Job ID = 10320346 sra ファイルのダウンロード中... Completed: 105281K bytes transferred in 19 seconds (43429K 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 6380089 spots for /home/okishinya/chipatlas/results/dm3/SRX3270983/SRR6159394.sra Written 6380089 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:36 6380089 reads; of these: 6380089 (100.00%) were unpaired; of these: 245687 (3.85%) aligned 0 times 3805138 (59.64%) aligned exactly 1 time 2329264 (36.51%) aligned >1 times 96.15% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:37 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_rmdupse_core] 360070 / 6134402 = 0.0587 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 @ Thu, 11 Jan 2018 02:09:15: # Command line: callpeak -t SRX3270983.bam -f BAM -g dm -n SRX3270983.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3270983.10 # format = BAM # ChIP-seq file = ['SRX3270983.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 @ Thu, 11 Jan 2018 02:09:15: # Command line: callpeak -t SRX3270983.bam -f BAM -g dm -n SRX3270983.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3270983.20 # format = BAM # ChIP-seq file = ['SRX3270983.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 @ Thu, 11 Jan 2018 02:09:15: # Command line: callpeak -t SRX3270983.bam -f BAM -g dm -n SRX3270983.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3270983.05 # format = BAM # ChIP-seq file = ['SRX3270983.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 @ Thu, 11 Jan 2018 02:09:15: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:09:15: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:09:15: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:09:15: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:09:15: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:09:15: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:09:21: 1000000 INFO @ Thu, 11 Jan 2018 02:09:21: 1000000 INFO @ Thu, 11 Jan 2018 02:09:21: 1000000 INFO @ Thu, 11 Jan 2018 02:09:27: 2000000 INFO @ Thu, 11 Jan 2018 02:09:27: 2000000 INFO @ Thu, 11 Jan 2018 02:09:27: 2000000 INFO @ Thu, 11 Jan 2018 02:09:33: 3000000 INFO @ Thu, 11 Jan 2018 02:09:33: 3000000 INFO @ Thu, 11 Jan 2018 02:09:33: 3000000 INFO @ Thu, 11 Jan 2018 02:09:39: 4000000 INFO @ Thu, 11 Jan 2018 02:09:39: 4000000 INFO @ Thu, 11 Jan 2018 02:09:39: 4000000 INFO @ Thu, 11 Jan 2018 02:09:45: 5000000 INFO @ Thu, 11 Jan 2018 02:09:45: 5000000 INFO @ Thu, 11 Jan 2018 02:09:46: 5000000 INFO @ Thu, 11 Jan 2018 02:09:50: #1 tag size is determined as 33 bps INFO @ Thu, 11 Jan 2018 02:09:50: #1 tag size = 33 INFO @ Thu, 11 Jan 2018 02:09:50: #1 total tags in treatment: 5774332 INFO @ Thu, 11 Jan 2018 02:09:50: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:09:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:09:50: #1 tag size is determined as 33 bps INFO @ Thu, 11 Jan 2018 02:09:50: #1 tag size = 33 INFO @ Thu, 11 Jan 2018 02:09:50: #1 total tags in treatment: 5774332 INFO @ Thu, 11 Jan 2018 02:09:50: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:09:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:09:50: #1 tags after filtering in treatment: 5774332 INFO @ Thu, 11 Jan 2018 02:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:09:50: #1 finished! INFO @ Thu, 11 Jan 2018 02:09:50: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:09:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:09:50: #1 tags after filtering in treatment: 5774332 INFO @ Thu, 11 Jan 2018 02:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:09:50: #1 finished! INFO @ Thu, 11 Jan 2018 02:09:50: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:09:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:09:50: #2 number of paired peaks: 551 WARNING @ Thu, 11 Jan 2018 02:09:50: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Thu, 11 Jan 2018 02:09:50: start model_add_line... INFO @ Thu, 11 Jan 2018 02:09:50: start X-correlation... INFO @ Thu, 11 Jan 2018 02:09:50: #2 number of paired peaks: 551 WARNING @ Thu, 11 Jan 2018 02:09:50: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Thu, 11 Jan 2018 02:09:50: start model_add_line... INFO @ Thu, 11 Jan 2018 02:09:50: start X-correlation... INFO @ Thu, 11 Jan 2018 02:09:51: end of X-cor INFO @ Thu, 11 Jan 2018 02:09:51: end of X-cor INFO @ Thu, 11 Jan 2018 02:09:51: #2 finished! INFO @ Thu, 11 Jan 2018 02:09:51: #2 finished! INFO @ Thu, 11 Jan 2018 02:09:51: #2 predicted fragment length is 32 bps INFO @ Thu, 11 Jan 2018 02:09:51: #2 predicted fragment length is 32 bps INFO @ Thu, 11 Jan 2018 02:09:51: #2 alternative fragment length(s) may be 32 bps INFO @ Thu, 11 Jan 2018 02:09:51: #2 alternative fragment length(s) may be 32 bps INFO @ Thu, 11 Jan 2018 02:09:51: #2.2 Generate R script for model : SRX3270983.20_model.r INFO @ Thu, 11 Jan 2018 02:09:51: #2.2 Generate R script for model : SRX3270983.05_model.r WARNING @ Thu, 11 Jan 2018 02:09:51: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:09:51: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Thu, 11 Jan 2018 02:09:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Thu, 11 Jan 2018 02:09:51: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Thu, 11 Jan 2018 02:09:51: #3 Call peaks... WARNING @ Thu, 11 Jan 2018 02:09:51: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Thu, 11 Jan 2018 02:09:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:09:51: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:09:51: #1 tag size is determined as 33 bps INFO @ Thu, 11 Jan 2018 02:09:51: #1 tag size = 33 INFO @ Thu, 11 Jan 2018 02:09:51: #1 total tags in treatment: 5774332 INFO @ Thu, 11 Jan 2018 02:09:51: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:09:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:09:51: #1 tags after filtering in treatment: 5774332 INFO @ Thu, 11 Jan 2018 02:09:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:09:51: #1 finished! INFO @ Thu, 11 Jan 2018 02:09:51: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:09:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:09:51: #2 number of paired peaks: 551 WARNING @ Thu, 11 Jan 2018 02:09:51: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Thu, 11 Jan 2018 02:09:51: start model_add_line... INFO @ Thu, 11 Jan 2018 02:09:51: start X-correlation... INFO @ Thu, 11 Jan 2018 02:09:51: end of X-cor INFO @ Thu, 11 Jan 2018 02:09:51: #2 finished! INFO @ Thu, 11 Jan 2018 02:09:51: #2 predicted fragment length is 32 bps INFO @ Thu, 11 Jan 2018 02:09:51: #2 alternative fragment length(s) may be 32 bps INFO @ Thu, 11 Jan 2018 02:09:51: #2.2 Generate R script for model : SRX3270983.10_model.r WARNING @ Thu, 11 Jan 2018 02:09:51: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:09:51: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Thu, 11 Jan 2018 02:09:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:09:51: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:10:04: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:10:04: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:10:04: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:10:11: #4 Write output xls file... SRX3270983.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:10:11: #4 Write peak in narrowPeak format file... SRX3270983.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:10:11: #4 Write summits bed file... SRX3270983.10_summits.bed INFO @ Thu, 11 Jan 2018 02:10:11: Done! INFO @ Thu, 11 Jan 2018 02:10:12: #4 Write output xls file... SRX3270983.20_peaks.xls pass1 - making usageList (8 chroms): 1 millis INFO @ Thu, 11 Jan 2018 02:10:12: #4 Write peak in narrowPeak format file... SRX3270983.20_peaks.narrowPeak pass2 - checking and writing primary data (1271 records, 4 fields): 4 millis INFO @ Thu, 11 Jan 2018 02:10:12: #4 Write summits bed file... SRX3270983.20_summits.bed CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:10:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (785 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:10:12: #4 Write output xls file... SRX3270983.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:10:12: #4 Write peak in narrowPeak format file... SRX3270983.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:10:12: #4 Write summits bed file... SRX3270983.05_summits.bed INFO @ Thu, 11 Jan 2018 02:10:12: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1622 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。