Job ID = 10320317 sra ファイルのダウンロード中... Completed: 880909K bytes transferred in 117 seconds (61205K 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 23231060 spots for /home/okishinya/chipatlas/results/ce10/SRX3043408/SRR5875892.sra Written 23231060 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: 00:08:18 23231060 reads; of these: 23231060 (100.00%) were unpaired; of these: 553294 (2.38%) aligned 0 times 19304544 (83.10%) aligned exactly 1 time 3373222 (14.52%) aligned >1 times 97.62% overall alignment rate Time searching: 00:08:18 Overall time: 00:08:18 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 12 files... [bam_rmdupse_core] 5018034 / 22677766 = 0.2213 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 @ Thu, 11 Jan 2018 02:22:02: # Command line: callpeak -t SRX3043408.bam -f BAM -g ce -n SRX3043408.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043408.10 # format = BAM # ChIP-seq file = ['SRX3043408.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 @ Thu, 11 Jan 2018 02:22:02: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:22:02: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:22:02: # Command line: callpeak -t SRX3043408.bam -f BAM -g ce -n SRX3043408.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043408.20 # format = BAM # ChIP-seq file = ['SRX3043408.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 @ Thu, 11 Jan 2018 02:22:02: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:22:02: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:22:02: # Command line: callpeak -t SRX3043408.bam -f BAM -g ce -n SRX3043408.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043408.05 # format = BAM # ChIP-seq file = ['SRX3043408.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 @ Thu, 11 Jan 2018 02:22:02: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:22:02: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:22:09: 1000000 INFO @ Thu, 11 Jan 2018 02:22:09: 1000000 INFO @ Thu, 11 Jan 2018 02:22:09: 1000000 INFO @ Thu, 11 Jan 2018 02:22:16: 2000000 INFO @ Thu, 11 Jan 2018 02:22:16: 2000000 INFO @ Thu, 11 Jan 2018 02:22:16: 2000000 INFO @ Thu, 11 Jan 2018 02:22:23: 3000000 INFO @ Thu, 11 Jan 2018 02:22:23: 3000000 INFO @ Thu, 11 Jan 2018 02:22:23: 3000000 INFO @ Thu, 11 Jan 2018 02:22:30: 4000000 INFO @ Thu, 11 Jan 2018 02:22:30: 4000000 INFO @ Thu, 11 Jan 2018 02:22:30: 4000000 INFO @ Thu, 11 Jan 2018 02:22:36: 5000000 INFO @ Thu, 11 Jan 2018 02:22:37: 5000000 INFO @ Thu, 11 Jan 2018 02:22:37: 5000000 INFO @ Thu, 11 Jan 2018 02:22:43: 6000000 INFO @ Thu, 11 Jan 2018 02:22:44: 6000000 INFO @ Thu, 11 Jan 2018 02:22:44: 6000000 INFO @ Thu, 11 Jan 2018 02:22:50: 7000000 INFO @ Thu, 11 Jan 2018 02:22:51: 7000000 INFO @ Thu, 11 Jan 2018 02:22:51: 7000000 INFO @ Thu, 11 Jan 2018 02:22:57: 8000000 INFO @ Thu, 11 Jan 2018 02:22:58: 8000000 INFO @ Thu, 11 Jan 2018 02:22:58: 8000000 INFO @ Thu, 11 Jan 2018 02:23:04: 9000000 INFO @ Thu, 11 Jan 2018 02:23:05: 9000000 INFO @ Thu, 11 Jan 2018 02:23:05: 9000000 INFO @ Thu, 11 Jan 2018 02:23:10: 10000000 INFO @ Thu, 11 Jan 2018 02:23:12: 10000000 INFO @ Thu, 11 Jan 2018 02:23:12: 10000000 INFO @ Thu, 11 Jan 2018 02:23:17: 11000000 INFO @ Thu, 11 Jan 2018 02:23:19: 11000000 INFO @ Thu, 11 Jan 2018 02:23:20: 11000000 INFO @ Thu, 11 Jan 2018 02:23:24: 12000000 INFO @ Thu, 11 Jan 2018 02:23:26: 12000000 INFO @ Thu, 11 Jan 2018 02:23:27: 12000000 INFO @ Thu, 11 Jan 2018 02:23:31: 13000000 INFO @ Thu, 11 Jan 2018 02:23:33: 13000000 INFO @ Thu, 11 Jan 2018 02:23:34: 13000000 INFO @ Thu, 11 Jan 2018 02:23:39: 14000000 INFO @ Thu, 11 Jan 2018 02:23:40: 14000000 INFO @ Thu, 11 Jan 2018 02:23:42: 14000000 INFO @ Thu, 11 Jan 2018 02:23:46: 15000000 INFO @ Thu, 11 Jan 2018 02:23:47: 15000000 INFO @ Thu, 11 Jan 2018 02:23:49: 15000000 INFO @ Thu, 11 Jan 2018 02:23:53: 16000000 INFO @ Thu, 11 Jan 2018 02:23:54: 16000000 INFO @ Thu, 11 Jan 2018 02:23:56: 16000000 INFO @ Thu, 11 Jan 2018 02:24:00: 17000000 INFO @ Thu, 11 Jan 2018 02:24:00: 17000000 INFO @ Thu, 11 Jan 2018 02:24:04: 17000000 INFO @ Thu, 11 Jan 2018 02:24:05: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:24:05: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:24:05: #1 total tags in treatment: 17659732 INFO @ Thu, 11 Jan 2018 02:24:05: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:24:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:24:05: #1 tags after filtering in treatment: 17659732 INFO @ Thu, 11 Jan 2018 02:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:24:05: #1 finished! INFO @ Thu, 11 Jan 2018 02:24:05: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:24:05: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:24:05: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:24:05: #1 total tags in treatment: 17659732 INFO @ Thu, 11 Jan 2018 02:24:05: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:24:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:24:05: #1 tags after filtering in treatment: 17659732 INFO @ Thu, 11 Jan 2018 02:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:24:05: #1 finished! INFO @ Thu, 11 Jan 2018 02:24:05: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:24:06: #2 number of paired peaks: 107 WARNING @ Thu, 11 Jan 2018 02:24:06: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Thu, 11 Jan 2018 02:24:06: start model_add_line... INFO @ Thu, 11 Jan 2018 02:24:06: start X-correlation... INFO @ Thu, 11 Jan 2018 02:24:06: end of X-cor INFO @ Thu, 11 Jan 2018 02:24:06: #2 finished! INFO @ Thu, 11 Jan 2018 02:24:06: #2 predicted fragment length is 49 bps INFO @ Thu, 11 Jan 2018 02:24:06: #2 alternative fragment length(s) may be 2,49,541,556,598 bps INFO @ Thu, 11 Jan 2018 02:24:06: #2.2 Generate R script for model : SRX3043408.05_model.r WARNING @ Thu, 11 Jan 2018 02:24:06: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:24:06: #2 You may need to consider one of the other alternative d(s): 2,49,541,556,598 WARNING @ Thu, 11 Jan 2018 02:24:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:24:06: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:24:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:24:06: #2 number of paired peaks: 107 WARNING @ Thu, 11 Jan 2018 02:24:06: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Thu, 11 Jan 2018 02:24:06: start model_add_line... INFO @ Thu, 11 Jan 2018 02:24:07: start X-correlation... INFO @ Thu, 11 Jan 2018 02:24:07: end of X-cor INFO @ Thu, 11 Jan 2018 02:24:07: #2 finished! INFO @ Thu, 11 Jan 2018 02:24:07: #2 predicted fragment length is 49 bps INFO @ Thu, 11 Jan 2018 02:24:07: #2 alternative fragment length(s) may be 2,49,541,556,598 bps INFO @ Thu, 11 Jan 2018 02:24:07: #2.2 Generate R script for model : SRX3043408.10_model.r WARNING @ Thu, 11 Jan 2018 02:24:07: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:24:07: #2 You may need to consider one of the other alternative d(s): 2,49,541,556,598 WARNING @ Thu, 11 Jan 2018 02:24:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:24:07: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:24:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:24:08: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:24:08: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:24:08: #1 total tags in treatment: 17659732 INFO @ Thu, 11 Jan 2018 02:24:08: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:24:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:24:09: #1 tags after filtering in treatment: 17659732 INFO @ Thu, 11 Jan 2018 02:24:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:24:09: #1 finished! INFO @ Thu, 11 Jan 2018 02:24:09: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:24:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:24:10: #2 number of paired peaks: 107 WARNING @ Thu, 11 Jan 2018 02:24:10: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Thu, 11 Jan 2018 02:24:10: start model_add_line... INFO @ Thu, 11 Jan 2018 02:24:10: start X-correlation... INFO @ Thu, 11 Jan 2018 02:24:10: end of X-cor INFO @ Thu, 11 Jan 2018 02:24:10: #2 finished! INFO @ Thu, 11 Jan 2018 02:24:10: #2 predicted fragment length is 49 bps INFO @ Thu, 11 Jan 2018 02:24:10: #2 alternative fragment length(s) may be 2,49,541,556,598 bps INFO @ Thu, 11 Jan 2018 02:24:10: #2.2 Generate R script for model : SRX3043408.20_model.r WARNING @ Thu, 11 Jan 2018 02:24:10: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:24:10: #2 You may need to consider one of the other alternative d(s): 2,49,541,556,598 WARNING @ Thu, 11 Jan 2018 02:24:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:24:10: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:24:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:24:38: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:24:40: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:24:43: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:24:55: #4 Write output xls file... SRX3043408.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:24:55: #4 Write peak in narrowPeak format file... SRX3043408.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:24:55: #4 Write summits bed file... SRX3043408.10_summits.bed INFO @ Thu, 11 Jan 2018 02:24:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (304 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:25:00: #4 Write output xls file... SRX3043408.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:25:00: #4 Write peak in narrowPeak format file... SRX3043408.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:25:00: #4 Write summits bed file... SRX3043408.05_summits.bed INFO @ Thu, 11 Jan 2018 02:25:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (607 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:25:01: #4 Write output xls file... SRX3043408.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:25:01: #4 Write peak in narrowPeak format file... SRX3043408.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:25:01: #4 Write summits bed file... SRX3043408.20_summits.bed INFO @ Thu, 11 Jan 2018 02:25:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (84 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。