Job ID = 10924617 sra ファイルのダウンロード中... Completed: 709957K bytes transferred in 15 seconds (373866K 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 32523795 spots for /home/okishinya/chipatlas/results/dm3/SRX2399657/SRR5081491.sra Written 32523795 spots for /home/okishinya/chipatlas/results/dm3/SRX2399657/SRR5081491.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: 00:11:53 32523795 reads; of these: 32523795 (100.00%) were unpaired; of these: 14908874 (45.84%) aligned 0 times 10554572 (32.45%) aligned exactly 1 time 7060349 (21.71%) aligned >1 times 54.16% overall alignment rate Time searching: 00:11:53 Overall time: 00:11:53 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] 4458729 / 17614921 = 0.2531 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 Aug 2018 10:44:36: # Command line: callpeak -t SRX2399657.bam -f BAM -g dm -n SRX2399657.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2399657.20 # format = BAM # ChIP-seq file = ['SRX2399657.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 Aug 2018 10:44:36: # Command line: callpeak -t SRX2399657.bam -f BAM -g dm -n SRX2399657.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2399657.10 # format = BAM # ChIP-seq file = ['SRX2399657.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 Aug 2018 10:44:36: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:44:36: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:44:36: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:44:36: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:44:36: # Command line: callpeak -t SRX2399657.bam -f BAM -g dm -n SRX2399657.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2399657.05 # format = BAM # ChIP-seq file = ['SRX2399657.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 Aug 2018 10:44:36: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:44:36: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:44:42: 1000000 INFO @ Mon, 06 Aug 2018 10:44:42: 1000000 INFO @ Mon, 06 Aug 2018 10:44:42: 1000000 INFO @ Mon, 06 Aug 2018 10:44:48: 2000000 INFO @ Mon, 06 Aug 2018 10:44:48: 2000000 INFO @ Mon, 06 Aug 2018 10:44:48: 2000000 INFO @ Mon, 06 Aug 2018 10:44:54: 3000000 INFO @ Mon, 06 Aug 2018 10:44:54: 3000000 INFO @ Mon, 06 Aug 2018 10:44:54: 3000000 INFO @ Mon, 06 Aug 2018 10:44:59: 4000000 INFO @ Mon, 06 Aug 2018 10:45:00: 4000000 INFO @ Mon, 06 Aug 2018 10:45:00: 4000000 INFO @ Mon, 06 Aug 2018 10:45:05: 5000000 INFO @ Mon, 06 Aug 2018 10:45:06: 5000000 INFO @ Mon, 06 Aug 2018 10:45:06: 5000000 INFO @ Mon, 06 Aug 2018 10:45:11: 6000000 INFO @ Mon, 06 Aug 2018 10:45:12: 6000000 INFO @ Mon, 06 Aug 2018 10:45:12: 6000000 INFO @ Mon, 06 Aug 2018 10:45:17: 7000000 INFO @ Mon, 06 Aug 2018 10:45:18: 7000000 INFO @ Mon, 06 Aug 2018 10:45:18: 7000000 INFO @ Mon, 06 Aug 2018 10:45:23: 8000000 INFO @ Mon, 06 Aug 2018 10:45:24: 8000000 INFO @ Mon, 06 Aug 2018 10:45:24: 8000000 INFO @ Mon, 06 Aug 2018 10:45:29: 9000000 INFO @ Mon, 06 Aug 2018 10:45:30: 9000000 INFO @ Mon, 06 Aug 2018 10:45:30: 9000000 INFO @ Mon, 06 Aug 2018 10:45:35: 10000000 INFO @ Mon, 06 Aug 2018 10:45:36: 10000000 INFO @ Mon, 06 Aug 2018 10:45:36: 10000000 INFO @ Mon, 06 Aug 2018 10:45:40: 11000000 INFO @ Mon, 06 Aug 2018 10:45:42: 11000000 INFO @ Mon, 06 Aug 2018 10:45:43: 11000000 INFO @ Mon, 06 Aug 2018 10:45:46: 12000000 INFO @ Mon, 06 Aug 2018 10:45:48: 12000000 INFO @ Mon, 06 Aug 2018 10:45:49: 12000000 INFO @ Mon, 06 Aug 2018 10:45:53: 13000000 INFO @ Mon, 06 Aug 2018 10:45:54: #1 tag size is determined as 51 bps INFO @ Mon, 06 Aug 2018 10:45:54: #1 tag size = 51 INFO @ Mon, 06 Aug 2018 10:45:54: #1 total tags in treatment: 13156192 INFO @ Mon, 06 Aug 2018 10:45:54: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:45:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:45:54: 13000000 INFO @ Mon, 06 Aug 2018 10:45:54: #1 tags after filtering in treatment: 13156192 INFO @ Mon, 06 Aug 2018 10:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:45:54: #1 finished! INFO @ Mon, 06 Aug 2018 10:45:54: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:45:55: #1 tag size is determined as 51 bps INFO @ Mon, 06 Aug 2018 10:45:55: #1 tag size = 51 INFO @ Mon, 06 Aug 2018 10:45:55: #1 total tags in treatment: 13156192 INFO @ Mon, 06 Aug 2018 10:45:55: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:45:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:45:55: 13000000 INFO @ Mon, 06 Aug 2018 10:45:55: #2 number of paired peaks: 615 WARNING @ Mon, 06 Aug 2018 10:45:55: Fewer paired peaks (615) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 615 pairs to build model! INFO @ Mon, 06 Aug 2018 10:45:55: start model_add_line... INFO @ Mon, 06 Aug 2018 10:45:55: #1 tags after filtering in treatment: 13156192 INFO @ Mon, 06 Aug 2018 10:45:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:45:55: #1 finished! INFO @ Mon, 06 Aug 