11:55:30: start X-correlation... INFO @ Mon, 06 Nov 2017 11:55:30: end of X-cor INFO @ Mon, 06 Nov 2017 11:55:30: #2 finished! INFO @ Mon, 06 Nov 2017 11:55:30: #2 predicted fragment length is 46 bps INFO @ Mon, 06 Nov 2017 11:55:30: #2 alternative fragment length(s) may be 2,46 bps INFO @ Mon, 06 Nov 2017 11:55:30: #2.2 Generate R script for model : SRX2458934.20_model.r WARNING @ Mon, 06 Nov 2017 11:55:30: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:55:30: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Mon, 06 Nov 2017 11:55:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:55:30: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:55:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:55:30: start X-correlation... INFO @ Mon, 06 Nov 2017 11:55:30: end of X-cor INFO @ Mon, 06 Nov 2017 11:55:30: #2 finished! INFO @ Mon, 06 Nov 2017 11:55:30: #2 predicted fragment length is 46 bps INFO @ Mon, 06 Nov 2017 11:55:30: #2 alternative fragment length(s) may be 2,46 bps INFO @ Mon, 06 Nov 2017 11:55:30: #2.2 Generate R script for model : SRX2458934.05_model.r WARNING @ Mon, 06 Nov 2017 11:55:30: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:55:30: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Mon, 06 Nov 2017 11:55:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:55:30: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:55:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:55:50: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:55:54: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:55:54: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:56:04: #4 Write output xls file... SRX2458934.10_peaks.xls INFO @ Mon, 06 Nov 2017 11:56:04: #4 Write peak in narrowPeak format file... SRX2458934.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:56:04: #4 Write summits bed file... SRX2458934.10_summits.bed INFO @ Mon, 06 Nov 2017 11:56:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1608 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:56:08: #4 Write output xls file... SRX2458934.05_peaks.xls INFO @ Mon, 06 Nov 2017 11:56:08: #4 Write peak in narrowPeak format file... SRX2458934.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:56:08: #4 Write summits bed file... SRX2458934.05_summits.bed INFO @ Mon, 06 Nov 2017 11:56:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2875 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:56:10: #4 Write output xls file... SRX2458934.20_peaks.xls INFO @ Mon, 06 Nov 2017 11:56:10: #4 Write peak in narrowPeak format file... SRX2458934.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:56:10: #4 Write summits bed file... SRX2458934.20_summits.bed INFO @ Mon, 06 Nov 2017 11:56:10: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (572 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。