Job ID = 10450728 sra ファイルのダウンロード中... Completed: 342284K bytes transferred in 22 seconds (127379K 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 18009319 spots for /home/okishinya/chipatlas/results/dm3/SRX3404016/SRR6303493.sra Written 18009319 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:10:12 18009319 reads; of these: 18009319 (100.00%) were unpaired; of these: 572054 (3.18%) aligned 0 times 13578404 (75.40%) aligned exactly 1 time 3858861 (21.43%) aligned >1 times 96.82% overall alignment rate Time searching: 00:10:12 Overall time: 00:10:12 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] 1274288 / 17437265 = 0.0731 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 11:04:49: # Command line: callpeak -t SRX3404016.bam -f BAM -g dm -n SRX3404016.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404016.05 # format = BAM # ChIP-seq file = ['SRX3404016.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 11:04:49: #1 read tag files... INFO @ Wed, 07 Feb 2018 11:04:49: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 11:04:49: # Command line: callpeak -t SRX3404016.bam -f BAM -g dm -n SRX3404016.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404016.10 # format = BAM # ChIP-seq file = ['SRX3404016.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 11:04:49: #1 read tag files... INFO @ Wed, 07 Feb 2018 11:04:49: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 11:04:49: # Command line: callpeak -t SRX3404016.bam -f BAM -g dm -n SRX3404016.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404016.20 # format = BAM # ChIP-seq file = ['SRX3404016.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 11:04:49: #1 read tag files... INFO @ Wed, 07 Feb 2018 11:04:49: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 11:04:57: 1000000 INFO @ Wed, 07 Feb 2018 11:04:57: 1000000 INFO @ Wed, 07 Feb 2018 11:04:58: 1000000 INFO @ Wed, 07 Feb 2018 11:05:06: 2000000 INFO @ Wed, 07 Feb 2018 11:05:06: 2000000 INFO @ Wed, 07 Feb 2018 11:05:06: 2000000 INFO @ Wed, 07 Feb 2018 11:05:15: 3000000 INFO @ Wed, 07 Feb 2018 11:05:15: 3000000 INFO @ Wed, 07 Feb 2018 11:05:15: 3000000 INFO @ Wed, 07 Feb 2018 11:05:23: 4000000 INFO @ Wed, 07 Feb 2018 11:05:24: 4000000 INFO @ Wed, 07 Feb 2018 11:05:24: 4000000 INFO @ Wed, 07 Feb 2018 11:05:32: 5000000 INFO @ Wed, 07 Feb 2018 11:05:33: 5000000 INFO @ Wed, 07 Feb 2018 11:05:33: 5000000 INFO @ Wed, 07 Feb 2018 11:05:41: 6000000 INFO @ Wed, 07 Feb 2018 11:05:42: 6000000 INFO @ Wed, 07 Feb 2018 11:05:43: 6000000 INFO @ Wed, 07 Feb 2018 11:05:50: 7000000 INFO @ Wed, 07 Feb 2018 11:05:51: 7000000 INFO @ Wed, 07 Feb 2018 11:05:52: 7000000 INFO @ Wed, 07 Feb 2018 11:05:59: 8000000 INFO @ Wed, 07 Feb 2018 11:06:00: 8000000 INFO @ Wed, 07 Feb 2018 11:06:01: 8000000 INFO @ Wed, 07 Feb 2018 11:06:07: 9000000 INFO @ Wed, 07 Feb 2018 11:06:09: 9000000 INFO @ Wed, 07 Feb 2018 11:06:11: 9000000 INFO @ Wed, 07 Feb 2018 11:06:16: 10000000 INFO @ Wed, 07 Feb 2018 11:06:18: 10000000 INFO @ Wed, 07 Feb 2018 11:06:20: 10000000 INFO @ Wed, 07 Feb 2018 11:06:25: 11000000 INFO @ Wed, 07 Feb 2018 11:06:27: 11000000 INFO @ Wed, 07 Feb 2018 11:06:29: 11000000 INFO @ Wed, 07 Feb 2018 11:06:34: 12000000 INFO @ Wed, 07 Feb 2018 11:06:36: 12000000 INFO @ Wed, 07 Feb 2018 11:06:38: 12000000 INFO @ Wed, 07 Feb 2018 11:06:43: 13000000 INFO @ Wed, 07 Feb 2018 11:06:46: 13000000 INFO @ Wed, 07 Feb 2018 11:06:47: 13000000 INFO @ Wed, 07 Feb 2018 11:06:51: 14000000 INFO @ Wed, 07 Feb 2018 11:06:55: 14000000 INFO @ Wed, 07 Feb 2018 11:06:57: 14000000 INFO @ Wed, 07 Feb 2018 11:07:00: 15000000 INFO @ Wed, 07 Feb 2018 11:07:04: 15000000 INFO @ Wed, 07 Feb 2018 11:07:06: 15000000 INFO @ Wed, 07 Feb 2018 11:07:09: 16000000 INFO @ Wed, 07 Feb 2018 11:07:11: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 11:07:11: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 11:07:11: #1 total tags in treatment: 16162977 INFO @ Wed, 07 Feb 2018 11:07:11: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 11:07:11: #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 11:07:11: #1 tags after filtering in treatment: 16162977 INFO @ Wed, 07 Feb 2018 11:07:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 11:07:11: #1 finished! INFO @ Wed, 07 Feb 2018 11:07:11: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 11:07:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 11:07:13: 16000000 INFO @ Wed, 07 Feb 2018 11:07:13: #2 number of paired peaks: 295 WARNING @ Wed, 07 Feb 2018 11:07:13: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Wed, 07 Feb 2018 11:07:13: start model_add_line... INFO @ Wed, 07 Feb 2018 11:07:13: start X-correlation... INFO @ Wed, 07 Feb 2018 11:07:13: end of X-cor INFO @ Wed, 07 Feb 2018 11:07:13: #2 finished! INFO @ Wed, 07 Feb 2018 11:07:13: #2 predicted fragment length is 91 bps INFO @ Wed, 07 Feb 2018 11:07:13: #2 alternative fragment length(s) may be 3,91 bps INFO @ Wed, 07 Feb 2018 11:07:13: #2.2 Generate R script for model : SRX3404016.20_model.r