2018 10:45:55: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:45:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:45:55: start X-correlation... INFO @ Mon, 06 Aug 2018 10:45:55: end of X-cor INFO @ Mon, 06 Aug 2018 10:45:55: #2 finished! INFO @ Mon, 06 Aug 2018 10:45:55: #2 predicted fragment length is 46 bps INFO @ Mon, 06 Aug 2018 10:45:55: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 06 Aug 2018 10:45:55: #2.2 Generate R script for model : SRX2399657.10_model.r WARNING @ Mon, 06 Aug 2018 10:45:55: #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 Aug 2018 10:45:55: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 06 Aug 2018 10:45:55: #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 Aug 2018 10:45:55: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:45:56: #1 tag size is determined as 51 bps INFO @ Mon, 06 Aug 2018 10:45:56: #1 tag size = 51 INFO @ Mon, 06 Aug 2018 10:45:56: #1 total tags in treatment: 13156192 INFO @ Mon, 06 Aug 2018 10:45:56: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:45:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:45:56: #2 number of paired peaks: 615 WARNING @ Mon, 06 Aug 2018 10:45:56: Fewer paired peaks (615) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 615 pairs to build model! INFO @ Mon, 06 Aug 2018 10:45:56: start model_add_line... INFO @ Mon, 06 Aug 2018 10:45:56: start X-correlation... INFO @ Mon, 06 Aug 2018 10:45:56: end of X-cor INFO @ Mon, 06 Aug 2018 10:45:56: #2 finished! INFO @ Mon, 06 Aug 2018 10:45:56: #2 predicted fragment length is 46 bps INFO @ Mon, 06 Aug 2018 10:45:56: #1 tags after filtering in treatment: 13156192 INFO @ Mon, 06 Aug 2018 10:45:56: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 06 Aug 2018 10:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:45:56: #2.2 Generate R script for model : SRX2399657.20_model.r INFO @ Mon, 06 Aug 2018 10:45:56: #1 finished! INFO @ Mon, 06 Aug 2018 10:45:56: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:45:56: #2 looking for paired plus/minus strand peaks... WARNING @ Mon, 06 Aug 2018 10:45:56: #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 Aug 2018 10:45:56: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 06 Aug 2018 10:45:56: #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 Aug 2018 10:45:56: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:45:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:45:57: #2 number of paired peaks: 615 WARNING @ Mon, 06 Aug 2018 10:45:57: Fewer paired peaks (615) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 615 pairs to build model! INFO @ Mon, 06 Aug 2018 10:45:57: start model_add_line... INFO @ Mon, 06 Aug 2018 10:45:57: start X-correlation... INFO @ Mon, 06 Aug 2018 10:45:57: end of X-cor INFO @ Mon, 06 Aug 2018 10:45:57: #2 finished! INFO @ Mon, 06 Aug 2018 10:45:57: #2 predicted fragment length is 46 bps INFO @ Mon, 06 Aug 2018 10:45:57: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 06 Aug 2018 10:45:57: #2.2 Generate R script for model : SRX2399657.05_model.r WARNING @ Mon, 06 Aug 2018 10:45:57: #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 Aug 2018 10:45:57: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 06 Aug 2018 10:45:57: #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 Aug 2018 10:45:57: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:45:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:46:23: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:46:25: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:46:25: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:46:40: #4 Write output xls file... SRX2399657.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:46:40: #4 Write peak in narrowPeak format file... SRX2399657.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:46:40: #4 Write summits bed file... SRX2399657.10_summits.bed INFO @ Mon, 06 Aug 2018 10:46:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1794 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:46:40: #4 Write output xls file... SRX2399657.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:46:40: #4 Write peak in narrowPeak format file... SRX2399657.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:46:40: #4 Write summits bed file... SRX2399657.20_summits.bed INFO @ Mon, 06 Aug 2018 10:46:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1377 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:46:42: #4 Write output xls file... SRX2399657.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:46:42: #4 Write peak in narrowPeak format file... SRX2399657.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:46:42: #4 Write summits bed file... SRX2399657.05_summits.bed INFO @ Mon, 06 Aug 2018 10:46:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2586 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。