Job ID = 10201974 sra ファイルのダウンロード中... Completed: 586879K bytes transferred in 18 seconds (265537K 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 18630839 spots for /home/okishinya/chipatlas/results/ce10/SRX2576643/SRR5272600.sra Written 18630839 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: 00:04:59 18630839 reads; of these: 18630839 (100.00%) were unpaired; of these: 416134 (2.23%) aligned 0 times 14985417 (80.43%) aligned exactly 1 time 3229288 (17.33%) aligned >1 times 97.77% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3411851 / 18214705 = 0.1873 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 @ Mon, 13 Nov 2017 13:18:55: # Command line: callpeak -t SRX2576643.bam -f BAM -g ce -n SRX2576643.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576643.20 # format = BAM # ChIP-seq file = ['SRX2576643.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 13 Nov 2017 13:18:55: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:18:55: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:18:55: # Command line: callpeak -t SRX2576643.bam -f BAM -g ce -n SRX2576643.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576643.05 # format = BAM # ChIP-seq file = ['SRX2576643.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 13 Nov 2017 13:18:55: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:18:55: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:18:55: # Command line: callpeak -t SRX2576643.bam -f BAM -g ce -n SRX2576643.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576643.10 # format = BAM # ChIP-seq file = ['SRX2576643.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 13 Nov 2017 13:18:55: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:18:55: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:19:01: 1000000 INFO @ Mon, 13 Nov 2017 13:19:01: 1000000 INFO @ Mon, 13 Nov 2017 13:19:01: 1000000 INFO @ Mon, 13 Nov 2017 13:19:08: 2000000 INFO @ Mon, 13 Nov 2017 13:19:08: 2000000 INFO @ Mon, 13 Nov 2017 13:19:08: 2000000 INFO @ Mon, 13 Nov 2017 13:19:14: 3000000 INFO @ Mon, 13 Nov 2017 13:19:14: 3000000 INFO @ Mon, 13 Nov 2017 13:19:15: 3000000 INFO @ Mon, 13 Nov 2017 13:19:20: 4000000 INFO @ Mon, 13 Nov 2017 13:19:20: 4000000 INFO @ Mon, 13 Nov 2017 13:19:21: 4000000 INFO @ Mon, 13 Nov 2017 13:19:26: 5000000 INFO @ Mon, 13 Nov 2017 13:19:27: 5000000 INFO @ Mon, 13 Nov 2017 13:19:28: 5000000 INFO @ Mon, 13 Nov 2017 13:19:33: 6000000 INFO @ Mon, 13 Nov 2017 13:19:33: 6000000 INFO @ Mon, 13 Nov 2017 13:19:34: 6000000 INFO @ Mon, 13 Nov 2017 13:19:39: 7000000 INFO @ Mon, 13 Nov 2017 13:19:39: 7000000 INFO @ Mon, 13 Nov 2017 13:19:41: 7000000 INFO @ Mon, 13 Nov 2017 13:19:46: 8000000 INFO @ Mon, 13 Nov 2017 13:19:46: 8000000 INFO @ Mon, 13 Nov 2017 13:19:47: 8000000 INFO @ Mon, 13 Nov 2017 13:19:52: 9000000 INFO @ Mon, 13 Nov 2017 13:19:52: 9000000 INFO @ Mon, 13 Nov 2017 13:19:54: 9000000 INFO @ Mon, 13 Nov 2017 13:19:58: 10000000 INFO @ Mon, 13 Nov 2017 13:19:59: 10000000 INFO @ Mon, 13 Nov 2017 13:20:00: 10000000 INFO @ Mon, 13 Nov 2017 13:20:05: 11000000 INFO @ Mon, 13 Nov 2017 13:20:05: 11000000 INFO @ Mon, 13 Nov 2017 13:20:06: 11000000 INFO @ Mon, 13 Nov 2017 13:20:11: 12000000 INFO @ Mon, 13 Nov 2017 13:20:12: 12000000 INFO @ Mon, 13 Nov 2017 13:20:13: 12000000 INFO @ Mon, 13 Nov 2017 13:20:18: 13000000 INFO @ Mon, 13 Nov 2017 13:20:18: 13000000 INFO @ Mon, 13 Nov 2017 13:20:19: 13000000 INFO @ Mon, 13 Nov 2017 13:20:24: 14000000 INFO @ Mon, 13 Nov 2017 13:20:25: 14000000 INFO @ Mon, 13 Nov 2017 13:20:26: 14000000 INFO @ Mon, 13 Nov 2017 13:20:29: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:20:29: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:20:29: #1 total tags in treatment: 14802854 INFO @ Mon, 13 Nov 2017 13:20:29: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:20:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:20:30: #1 tags after filtering in treatment: 14802854 INFO @ Mon, 13 Nov 2017 13:20:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:20:30: #1 finished! INFO @ Mon, 13 Nov 2017 13:20:30: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:20:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:20:30: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:20:30: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:20:30: #1 total tags in treatment: 14802854 INFO @ Mon, 13 Nov 2017 13:20:30: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:20:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:20:30: #1 tags after filtering in treatment: 14802854 INFO @ Mon, 13 Nov 2017 13:20:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:20:30: #1 finished! INFO @ Mon, 13 Nov 2017 13:20:30: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:20:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:20:31: #2 number of paired peaks: 278 WARNING @ Mon, 13 Nov 2017 13:20:31: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Mon, 13 Nov 2017 13:20:31: start model_add_line... INFO @ Mon, 13 Nov 2017 13:20:31: start X-correlation... INFO @ Mon, 13 Nov 2017 13:20:31: end of X-cor INFO @ Mon, 13 Nov 2017 13:20:31: #2 finished! INFO @ Mon, 13 Nov 2017 13:20:31: #2 predicted fragment length is 49 bps INFO @ Mon, 13 Nov 2017 13:20:31: #2 alternative fragment length(s) may be 3,49,560 bps INFO @ Mon, 13 Nov 2017 13:20:31: #2.2 Generate R script for model : SRX2576643.05_model.r WARNING @ Mon, 13 Nov 2017 13:20:31: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:20:31: #2 You may need to consider one of the other alternative d(s): 3,49,560 WARNING @ Mon, 13 Nov 2017 13:20:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:20:31: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:20:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:20:31: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:20:31: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:20:31: #1 total tags in treatment: 14802854 INFO @ Mon, 13 Nov 2017 13:20:31: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:20:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:20:31: #2 number of paired peaks: 278 WARNING @ Mon, 13 Nov 2017 13:20:31: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Mon, 13 Nov 2017 13:20:31: start model_add_line... INFO @ Mon, 13 Nov 2017 13:20:31: start X-correlation... INFO @ Mon, 13 Nov 2017 13:20:31: end of X-cor INFO @ Mon, 13 Nov 2017 13:20:31: #2 finished! INFO @ Mon, 13 Nov 2017 13:20:31: #2 predicted fragment length is 49 bps INFO @ Mon, 13 Nov 2017 13:20:31: #2 alternative fragment length(s) may be 3,49,560 bps INFO @ Mon, 13 Nov 2017 13:20:31: #2.2 Generate R script for model : SRX2576643.10_model.r WARNING @ Mon, 13 Nov 2017 13:20:31: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:20:31: #2 You may need to consider one of the other alternative d(s): 3,49,560 WARNING @ Mon, 13 Nov 2017 13:20:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:20:31: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:20:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:20:31: #1 tags after filtering in treatment: 14802854 INFO @ Mon, 13 Nov 2017 13:20:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:20:31: #1 finished! INFO @ Mon, 13 Nov 2017 13:20:31: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:20:32: #2 number of paired peaks: 278 WARNING @ Mon, 13 Nov 2017 13:20:32: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Mon, 13 Nov 2017 13:20:32: start model_add_line... INFO @ Mon, 13 Nov 2017 13:20:33: start X-correlation... INFO @ Mon, 13 Nov 2017 13:20:33: end of X-cor INFO @ Mon, 13 Nov 2017 13:20:33: #2 finished! INFO @ Mon, 13 Nov 2017 13:20:33: #2 predicted fragment length is 49 bps INFO @ Mon, 13 Nov 2017 13:20:33: #2 alternative fragment length(s) may be 3,49,560 bps INFO @ Mon, 13 Nov 2017 13:20:33: #2.2 Generate R script for model : SRX2576643.20_model.r WARNING @ Mon, 13 Nov 2017 13:20:33: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:20:33: #2 You may need to consider one of the other alternative d(s): 3,49,560 WARNING @ Mon, 13 Nov 2017 13:20:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:20:33: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:20:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:21:00: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:21:00: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:21:02: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:21:15: #4 Write output xls file... SRX2576643.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:21:15: #4 Write peak in narrowPeak format file... SRX2576643.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:21:15: #4 Write summits bed file... SRX2576643.10_summits.bed INFO @ Mon, 13 Nov 2017 13:21:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (730 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:21:15: #4 Write output xls file... SRX2576643.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:21:15: #4 Write peak in narrowPeak format file... SRX2576643.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:21:15: #4 Write summits bed file... SRX2576643.05_summits.bed INFO @ Mon, 13 Nov 2017 13:21:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1228 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:21:17: #4 Write output xls file... SRX2576643.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:21:17: #4 Write peak in narrowPeak format file... SRX2576643.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:21:17: #4 Write summits bed file... SRX2576643.20_summits.bed INFO @ Mon, 13 Nov 2017 13:21:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (249 records, 4 fields): 31 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。