Job ID = 10320316 sra ファイルのダウンロード中... Completed: 583539K bytes transferred in 80 seconds (59331K 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 17069793 spots for /home/okishinya/chipatlas/results/ce10/SRX3043407/SRR5875891.sra Written 17069793 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: 00:05:59 17069793 reads; of these: 17069793 (100.00%) were unpaired; of these: 192579 (1.13%) aligned 0 times 14337658 (83.99%) aligned exactly 1 time 2539556 (14.88%) aligned >1 times 98.87% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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] 2329362 / 16877214 = 0.1380 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 02:17:18: # Command line: callpeak -t SRX3043407.bam -f BAM -g ce -n SRX3043407.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043407.05 # format = BAM # ChIP-seq file = ['SRX3043407.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 02:17:18: # Command line: callpeak -t SRX3043407.bam -f BAM -g ce -n SRX3043407.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043407.10 # format = BAM # ChIP-seq file = ['SRX3043407.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 02:17:18: # Command line: callpeak -t SRX3043407.bam -f BAM -g ce -n SRX3043407.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043407.20 # format = BAM # ChIP-seq file = ['SRX3043407.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 02:17:18: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:17:18: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:17:18: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:17:18: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:17:18: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:17:18: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:17:25: 1000000 INFO @ Thu, 11 Jan 2018 02:17:25: 1000000 INFO @ Thu, 11 Jan 2018 02:17:25: 1000000 INFO @ Thu, 11 Jan 2018 02:17:31: 2000000 INFO @ Thu, 11 Jan 2018 02:17:31: 2000000 INFO @ Thu, 11 Jan 2018 02:17:31: 2000000 INFO @ Thu, 11 Jan 2018 02:17:37: 3000000 INFO @ Thu, 11 Jan 2018 02:17:38: 3000000 INFO @ Thu, 11 Jan 2018 02:17:38: 3000000 INFO @ Thu, 11 Jan 2018 02:17:44: 4000000 INFO @ Thu, 11 Jan 2018 02:17:44: 4000000 INFO @ Thu, 11 Jan 2018 02:17:44: 4000000 INFO @ Thu, 11 Jan 2018 02:17:50: 5000000 INFO @ Thu, 11 Jan 2018 02:17:51: 5000000 INFO @ Thu, 11 Jan 2018 02:17:51: 5000000 INFO @ Thu, 11 Jan 2018 02:17:57: 6000000 INFO @ Thu, 11 Jan 2018 02:17:57: 6000000 INFO @ Thu, 11 Jan 2018 02:17:57: 6000000 INFO @ Thu, 11 Jan 2018 02:18:03: 7000000 INFO @ Thu, 11 Jan 2018 02:18:03: 7000000 INFO @ Thu, 11 Jan 2018 02:18:04: 7000000 INFO @ Thu, 11 Jan 2018 02:18:09: 8000000 INFO @ Thu, 11 Jan 2018 02:18:10: 8000000 INFO @ Thu, 11 Jan 2018 02:18:10: 8000000 INFO @ Thu, 11 Jan 2018 02:18:16: 9000000 INFO @ Thu, 11 Jan 2018 02:18:16: 9000000 INFO @ Thu, 11 Jan 2018 02:18:17: 9000000 INFO @ Thu, 11 Jan 2018 02:18:22: 10000000 INFO @ Thu, 11 Jan 2018 02:18:22: 10000000 INFO @ Thu, 11 Jan 2018 02:18:23: 10000000 INFO @ Thu, 11 Jan 2018 02:18:29: 11000000 INFO @ Thu, 11 Jan 2018 02:18:29: 11000000 INFO @ Thu, 11 Jan 2018 02:18:30: 11000000 INFO @ Thu, 11 Jan 2018 02:18:35: 12000000 INFO @ Thu, 11 Jan 2018 02:18:35: 12000000 INFO @ Thu, 11 Jan 2018 02:18:36: 12000000 INFO @ Thu, 11 Jan 2018 02:18:41: 13000000 INFO @ Thu, 11 Jan 2018 02:18:42: 13000000 INFO @ Thu, 11 Jan 2018 02:18:43: 13000000 INFO @ Thu, 11 Jan 2018 02:18:48: 14000000 INFO @ Thu, 11 Jan 2018 02:18:48: 14000000 INFO @ Thu, 11 Jan 2018 02:18:49: 14000000 INFO @ Thu, 11 Jan 2018 02:18:51: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:18:51: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:18:51: #1 total tags in treatment: 14547852 INFO @ Thu, 11 Jan 2018 02:18:51: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:18:51: #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 02:18:52: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:18:52: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:18:52: #1 total tags in treatment: 14547852 INFO @ Thu, 11 Jan 2018 02:18:52: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:18:52: #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 02:18:52: #1 tags after filtering in treatment: 14547852 INFO @ Thu, 11 Jan 2018 02:18:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:18:52: #1 finished! INFO @ Thu, 11 Jan 2018 02:18:52: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:18:52: #1 tags after filtering in treatment: 14547852 INFO @ Thu, 11 Jan 2018 02:18:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:18:52: #1 finished! INFO @ Thu, 11 Jan 2018 02:18:52: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:18:53: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:18:53: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:18:53: #1 total tags in treatment: 14547852 