Job ID = 10450714 sra ファイルのダウンロード中... Completed: 370325K bytes transferred in 9 seconds (323812K 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 19218421 spots for /home/okishinya/chipatlas/results/dm3/SRX3404009/SRR6303486.sra Written 19218421 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: 00:07:24 19218421 reads; of these: 19218421 (100.00%) were unpaired; of these: 472295 (2.46%) aligned 0 times 13768569 (71.64%) aligned exactly 1 time 4977557 (25.90%) aligned >1 times 97.54% overall alignment rate Time searching: 00:07:24 Overall time: 00:07:24 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] 1610081 / 18746126 = 0.0859 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, 07 Feb 2018 10:12:23: # Command line: callpeak -t SRX3404009.bam -f BAM -g dm -n SRX3404009.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404009.05 # format = BAM # ChIP-seq file = ['SRX3404009.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, 07 Feb 2018 10:12:23: #1 read tag files... INFO @ Wed, 07 Feb 2018 10:12:23: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 10:12:23: # Command line: callpeak -t SRX3404009.bam -f BAM -g dm -n SRX3404009.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404009.10 # format = BAM # ChIP-seq file = ['SRX3404009.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, 07 Feb 2018 10:12:23: #1 read tag files... INFO @ Wed, 07 Feb 2018 10:12:23: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 10:12:23: # Command line: callpeak -t SRX3404009.bam -f BAM -g dm -n SRX3404009.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404009.20 # format = BAM # ChIP-seq file = ['SRX3404009.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, 07 Feb 2018 10:12:23: #1 read tag files... INFO @ Wed, 07 Feb 2018 10:12:23: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 10:12:31: 1000000 INFO @ Wed, 07 Feb 2018 10:12:31: 1000000 INFO @ Wed, 07 Feb 2018 10:12:31: 1000000 INFO @ Wed, 07 Feb 2018 10:12:40: 2000000 INFO @ Wed, 07 Feb 2018 10:12:40: 2000000 INFO @ Wed, 07 Feb 2018 10:12:40: 2000000 INFO @ Wed, 07 Feb 2018 10:12:48: 3000000 INFO @ Wed, 07 Feb 2018 10:12:48: 3000000 INFO @ Wed, 07 Feb 2018 10:12:48: 3000000 INFO @ Wed, 07 Feb 2018 10:12:56: 4000000 INFO @ Wed, 07 Feb 2018 10:12:56: 4000000 INFO @ Wed, 07 Feb 2018 10:12:56: 4000000 INFO @ Wed, 07 Feb 2018 10:13:04: 5000000 INFO @ Wed, 07 Feb 2018 10:13:04: 5000000 INFO @ Wed, 07 Feb 2018 10:13:04: 5000000 INFO @ Wed, 07 Feb 2018 10:13:12: 6000000 INFO @ Wed, 07 Feb 2018 10:13:12: 6000000 INFO @ Wed, 07 Feb 2018 10:13:12: 6000000 INFO @ Wed, 07 Feb 2018 10:13:20: 7000000 INFO @ Wed, 07 Feb 2018 10:13:20: 7000000 INFO @ Wed, 07 Feb 2018 10:13:20: 7000000 INFO @ Wed, 07 Feb 2018 10:13:28: 8000000 INFO @ Wed, 07 Feb 2018 10:13:28: 8000000 INFO @ Wed, 07 Feb 2018 10:13:28: 8000000 INFO @ Wed, 07 Feb 2018 10:13:36: 9000000 INFO @ Wed, 07 Feb 2018 10:13:36: 9000000 INFO @ Wed, 07 Feb 2018 10:13:36: 9000000 INFO @ Wed, 07 Feb 2018 10:13:44: 10000000 INFO @ Wed, 07 Feb 2018 10:13:44: 10000000 INFO @ Wed, 07 Feb 2018 10:13:44: 10000000 INFO @ Wed, 07 Feb 2018 10:13:52: 11000000 INFO @ Wed, 07 Feb 2018 10:13:52: 11000000 INFO @ Wed, 07 Feb 2018 10:13:52: 11000000 INFO @ Wed, 07 Feb 2018 10:14:00: 12000000 INFO @ Wed, 07 Feb 2018 10:14:00: 12000000 INFO @ Wed, 07 Feb 2018 10:14:00: 12000000 INFO @ Wed, 07 Feb 2018 10:14:08: 13000000 INFO @ Wed, 07 Feb 2018 10:14:08: 13000000 INFO @ Wed, 07 Feb 2018 10:14:08: 13000000 INFO @ Wed, 07 Feb 2018 10:14:16: 14000000 INFO @ Wed, 07 Feb 2018 10:14:16: 14000000 INFO @ Wed, 07 Feb 2018 10:14:16: 14000000 INFO @ Wed, 07 Feb 2018 10:14:24: 15000000 INFO @ Wed, 07 Feb 2018 10:14:24: 15000000 INFO @ Wed, 07 Feb 2018 10:14:24: 15000000 INFO @ Wed, 07 Feb 2018 10:14:32: 16000000 INFO @ Wed, 07 Feb 2018 10:14:32: 16000000 INFO @ Wed, 07 Feb 2018 10:14:32: 16000000 INFO @ Wed, 07 Feb 2018 10:14:40: 17000000 INFO @ Wed, 07 Feb 2018 10:14:40: 17000000 INFO @ Wed, 07 Feb 2018 10:14:40: 17000000 INFO @ Wed, 07 Feb 2018 10:14:41: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 10:14:41: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 10:14:41: #1 total tags in treatment: 17136045 INFO @ Wed, 07 Feb 2018 10:14:41: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 10:14:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 10:14:41: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 10:14:41: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 10:14:41: #1 total tags in treatment: 17136045 INFO @ Wed, 07 Feb 2018 10:14:41: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 10:14:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 10:14:41: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 10:14:41: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 10:14:41: #1 total tags in treatment: 17136045 INFO @ Wed, 07 Feb 2018 10:14:41: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 10:14:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 10:14:42: #1 tags after filtering in treatment: 17136045 INFO @ Wed, 