Job ID = 10845183 sra ファイルのダウンロード中... Completed: 148078K bytes transferred in 12 seconds (98396K 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 3401169 spots for /home/okishinya/chipatlas/results/dm3/SRX2642399/SRR5345739.sra Written 3401169 spots for /home/okishinya/chipatlas/results/dm3/SRX2642399/SRR5345739.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: 00:01:54 3401169 reads; of these: 3401169 (100.00%) were unpaired; of these: 613263 (18.03%) aligned 0 times 2068098 (60.81%) aligned exactly 1 time 719808 (21.16%) aligned >1 times 81.97% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 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] 60622 / 2787906 = 0.0217 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 @ Wed, 04 Jul 2018 09:29:32: # Command line: callpeak -t SRX2642399.bam -f BAM -g dm -n SRX2642399.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2642399.20 # format = BAM # ChIP-seq file = ['SRX2642399.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 @ Wed, 04 Jul 2018 09:29:32: # Command line: callpeak -t SRX2642399.bam -f BAM -g dm -n SRX2642399.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2642399.05 # format = BAM # ChIP-seq file = ['SRX2642399.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 @ Wed, 04 Jul 2018 09:29:32: # Command line: callpeak -t SRX2642399.bam -f BAM -g dm -n SRX2642399.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2642399.10 # format = BAM # ChIP-seq file = ['SRX2642399.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 @ Wed, 04 Jul 2018 09:29:32: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:29:32: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:29:32: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:29:32: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:29:32: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:29:32: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:29:40: 1000000 INFO @ Wed, 04 Jul 2018 09:29:40: 1000000 INFO @ Wed, 04 Jul 2018 09:29:40: 1000000 INFO @ Wed, 04 Jul 2018 09:29:48: 2000000 INFO @ Wed, 04 Jul 2018 09:29:48: 2000000 INFO @ Wed, 04 Jul 2018 09:29:48: 2000000 INFO @ Wed, 04 Jul 2018 09:29:53: #1 tag size is determined as 89 bps INFO @ Wed, 04 Jul 2018 09:29:53: #1 tag size = 89 INFO @ Wed, 04 Jul 2018 09:29:53: #1 total tags in treatment: 2727284 INFO @ Wed, 04 Jul 2018 09:29:53: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:29:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:29:53: #1 tags after filtering in treatment: 2727284 INFO @ Wed, 04 Jul 2018 09:29:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:29:53: #1 finished! INFO @ Wed, 04 Jul 2018 09:29:53: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:29:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:29:54: #1 tag size is determined as 89 bps INFO @ Wed, 04 Jul 2018 09:29:54: #1 tag size = 89 INFO @ Wed, 04 Jul 2018 09:29:54: #1 total tags in treatment: 2727284 INFO @ Wed, 04 Jul 2018 09:29:54: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:29:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:29:54: #1 tag size is determined as 89 bps INFO @ Wed, 04 Jul 2018 09:29:54: #1 tag size = 89 INFO @ Wed, 04 Jul 2018 09:29:54: #1 total tags in treatment: 2727284 INFO @ Wed, 04 Jul 2018 09:29:54: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:29:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:29:54: #1 tags after filtering in treatment: 2727284 INFO @ Wed, 04 Jul 2018 09:29:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:29:54: #1 finished! INFO @ Wed, 04 Jul 2018 09:29:54: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:29:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:29:54: #2 number of paired peaks: 201 WARNING @ Wed, 04 Jul 2018 09:29:54: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Wed, 04 Jul 2018 09:29:54: start model_add_line... INFO @ Wed, 04 Jul 2018 09:29:54: start X-correlation... INFO @ Wed, 04 Jul 2018 09:29:54: #1 tags after filtering in treatment: 2727284 INFO @ Wed, 04 Jul 2018 09:29:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:29:54: #1 finished! INFO @ Wed, 04 Jul 2018 09:29:54: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:29:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:29:54: #2 number of paired peaks: 201 WARNING @ Wed, 04 Jul 2018 09:29:54: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Wed, 04 Jul 2018 09:29:54: start model_add_line... INFO @ Wed, 04 Jul 2018 09:29:54: start X-correlation... INFO @ Wed, 04 Jul 2018 09:29:54: end of X-cor INFO @ Wed, 04 Jul 2018 09:29:54: end of X-cor INFO @ Wed, 04 Jul 2018 09:29:54: #2 finished! INFO @ Wed, 04 Jul 2018 09:29:54: #2 finished! INFO @ Wed, 04 Jul 2018 09:29:54: #2 predicted fragment length is 94 bps INFO @ Wed, 04 Jul 2018 09:29:54: #2 predicted fragment length is 94 bps INFO @ Wed, 04 Jul 2018 09:29:54: #2 alternative fragment length(s) may be 94 bps INFO @ Wed, 04 Jul 2018 09:29:54: #2 alternative fragment length(s) may be 94 bps INFO @ Wed, 04 Jul 2018 09:29:54: #2.2 Generate R script for model : SRX2642399.20_model.r INFO @ Wed, 04 Jul 2018 09:29:54: #2.2 Generate R script for model : SRX2642399.05_model.r WARNING @ Wed, 04 Jul 2018 09:29:54: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:29:54: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Wed, 04 Jul 2018 09:29:54: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:29:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Wed, 04 Jul 2018 09:29:54: #2 You may need to consider one of the other alternative d(s): 94 INFO @ Wed, 04 Jul 2018 09:29:54: #3 Call peaks... WARNING @ Wed, 04 Jul 2018 09:29:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:29:54: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:29:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:29:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:29:54: #2 number of paired peaks: 201 WARNING @ Wed, 04 Jul 2018 09:29:54: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Wed, 04 Jul 2018 09:29:54: start model_add_line... INFO @ Wed, 04 Jul 2018 09:29:54: start X-correlation... INFO @ Wed, 04 Jul 2018 09:29:54: end of X-cor INFO @ Wed, 04 Jul 2018 09:29:54: #2 finished! INFO @ Wed, 04 Jul 2018 09:29:54: #2 predicted fragment length is 94 bps INFO @ Wed, 04 Jul 2018 09:29:54: #2 alternative fragment length(s) may be 94 bps INFO @ Wed, 04 Jul 2018 09:29:54: #2.2 Generate R script for model : SRX2642399.10_model.r WARNING @ Wed, 04 Jul 2018 09:29:54: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:29:54: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Wed, 04 Jul 2018 09:29:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:29:54: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:29:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:30:00: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:30:01: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:30:01: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:30:04: #4 Write output xls file... SRX2642399.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:30:04: #4 Write peak in narrowPeak format file... SRX2642399.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:30:04: #4 Write summits bed file... SRX2642399.20_summits.bed INFO @ Wed, 04 Jul 2018 09:30:04: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (180 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:30:04: #4 Write output xls file... SRX2642399.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:30:04: #4 Write peak in narrowPeak format file... SRX2642399.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:30:04: #4 Write summits bed file... SRX2642399.10_summits.bed INFO @ Wed, 04 Jul 2018 09:30:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (323 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:30:04: #4 Write output xls file... SRX2642399.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:30:04: #4 Write peak in narrowPeak format file... SRX2642399.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:30:04: #4 Write summits bed file... SRX2642399.05_summits.bed INFO @ Wed, 04 Jul 2018 09:30:04: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (502 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。