Job ID = 10201989 sra ファイルのダウンロード中... Completed: 450512K bytes transferred in 13 seconds (273286K 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 19530987 spots for /home/okishinya/chipatlas/results/ce10/SRX2576658/SRR5272615.sra Written 19530987 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: 00:07:30 19530987 reads; of these: 19530987 (100.00%) were unpaired; of these: 138747 (0.71%) aligned 0 times 16096553 (82.42%) aligned exactly 1 time 3295687 (16.87%) aligned >1 times 99.29% overall alignment rate Time searching: 00:07:30 Overall time: 00:07:30 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] 2125565 / 19392240 = 0.1096 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 13:23:44: # Command line: callpeak -t SRX2576658.bam -f BAM -g ce -n SRX2576658.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576658.05 # format = BAM # ChIP-seq file = ['SRX2576658.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 13:23:44: # Command line: callpeak -t SRX2576658.bam -f BAM -g ce -n SRX2576658.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576658.20 # format = BAM # ChIP-seq file = ['SRX2576658.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 13:23:44: # Command line: callpeak -t SRX2576658.bam -f BAM -g ce -n SRX2576658.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576658.10 # format = BAM # ChIP-seq file = ['SRX2576658.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 13:23:44: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:23:44: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:23:44: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:23:44: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:23:44: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:23:44: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:23:56: 1000000 INFO @ Mon, 13 Nov 2017 13:23:58: 1000000 INFO @ Mon, 13 Nov 2017 13:23:59: 1000000 INFO @ Mon, 13 Nov 2017 13:24:09: 2000000 INFO @ Mon, 13 Nov 2017 13:24:10: 2000000 INFO @ Mon, 13 Nov 2017 13:24:18: 2000000 INFO @ Mon, 13 Nov 2017 13:24:23: 3000000 INFO @ Mon, 13 Nov 2017 13:24:23: 3000000 INFO @ Mon, 13 Nov 2017 13:24:35: 4000000 INFO @ Mon, 13 Nov 2017 13:24:35: 4000000 INFO @ Mon, 13 Nov 2017 13:24:37: 3000000 INFO @ Mon, 13 Nov 2017 13:24:47: 5000000 INFO @ Mon, 13 Nov 2017 13:24:48: 5000000 INFO @ Mon, 13 Nov 2017 13:24:56: 4000000 INFO @ Mon, 13 Nov 2017 13:25:00: 6000000 INFO @ Mon, 13 Nov 2017 13:25:01: 6000000 INFO @ Mon, 13 Nov 2017 13:25:12: 7000000 INFO @ Mon, 13 Nov 2017 13:25:13: 5000000 INFO @ Mon, 13 Nov 2017 13:25:14: 7000000 INFO @ Mon, 13 Nov 2017 13:25:26: 8000000 INFO @ Mon, 13 Nov 2017 13:25:29: 8000000 INFO @ Mon, 13 Nov 2017 13:25:31: 6000000 INFO @ Mon, 13 Nov 2017 13:25:42: 9000000 INFO @ Mon, 13 Nov 2017 13:25:42: 9000000 INFO @ Mon, 13 Nov 2017 13:25:50: 7000000 INFO @ Mon, 13 Nov 2017 13:25:55: 10000000 INFO @ Mon, 13 Nov 2017 13:25:57: 10000000 INFO @ Mon, 13 Nov 2017 13:26:07: 8000000 INFO @ Mon, 13 Nov 2017 13:26:08: 11000000 INFO @ Mon, 13 Nov 2017 13:26:14: 11000000 INFO @ Mon, 13 Nov 2017 13:26:24: 12000000 INFO @ Mon, 13 Nov 2017 13:26:24: 9000000 INFO @ Mon, 13 Nov 2017 13:26:30: 12000000 INFO @ Mon, 13 Nov 2017 13:26:40: 13000000 INFO @ Mon, 13 Nov 2017 13:26:41: 10000000 INFO @ Mon, 13 Nov 2017 13:26:46: 13000000 INFO @ Mon, 13 Nov 2017 13:26:57: 14000000 INFO @ Mon, 13 Nov 2017 13:26:58: 11000000 INFO @ Mon, 13 Nov 2017 13:27:03: 14000000 INFO @ Mon, 13 Nov 2017 13:27:15: 15000000 INFO @ Mon, 13 Nov 2017 13:27:15: 12000000 INFO @ Mon, 13 Nov 2017 13:27:19: 15000000 INFO @ Mon, 13 Nov 2017 13:27:33: 16000000 INFO @ Mon, 13 Nov 2017 13:27:34: 13000000 INFO @ Mon, 13 Nov 2017 13:27:36: 16000000 INFO @ Mon, 13 Nov 2017 13:27:51: 17000000 INFO @ Mon, 13 Nov 2017 13:27:52: 17000000 INFO @ Mon, 13 Nov 2017 13:27:54: 14000000 INFO @ Mon, 13 Nov 2017 13:27:55: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:27:55: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:27:55: #1 total tags in treatment: 17266675 INFO @ Mon, 13 Nov 2017 13:27:55: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:27:55: #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 13:27:55: #1 tags after filtering in treatment: 17266675 INFO @ Mon, 13 Nov 2017 13:27:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:27:55: #1 finished! INFO @ Mon, 13 Nov 2017 13:27:55: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:27:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:27:56: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:27:56: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:27:56: #1 total tags in treatment: 17266675 INFO @ Mon, 13 Nov 2017 13:27:56: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:27:56: #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 13:27:57: #2 number of paired peaks: 227 WARNING @ Mon, 13 Nov 2017 13:27:57: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Mon, 13 Nov 2017 13:27:57: start