INFO @ Thu, 11 Jan 2018 02:18:53: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:18:53: #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 02:18:53: #2 number of paired peaks: 111 WARNING @ Thu, 11 Jan 2018 02:18:53: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Thu, 11 Jan 2018 02:18:53: start model_add_line... INFO @ Thu, 11 Jan 2018 02:18:53: #2 number of paired peaks: 111 WARNING @ Thu, 11 Jan 2018 02:18:53: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Thu, 11 Jan 2018 02:18:53: start model_add_line... INFO @ Thu, 11 Jan 2018 02:18:53: start X-correlation... INFO @ Thu, 11 Jan 2018 02:18:53: #1 tags after filtering in treatment: 14547852 INFO @ Thu, 11 Jan 2018 02:18:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:18:53: #1 finished! INFO @ Thu, 11 Jan 2018 02:18:53: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:18:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:18:53: start X-correlation... INFO @ Thu, 11 Jan 2018 02:18:53: end of X-cor INFO @ Thu, 11 Jan 2018 02:18:53: end of X-cor INFO @ Thu, 11 Jan 2018 02:18:53: #2 finished! INFO @ Thu, 11 Jan 2018 02:18:53: #2 finished! INFO @ Thu, 11 Jan 2018 02:18:53: #2 predicted fragment length is 56 bps INFO @ Thu, 11 Jan 2018 02:18:53: #2 predicted fragment length is 56 bps INFO @ Thu, 11 Jan 2018 02:18:53: #2 alternative fragment length(s) may be 1,56,153,379,500,575 bps INFO @ Thu, 11 Jan 2018 02:18:53: #2 alternative fragment length(s) may be 1,56,153,379,500,575 bps INFO @ Thu, 11 Jan 2018 02:18:53: #2.2 Generate R script for model : SRX3043407.05_model.r INFO @ Thu, 11 Jan 2018 02:18:53: #2.2 Generate R script for model : SRX3043407.20_model.r WARNING @ Thu, 11 Jan 2018 02:18:53: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:18:53: #2 You may need to consider one of the other alternative d(s): 1,56,153,379,500,575 WARNING @ Thu, 11 Jan 2018 02:18:53: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:18:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Thu, 11 Jan 2018 02:18:53: #2 You may need to consider one of the other alternative d(s): 1,56,153,379,500,575 INFO @ Thu, 11 Jan 2018 02:18:53: #3 Call peaks... WARNING @ Thu, 11 Jan 2018 02:18:53: #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 02:18:53: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:18:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:18:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:18:54: #2 number of paired peaks: 111 WARNING @ Thu, 11 Jan 2018 02:18:54: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Thu, 11 Jan 2018 02:18:54: start model_add_line... INFO @ Thu, 11 Jan 2018 02:18:54: start X-correlation... INFO @ Thu, 11 Jan 2018 02:18:54: end of X-cor INFO @ Thu, 11 Jan 2018 02:18:54: #2 finished! INFO @ Thu, 11 Jan 2018 02:18:54: #2 predicted fragment length is 56 bps INFO @ Thu, 11 Jan 2018 02:18:54: #2 alternative fragment length(s) may be 1,56,153,379,500,575 bps INFO @ Thu, 11 Jan 2018 02:18:54: #2.2 Generate R script for model : SRX3043407.10_model.r WARNING @ Thu, 11 Jan 2018 02:18:54: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:18:54: #2 You may need to consider one of the other alternative d(s): 1,56,153,379,500,575 WARNING @ Thu, 11 Jan 2018 02:18:54: #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 02:18:54: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:18:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:19:20: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:19:21: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:19:23: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:19:34: #4 Write output xls file... SRX3043407.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:19:34: #4 Write peak in narrowPeak format file... SRX3043407.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:19:34: #4 Write summits bed file... SRX3043407.05_summits.bed INFO @ Thu, 11 Jan 2018 02:19:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (548 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:19:35: #4 Write output xls file... SRX3043407.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:19:35: #4 Write peak in narrowPeak format file... SRX3043407.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:19:35: #4 Write summits bed file... SRX3043407.10_summits.bed INFO @ Thu, 11 Jan 2018 02:19:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (291 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:19:37: #4 Write output xls file... SRX3043407.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:19:37: #4 Write peak in narrowPeak format file... SRX3043407.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:19:37: #4 Write summits bed file... SRX3043407.20_summits.bed INFO @ Thu, 11 Jan 2018 02:19:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (83 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。