Job ID = 10480731 sra ファイルのダウンロード中... Completed: 162384K bytes transferred in 12 seconds (104951K 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 8883488 spots for /home/okishinya/chipatlas/results/dm3/SRX3380790/SRR6278153.sra Written 8883488 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: 00:05:38 8883488 reads; of these: 8883488 (100.00%) were unpaired; of these: 1032742 (11.63%) aligned 0 times 4020591 (45.26%) aligned exactly 1 time 3830155 (43.12%) aligned >1 times 88.37% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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] 2051538 / 7850746 = 0.2613 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 @ Fri, 16 Mar 2018 07:52:03: # Command line: callpeak -t SRX3380790.bam -f BAM -g dm -n SRX3380790.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380790.05 # format = BAM # ChIP-seq file = ['SRX3380790.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 @ Fri, 16 Mar 2018 07:52:03: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:52:03: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:52:03: # Command line: callpeak -t SRX3380790.bam -f BAM -g dm -n SRX3380790.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380790.20 # format = BAM # ChIP-seq file = ['SRX3380790.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 @ Fri, 16 Mar 2018 07:52:03: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:52:03: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:52:03: # Command line: callpeak -t SRX3380790.bam -f BAM -g dm -n SRX3380790.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380790.10 # format = BAM # ChIP-seq file = ['SRX3380790.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 @ Fri, 16 Mar 2018 07:52:03: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:52:03: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:52:10: 1000000 INFO @ Fri, 16 Mar 2018 07:52:10: 1000000 INFO @ Fri, 16 Mar 2018 07:52:10: 1000000 INFO @ Fri, 16 Mar 2018 07:52:16: 2000000 INFO @ Fri, 16 Mar 2018 07:52:17: 2000000 INFO @ Fri, 16 Mar 2018 07:52:17: 2000000 INFO @ Fri, 16 Mar 2018 07:52:23: 3000000 INFO @ Fri, 16 Mar 2018 07:52:24: 3000000 INFO @ Fri, 16 Mar 2018 07:52:24: 3000000 INFO @ Fri, 16 Mar 2018 07:52:29: 4000000 INFO @ Fri, 16 Mar 2018 07:52:31: 4000000 INFO @ Fri, 16 Mar 2018 07:52:31: 4000000 INFO @ Fri, 16 Mar 2018 07:52:36: 5000000 INFO @ Fri, 16 Mar 2018 07:52:38: 5000000 INFO @ Fri, 16 Mar 2018 07:52:38: 5000000 INFO @ Fri, 16 Mar 2018 07:52:41: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:52:41: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:52:41: #1 total tags in treatment: 5799208 INFO @ Fri, 16 Mar 2018 07:52:41: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:52:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:52:41: #1 tags after filtering in treatment: 5799208 INFO @ Fri, 16 Mar 2018 07:52:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:52:41: #1 finished! INFO @ Fri, 16 Mar 2018 07:52:41: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:52:42: #2 number of paired peaks: 731 WARNING @ Fri, 16 Mar 2018 07:52:42: Fewer paired peaks (731) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 731 pairs to build model! INFO @ Fri, 16 Mar 2018 07:52:42: start model_add_line... INFO @ Fri, 16 Mar 2018 07:52:42: start X-correlation... INFO @ Fri, 16 Mar 2018 07:52:42: end of X-cor INFO @ Fri, 16 Mar 2018 07:52:42: #2 finished! INFO @ Fri, 16 Mar 2018 07:52:42: #2 predicted fragment length is 50 bps INFO @ Fri, 16 Mar 2018 07:52:42: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 16 Mar 2018 07:52:42: #2.2 Generate R script for model : SRX3380790.10_model.r WARNING @ Fri, 16 Mar 2018 07:52:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:52:42: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 16 Mar 2018 07:52:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:52:42: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:52:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:52:43: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:52:43: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:52:43: #1 total tags in treatment: 5799208 INFO @ Fri, 16 Mar 2018 07:52:43: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:52:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:52:43: #1 tags after filtering in treatment: 5799208 INFO @ Fri, 16 Mar 2018 07:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:52:43: #1 finished! INFO @ Fri, 16 Mar 2018 07:52:43: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:52:43: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:52:43: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:52:43: #1 total tags in treatment: 5799208 INFO @ Fri, 16 Mar 2018 07:52:43: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:52:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:52:43: #1 tags after filtering in treatment: 5799208 INFO @ Fri, 16 Mar 2018 07:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:52:43: #1 finished! INFO @ Fri, 16 Mar 2018 07:52:43: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:52:44: #2 number of paired peaks: 731 WARNING @ Fri, 16 Mar 2018 07:52:44: Fewer paired peaks (731) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 731 pairs to build model! INFO @ Fri, 16 Mar 2018 07:52:44: start model_add_line... INFO @ Fri, 16 Mar 2018 07:52:44: start X-correlation... INFO @ Fri, 16 Mar 2018 07:52:44: end of X-cor INFO @ Fri, 16 Mar 2018 07:52:44: #2 finished! INFO @ Fri, 16 Mar 2018 07:52:44: #2 predicted fragment length is 50 bps INFO @ Fri, 16 Mar 2018 07:52:44: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 16 Mar 2018 07:52:44: #2.2 Generate R script for model : SRX3380790.20_model.r WARNING @ Fri, 16 Mar 2018 07:52:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:52:44: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 16 Mar 2018 07:52:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:52:44: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:52:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:52:44: #2 number of paired peaks: 731 WARNING @ Fri, 16 Mar 2018 07:52:44: Fewer paired peaks (731) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 731 pairs to build model! INFO @ Fri, 16 Mar 2018 07:52:44: start model_add_line... INFO @ Fri, 16 Mar 2018 07:52:44: start X-correlation... INFO @ Fri, 16 Mar 2018 07:52:44: end of X-cor INFO @ Fri, 16 Mar 2018 07:52:44: #2 finished! INFO @ Fri, 16 Mar 2018 07:52:44: #2 predicted fragment length is 50 bps INFO @ Fri, 16 Mar 2018 07:52:44: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 16 Mar 2018 07:52:44: #2.2 Generate R script for model : SRX3380790.05_model.r WARNING @ Fri, 16 Mar 2018 07:52:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:52:44: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 16 Mar 2018 07:52:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:52:44: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:52:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:52:55: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:52:57: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:52:58: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:53:02: #4 Write output xls file... SRX3380790.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:53:02: #4 Write peak in narrowPeak format file... SRX3380790.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:53:02: #4 Write summits bed file... SRX3380790.10_summits.bed INFO @ Fri, 16 Mar 2018 07:53:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1538 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:53:03: #4 Write output xls file... SRX3380790.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:53:03: #4 Write peak in narrowPeak format file... SRX3380790.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:53:03: #4 Write summits bed file... SRX3380790.20_summits.bed INFO @ Fri, 16 Mar 2018 07:53:03: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (963 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:53:04: #4 Write output xls file... SRX3380790.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:53:04: #4 Write peak in narrowPeak format file... SRX3380790.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:53:04: #4 Write summits bed file... SRX3380790.05_summits.bed INFO @ Fri, 16 Mar 2018 07:53:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2113 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。