model_add_line... INFO @ Mon, 13 Nov 2017 13:27:57: #1 tags after filtering in treatment: 17266675 INFO @ Mon, 13 Nov 2017 13:27:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:27:57: #1 finished! INFO @ Mon, 13 Nov 2017 13:27:57: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:27:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:27:57: start X-correlation... INFO @ Mon, 13 Nov 2017 13:27:57: end of X-cor INFO @ Mon, 13 Nov 2017 13:27:57: #2 finished! INFO @ Mon, 13 Nov 2017 13:27:57: #2 predicted fragment length is 1 bps INFO @ Mon, 13 Nov 2017 13:27:57: #2 alternative fragment length(s) may be 1,33,526,576 bps INFO @ Mon, 13 Nov 2017 13:27:57: #2.2 Generate R script for model : SRX2576658.10_model.r WARNING @ Mon, 13 Nov 2017 13:27:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:27:57: #2 You may need to consider one of the other alternative d(s): 1,33,526,576 WARNING @ Mon, 13 Nov 2017 13:27:57: #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 13:27:57: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:27:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:27:58: #2 number of paired peaks: 227 WARNING @ Mon, 13 Nov 2017 13:27:58: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Mon, 13 Nov 2017 13:27:58: start model_add_line... INFO @ Mon, 13 Nov 2017 13:27:59: start X-correlation... INFO @ Mon, 13 Nov 2017 13:27:59: end of X-cor INFO @ Mon, 13 Nov 2017 13:27:59: #2 finished! INFO @ Mon, 13 Nov 2017 13:27:59: #2 predicted fragment length is 1 bps INFO @ Mon, 13 Nov 2017 13:27:59: #2 alternative fragment length(s) may be 1,33,526,576 bps INFO @ Mon, 13 Nov 2017 13:27:59: #2.2 Generate R script for model : SRX2576658.05_model.r WARNING @ Mon, 13 Nov 2017 13:27:59: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:27:59: #2 You may need to consider one of the other alternative d(s): 1,33,526,576 WARNING @ Mon, 13 Nov 2017 13:27:59: #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 13:27:59: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:27:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:28:14: 15000000 INFO @ Mon, 13 Nov 2017 13:28:30: 16000000 INFO @ Mon, 13 Nov 2017 13:28:35: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:28:38: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:28:49: 17000000 INFO @ Mon, 13 Nov 2017 13:28:54: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:28:54: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:28:54: #1 total tags in treatment: 17266675 INFO @ Mon, 13 Nov 2017 13:28:54: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:28:54: #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 13:28:55: #1 tags after filtering in treatment: 17266675 INFO @ Mon, 13 Nov 2017 13:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:28:55: #1 finished! INFO @ Mon, 13 Nov 2017 13:28:55: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:28:55: #4 Write output xls file... SRX2576658.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:28:55: #4 Write peak in narrowPeak format file... SRX2576658.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:28:55: #4 Write summits bed file... SRX2576658.10_summits.bed INFO @ Mon, 13 Nov 2017 13:28:55: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:28:56: #2 number of paired peaks: 227 WARNING @ Mon, 13 Nov 2017 13:28:56: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Mon, 13 Nov 2017 13:28:56: start model_add_line... INFO @ Mon, 13 Nov 2017 13:28:56: start X-correlation... INFO @ Mon, 13 Nov 2017 13:28:56: end of X-cor INFO @ Mon, 13 Nov 2017 13:28:56: #2 finished! INFO @ Mon, 13 Nov 2017 13:28:56: #2 predicted fragment length is 1 bps INFO @ Mon, 13 Nov 2017 13:28:56: #2 alternative fragment length(s) may be 1,33,526,576 bps INFO @ Mon, 13 Nov 2017 13:28:56: #2.2 Generate R script for model : SRX2576658.20_model.r WARNING @ Mon, 13 Nov 2017 13:28:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:28:56: #2 You may need to consider one of the other alternative d(s): 1,33,526,576 WARNING @ Mon, 13 Nov 2017 13:28:56: #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 13:28:56: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:28:59: #4 Write output xls file... SRX2576658.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:28:59: #4 Write peak in narrowPeak format file... SRX2576658.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:28:59: #4 Write summits bed file... SRX2576658.05_summits.bed INFO @ Mon, 13 Nov 2017 13:28:59: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:29:34: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:29:54: #4 Write output xls file... SRX2576658.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:29:54: #4 Write peak in narrowPeak format file... SRX2576658.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:29:54: #4 Write summits bed file... SRX2576658.20_summits.bed INFO @ Mon, 13 Nov 2017 13:29:54: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。