WARNING @ Wed, 07 Feb 2018 11:07:13: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 11:07:13: #2 You may need to consider one of the other alternative d(s): 3,91 WARNING @ Wed, 07 Feb 2018 11:07:13: #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 11:07:13: #3 Call peaks... INFO @ Wed, 07 Feb 2018 11:07:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:07:14: 16000000 INFO @ Wed, 07 Feb 2018 11:07:14: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 11:07:14: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 11:07:14: #1 total tags in treatment: 16162977 INFO @ Wed, 07 Feb 2018 11:07:14: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 11:07:14: #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 11:07:15: #1 tags after filtering in treatment: 16162977 INFO @ Wed, 07 Feb 2018 11:07:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 11:07:15: #1 finished! INFO @ Wed, 07 Feb 2018 11:07:15: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 11:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 11:07:16: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 11:07:16: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 11:07:16: #1 total tags in treatment: 16162977 INFO @ Wed, 07 Feb 2018 11:07:16: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 11:07:16: #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 11:07:16: #1 tags after filtering in treatment: 16162977 INFO @ Wed, 07 Feb 2018 11:07:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 11:07:16: #1 finished! INFO @ Wed, 07 Feb 2018 11:07:16: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 11:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 11:07:16: #2 number of paired peaks: 295 WARNING @ Wed, 07 Feb 2018 11:07:16: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Wed, 07 Feb 2018 11:07:16: start model_add_line... INFO @ Wed, 07 Feb 2018 11:07:16: start X-correlation... INFO @ Wed, 07 Feb 2018 11:07:16: end of X-cor INFO @ Wed, 07 Feb 2018 11:07:16: #2 finished! INFO @ Wed, 07 Feb 2018 11:07:16: #2 predicted fragment length is 91 bps INFO @ Wed, 07 Feb 2018 11:07:16: #2 alternative fragment length(s) may be 3,91 bps INFO @ Wed, 07 Feb 2018 11:07:16: #2.2 Generate R script for model : SRX3404016.05_model.r WARNING @ Wed, 07 Feb 2018 11:07:17: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 11:07:17: #2 You may need to consider one of the other alternative d(s): 3,91 WARNING @ Wed, 07 Feb 2018 11:07:17: #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 11:07:17: #3 Call peaks... INFO @ Wed, 07 Feb 2018 11:07:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:07:18: #2 number of paired peaks: 295 WARNING @ Wed, 07 Feb 2018 11:07:18: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Wed, 07 Feb 2018 11:07:18: start model_add_line... INFO @ Wed, 07 Feb 2018 11:07:18: start X-correlation... INFO @ Wed, 07 Feb 2018 11:07:18: end of X-cor INFO @ Wed, 07 Feb 2018 11:07:18: #2 finished! INFO @ Wed, 07 Feb 2018 11:07:18: #2 predicted fragment length is 91 bps INFO @ Wed, 07 Feb 2018 11:07:18: #2 alternative fragment length(s) may be 3,91 bps INFO @ Wed, 07 Feb 2018 11:07:18: #2.2 Generate R script for model : SRX3404016.10_model.r WARNING @ Wed, 07 Feb 2018 11:07:18: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 11:07:18: #2 You may need to consider one of the other alternative d(s): 3,91 WARNING @ Wed, 07 Feb 2018 11:07:18: #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 11:07:18: #3 Call peaks... INFO @ Wed, 07 Feb 2018 11:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:07:55: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:08:01: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:08:01: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:08:18: #4 Write output xls file... SRX3404016.20_peaks.xls INFO @ Wed, 07 Feb 2018 11:08:18: #4 Write peak in narrowPeak format file... SRX3404016.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:08:18: #4 Write summits bed file... SRX3404016.20_summits.bed INFO @ Wed, 07 Feb 2018 11:08:18: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (699 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 11:08:25: #4 Write output xls file... SRX3404016.10_peaks.xls INFO @ Wed, 07 Feb 2018 11:08:25: #4 Write peak in narrowPeak format file... SRX3404016.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:08:25: #4 Write summits bed file... SRX3404016.10_summits.bed INFO @ Wed, 07 Feb 2018 11:08:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1565 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 11:08:25: #4 Write output xls file... SRX3404016.05_peaks.xls INFO @ Wed, 07 Feb 2018 11:08:25: #4 Write peak in narrowPeak format file... SRX3404016.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:08:25: #4 Write summits bed file... SRX3404016.05_summits.bed INFO @ Wed, 07 Feb 2018 11:08:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2879 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。