Job ID = 10320320 sra ファイルのダウンロード中... Completed: 687010K bytes transferred in 100 seconds (55821K 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 18934290 spots for /home/okishinya/chipatlas/results/ce10/SRX3043411/SRR5875895.sra Written 18934290 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: 00:06:26 18934290 reads; of these: 18934290 (100.00%) were unpaired; of these: 597577 (3.16%) aligned 0 times 15765681 (83.27%) aligned exactly 1 time 2571032 (13.58%) aligned >1 times 96.84% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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] 2582364 / 18336713 = 0.1408 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 02:18:37: # Command line: callpeak -t SRX3043411.bam -f BAM -g ce -n SRX3043411.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043411.20 # format = BAM # ChIP-seq file = ['SRX3043411.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 02:18:37: # Command line: callpeak -t SRX3043411.bam -f BAM -g ce -n SRX3043411.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043411.05 # format = BAM # ChIP-seq file = ['SRX3043411.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 02:18:37: # Command line: callpeak -t SRX3043411.bam -f BAM -g ce -n SRX3043411.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043411.10 # format = BAM # ChIP-seq file = ['SRX3043411.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 02:18:37: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:18:37: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:18:37: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:18:37: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:18:37: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:18:37: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:18:44: 1000000 INFO @ Thu, 11 Jan 2018 02:18:44: 1000000 INFO @ Thu, 11 Jan 2018 02:18:44: 1000000 INFO @ Thu, 11 Jan 2018 02:18:51: 2000000 INFO @ Thu, 11 Jan 2018 02:18:51: 2000000 INFO @ Thu, 11 Jan 2018 02:18:51: 2000000 INFO @ Thu, 11 Jan 2018 02:18:58: 3000000 INFO @ Thu, 11 Jan 2018 02:18:58: 3000000 INFO @ Thu, 11 Jan 2018 02:18:58: 3000000 INFO @ Thu, 11 Jan 2018 02:19:05: 4000000 INFO @ Thu, 11 Jan 2018 02:19:05: 4000000 INFO @ Thu, 11 Jan 2018 02:19:05: 4000000 INFO @ Thu, 11 Jan 2018 02:19:12: 5000000 INFO @ Thu, 11 Jan 2018 02:19:12: 5000000 INFO @ Thu, 11 Jan 2018 02:19:12: 5000000 INFO @ Thu, 11 Jan 2018 02:19:19: 6000000 INFO @ Thu, 11 Jan 2018 02:19:19: 6000000 INFO @ Thu, 11 Jan 2018 02:19:20: 6000000 INFO @ Thu, 11 Jan 2018 02:19:26: 7000000 INFO @ Thu, 11 Jan 2018 02:19:26: 7000000 INFO @ Thu, 11 Jan 2018 02:19:27: 7000000 INFO @ Thu, 11 Jan 2018 02:19:33: 8000000 INFO @ Thu, 11 Jan 2018 02:19:34: 8000000 INFO @ Thu, 11 Jan 2018 02:19:34: 8000000 INFO @ Thu, 11 Jan 2018 02:19:40: 9000000 INFO @ Thu, 11 Jan 2018 02:19:41: 9000000 INFO @ Thu, 11 Jan 2018 02:19:42: 9000000 INFO @ Thu, 11 Jan 2018 02:19:47: 10000000 INFO @ Thu, 11 Jan 2018 02:19:48: 10000000 INFO @ Thu, 11 Jan 2018 02:19:49: 10000000 INFO @ Thu, 11 Jan 2018 02:19:53: 11000000 INFO @ Thu, 11 Jan 2018 02:19:55: 11000000 INFO @ Thu, 11 Jan 2018 02:19:56: 11000000 INFO @ Thu, 11 Jan 2018 02:20:00: 12000000 INFO @ Thu, 11 Jan 2018 02:20:03: 12000000 INFO @ Thu, 11 Jan 2018 02:20:04: 12000000 INFO @ Thu, 11 Jan 2018 02:20:07: 13000000 INFO @ Thu, 11 Jan 2018 02:20:10: 13000000 INFO @ Thu, 11 Jan 2018 02:20:11: 13000000 INFO @ Thu, 11 Jan 2018 02:20:14: 14000000 INFO @ Thu, 11 Jan 2018 02:20:18: 14000000 INFO @ Thu, 11 Jan 2018 02:20:18: 14000000 INFO @ Thu, 11 Jan 2018 02:20:21: 15000000 INFO @ Thu, 11 Jan 2018 02:20:25: 15000000 INFO @ Thu, 11 Jan 2018 02:20:26: 15000000 INFO @ Thu, 11 Jan 2018 02:20:26: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:20:26: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:20:26: #1 total tags in treatment: 15754349 INFO @ Thu, 11 Jan 2018 02:20:26: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:20:26: #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 02:20:26: #1 tags after filtering in treatment: 15754349 INFO @ Thu, 11 Jan 2018 02:20:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:20:26: #1 finished! INFO @ Thu, 11 Jan 2018 02:20:26: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:20:28: #2 number of paired peaks: 118 WARNING @ Thu, 11 Jan 2018 02:20:28: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 11 Jan 2018 02:20:28: start model_add_line... INFO @ Thu, 11 Jan 2018 02:20:28: start X-correlation... INFO @ Thu, 11 Jan 2018 02:20:28: end of X-cor INFO @ Thu, 11 Jan 2018 02:20:28: #2 finished! INFO @ Thu, 11 Jan 2018 02:20:28: #2 predicted fragment length is 55 bps INFO @ Thu, 11 Jan 2018 02:20:28: #2 alternative fragment length(s) may be 1,55,117,154,209,356,382,559,563,571,592 bps INFO @ Thu, 11 Jan 2018 02:20:28: #2.2 Generate R script for model : SRX3043411.05_model.r WARNING @ Thu, 11 Jan 2018 02:20:28: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:20:28: #2 You