07 Feb 2018 10:14:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 10:14:42: #1 finished! INFO @ Wed, 07 Feb 2018 10:14:42: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 10:14:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 10:14:42: #1 tags after filtering in treatment: 17136045 INFO @ Wed, 07 Feb 2018 10:14:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 10:14:42: #1 finished! INFO @ Wed, 07 Feb 2018 10:14:42: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 10:14:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 10:14:42: #1 tags after filtering in treatment: 17136045 INFO @ Wed, 07 Feb 2018 10:14:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 10:14:42: #1 finished! INFO @ Wed, 07 Feb 2018 10:14:42: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 10:14:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 10:14:43: #2 number of paired peaks: 299 WARNING @ Wed, 07 Feb 2018 10:14:43: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Wed, 07 Feb 2018 10:14:43: start model_add_line... INFO @ Wed, 07 Feb 2018 10:14:43: #2 number of paired peaks: 299 WARNING @ Wed, 07 Feb 2018 10:14:43: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Wed, 07 Feb 2018 10:14:43: start model_add_line... INFO @ Wed, 07 Feb 2018 10:14:43: start X-correlation... INFO @ Wed, 07 Feb 2018 10:14:43: end of X-cor INFO @ Wed, 07 Feb 2018 10:14:43: #2 finished! INFO @ Wed, 07 Feb 2018 10:14:43: #2 predicted fragment length is 69 bps INFO @ Wed, 07 Feb 2018 10:14:43: #2 alternative fragment length(s) may be 3,69 bps INFO @ Wed, 07 Feb 2018 10:14:43: #2.2 Generate R script for model : SRX3404009.20_model.r INFO @ Wed, 07 Feb 2018 10:14:43: start X-correlation... INFO @ Wed, 07 Feb 2018 10:14:43: end of X-cor INFO @ Wed, 07 Feb 2018 10:14:43: #2 finished! INFO @ Wed, 07 Feb 2018 10:14:43: #2 predicted fragment length is 69 bps INFO @ Wed, 07 Feb 2018 10:14:43: #2 alternative fragment length(s) may be 3,69 bps INFO @ Wed, 07 Feb 2018 10:14:43: #2.2 Generate R script for model : SRX3404009.05_model.r WARNING @ Wed, 07 Feb 2018 10:14:43: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 10:14:43: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Wed, 07 Feb 2018 10:14:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 10:14:43: #3 Call peaks... INFO @ Wed, 07 Feb 2018 10:14:43: #3 Pre-compute pvalue-qvalue table... WARNING @ Wed, 07 Feb 2018 10:14:43: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 10:14:43: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Wed, 07 Feb 2018 10:14:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 10:14:43: #3 Call peaks... INFO @ Wed, 07 Feb 2018 10:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 10:14:43: #2 number of paired peaks: 299 WARNING @ Wed, 07 Feb 2018 10:14:43: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Wed, 07 Feb 2018 10:14:43: start model_add_line... INFO @ Wed, 07 Feb 2018 10:14:43: start X-correlation... INFO @ Wed, 07 Feb 2018 10:14:43: end of X-cor INFO @ Wed, 07 Feb 2018 10:14:43: #2 finished! INFO @ Wed, 07 Feb 2018 10:14:43: #2 predicted fragment length is 69 bps INFO @ Wed, 07 Feb 2018 10:14:43: #2 alternative fragment length(s) may be 3,69 bps INFO @ Wed, 07 Feb 2018 10:14:43: #2.2 Generate R script for model : SRX3404009.10_model.r WARNING @ Wed, 07 Feb 2018 10:14:43: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 10:14:43: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Wed, 07 Feb 2018 10:14:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 10:14:43: #3 Call peaks... INFO @ Wed, 07 Feb 2018 10:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 10:15:18: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 10:15:18: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 10:15:22: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 10:15:36: #4 Write output xls file... SRX3404009.05_peaks.xls INFO @ Wed, 07 Feb 2018 10:15:36: #4 Write peak in narrowPeak format file... SRX3404009.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 10:15:36: #4 Write summits bed file... SRX3404009.05_summits.bed INFO @ Wed, 07 Feb 2018 10:15:36: Done! INFO @ Wed, 07 Feb 2018 10:15:36: #4 Write output xls file... SRX3404009.10_peaks.xls INFO @ Wed, 07 Feb 2018 10:15:36: #4 Write peak in narrowPeak format file... SRX3404009.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 10:15:36: #4 Write summits bed file... SRX3404009.10_summits.bed INFO @ Wed, 07 Feb 2018 10:15:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2193 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1206 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 10:15:44: #4 Write output xls file... SRX3404009.20_peaks.xls INFO @ Wed, 07 Feb 2018 10:15:44: #4 Write peak in narrowPeak format file... SRX3404009.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 10:15:44: #4 Write summits bed file... SRX3404009.20_summits.bed INFO @ Wed, 07 Feb 2018 10:15:44: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (532 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。