may need to consider one of the other alternative d(s): 1,55,117,154,209,356,382,559,563,571,592 WARNING @ Thu, 11 Jan 2018 02:20:28: #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 02:20:28: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:20:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:20:31: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:20:31: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:20:31: #1 total tags in treatment: 15754349 INFO @ Thu, 11 Jan 2018 02:20:31: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:20:31: #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 02:20:31: #1 tags after filtering in treatment: 15754349 INFO @ Thu, 11 Jan 2018 02:20:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:20:31: #1 finished! INFO @ Thu, 11 Jan 2018 02:20:31: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:20:31: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:20:31: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:20:31: #1 total tags in treatment: 15754349 INFO @ Thu, 11 Jan 2018 02:20:31: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:20:31: #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 02:20:32: #1 tags after filtering in treatment: 15754349 INFO @ Thu, 11 Jan 2018 02:20:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:20:32: #1 finished! INFO @ Thu, 11 Jan 2018 02:20:32: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:20:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:20:32: #2 number of paired peaks: 118 WARNING @ Thu, 11 Jan 2018 02:20:32: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 11 Jan 2018 02:20:32: start model_add_line... INFO @ Thu, 11 Jan 2018 02:20:32: start X-correlation... INFO @ Thu, 11 Jan 2018 02:20:32: end of X-cor INFO @ Thu, 11 Jan 2018 02:20:32: #2 finished! INFO @ Thu, 11 Jan 2018 02:20:32: #2 predicted fragment length is 55 bps INFO @ Thu, 11 Jan 2018 02:20:32: #2 alternative fragment length(s) may be 1,55,117,154,209,356,382,559,563,571,592 bps INFO @ Thu, 11 Jan 2018 02:20:32: #2.2 Generate R script for model : SRX3043411.20_model.r WARNING @ Thu, 11 Jan 2018 02:20:32: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:20:32: #2 You may need to consider one of the other alternative d(s): 1,55,117,154,209,356,382,559,563,571,592 WARNING @ Thu, 11 Jan 2018 02:20:32: #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 02:20:32: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:20:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:20:33: #2 number of paired peaks: 118 WARNING @ Thu, 11 Jan 2018 02:20:33: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 11 Jan 2018 02:20:33: start model_add_line... INFO @ Thu, 11 Jan 2018 02:20:33: start X-correlation... INFO @ Thu, 11 Jan 2018 02:20:33: end of X-cor INFO @ Thu, 11 Jan 2018 02:20:33: #2 finished! INFO @ Thu, 11 Jan 2018 02:20:33: #2 predicted fragment length is 55 bps INFO @ Thu, 11 Jan 2018 02:20:33: #2 alternative fragment length(s) may be 1,55,117,154,209,356,382,559,563,571,592 bps INFO @ Thu, 11 Jan 2018 02:20:33: #2.2 Generate R script for model : SRX3043411.10_model.r WARNING @ Thu, 11 Jan 2018 02:20:33: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:20:33: #2 You may need to consider one of the other alternative d(s): 1,55,117,154,209,356,382,559,563,571,592 WARNING @ Thu, 11 Jan 2018 02:20:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:20:33: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:20:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:20:58: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:21:02: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:21:05: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:21:15: #4 Write output xls file... SRX3043411.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:21:15: #4 Write peak in narrowPeak format file... SRX3043411.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:21:15: #4 Write summits bed file... SRX3043411.05_summits.bed INFO @ Thu, 11 Jan 2018 02:21:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (505 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:21:18: #4 Write output xls file... SRX3043411.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:21:18: #4 Write peak in narrowPeak format file... SRX3043411.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:21:18: #4 Write summits bed file... SRX3043411.20_summits.bed INFO @ Thu, 11 Jan 2018 02:21:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (62 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:21:20: #4 Write output xls file... SRX3043411.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:21:20: #4 Write peak in narrowPeak format file... SRX3043411.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:21:20: #4 Write summits bed file... SRX3043411.10_summits.bed INFO @ Thu, 11 Jan 2018 02:21:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (275 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。