Job ID = 10608867 sra ファイルのダウンロード中... Completed: 580752K bytes transferred in 33 seconds (141605K 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 12783139 spots for /home/okishinya/chipatlas/results/rn6/SRX2727601/SRR5437664.sra Written 12783139 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:23:31 12783139 reads; of these: 12783139 (100.00%) were unpaired; of these: 437268 (3.42%) aligned 0 times 9471501 (74.09%) aligned exactly 1 time 2874370 (22.49%) aligned >1 times 96.58% overall alignment rate Time searching: 00:23:34 Overall time: 00:23:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 432313 / 12345871 = 0.0350 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, 03 May 2018 22:43:20: # Command line: callpeak -t SRX2727601.bam -f BAM -g 2.15e9 -n SRX2727601.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2727601.10 # format = BAM # ChIP-seq file = ['SRX2727601.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 03 May 2018 22:43:20: #1 read tag files... INFO @ Thu, 03 May 2018 22:43:20: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:43:20: # Command line: callpeak -t SRX2727601.bam -f BAM -g 2.15e9 -n SRX2727601.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2727601.20 # format = BAM # ChIP-seq file = ['SRX2727601.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 03 May 2018 22:43:20: #1 read tag files... INFO @ Thu, 03 May 2018 22:43:20: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:43:20: # Command line: callpeak -t SRX2727601.bam -f BAM -g 2.15e9 -n SRX2727601.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2727601.05 # format = BAM # ChIP-seq file = ['SRX2727601.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 03 May 2018 22:43:20: #1 read tag files... INFO @ Thu, 03 May 2018 22:43:20: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:43:32: 1000000 INFO @ Thu, 03 May 2018 22:43:32: 1000000 INFO @ Thu, 03 May 2018 22:43:32: 1000000 INFO @ Thu, 03 May 2018 22:43:44: 2000000 INFO @ Thu, 03 May 2018 22:43:44: 2000000 INFO @ Thu, 03 May 2018 22:43:44: 2000000 INFO @ Thu, 03 May 2018 22:43:56: 3000000 INFO @ Thu, 03 May 2018 22:43:56: 3000000 INFO @ Thu, 03 May 2018 22:43:56: 3000000 INFO @ Thu, 03 May 2018 22:44:07: 4000000 INFO @ Thu, 03 May 2018 22:44:07: 4000000 INFO @ Thu, 03 May 2018 22:44:07: 4000000 INFO @ Thu, 03 May 2018 22:44:17: 5000000 INFO @ Thu, 03 May 2018 22:44:17: 5000000 INFO @ Thu, 03 May 2018 22:44:18: 5000000 INFO @ Thu, 03 May 2018 22:44:28: 6000000 INFO @ Thu, 03 May 2018 22:44:28: 6000000 INFO @ Thu, 03 May 2018 22:44:28: 6000000 INFO @ Thu, 03 May 2018 22:44:38: 7000000 INFO @ Thu, 03 May 2018 22:44:38: 7000000 INFO @ Thu, 03 May 2018 22:44:38: 7000000 INFO @ Thu, 03 May 2018 22:44:48: 8000000 INFO @ Thu, 03 May 2018 22:44:48: 8000000 INFO @ Thu, 03 May 2018 22:44:48: 8000000 INFO @ Thu, 03 May 2018 22:44:58: 9000000 INFO @ Thu, 03 May 2018 22:44:58: 9000000 INFO @ Thu, 03 May 2018 22:44:58: 9000000 INFO @ Thu, 03 May 2018 22:45:08: 10000000 INFO @ Thu, 03 May 2018 22:45:09: 10000000 INFO @ Thu, 03 May 2018 22:45:09: 10000000 INFO @ Thu, 03 May 2018 22:45:18: 11000000 INFO @ Thu, 03 May 2018 22:45:19: 11000000 INFO @ Thu, 03 May 2018 22:45:19: 11000000 INFO @ Thu, 03 May 2018 22:45:27: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:45:27: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:45:27: #1 total tags in treatment: 11913558 INFO @ Thu, 03 May 2018 22:45:27: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:45:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:45:27: #1 tags after filtering in treatment: 11913370 INFO @ Thu, 03 May 2018 22:45:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:45:27: #1 finished! INFO @ Thu, 03 May 2018 22:45:27: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:45:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:45:29: #2 number of paired peaks: 5430 INFO @ Thu, 03 May 2018 22:45:29: start model_add_line... INFO @ Thu, 03 May 2018 22:45:29: start X-correlation... INFO @ Thu, 03 May 2018 22:45:29: end of X-cor INFO @ Thu, 03 May 2018 22:45:29: #2 finished! INFO @ Thu, 03 May 2018 22:45:29: #2 predicted fragment length is 100 bps INFO @ Thu, 03 May 2018 22:45:29: #2 alternative fragment length(s) may be 100 bps INFO @ Thu, 03 May 2018 22:45:29: #2.2 Generate R script for model : SRX2727601.05_model.r WARNING @ Thu, 03 May 2018 22:45:29: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:45:29: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Thu, 03 May 2018 22:45:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:45:29: #3 Call peaks... INFO @ Thu, 03 May 2018 22:45:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:45:29: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:45:29: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:45:29: #1 total tags in treatment: 11913558 INFO @ Thu, 03 May 2018 22:45:29: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:45:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:45:29: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:45:29: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:45:29: #1 total tags in treatment: 11913558 INFO @ Thu, 03 May 2018 22:45:29: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:45:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:45:29: #1 tags after filtering in treatment: 11913370 INFO @ Thu, 03 May 2018 22:45:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:45:29: #1 finished! INFO @ Thu, 03 May 2018 22:45:29: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:45:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:45:29: #1 tags after filtering in treatment: 11913370 INFO @ Thu, 03 May 2018 22:45:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:45:29: #1 finished! INFO @ Thu, 03 May 2018 22:45:29: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:45:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:45:31: #2 number of paired peaks: 5430 INFO @ Thu, 03 May 2018 22:45:31: start model_add_line... INFO @ Thu, 03 May 2018 22:45:31: #2 number of paired peaks: 5430 INFO @ Thu, 03 May 2018 22:45:31: start model_add_line... INFO @ Thu, 03 May 2018 22:45:31: start X-correlation... INFO @ Thu, 03 May 2018 22:45:31: end of X-cor INFO @ Thu, 03 May 2018 22:45:31: #2 finished! INFO @ Thu, 03 May 2018 22:45:31: #2 predicted fragment length is 100 bps INFO @ Thu, 03 May 2018 22:45:31: #2 alternative fragment length(s) may be 100 bps INFO @ Thu, 03 May 2018 22:45:31: #2.2 Generate R script for model : SRX2727601.20_model.r WARNING @ Thu, 03 May 2018 22:45:31: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:45:31: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Thu, 03 May 2018 22:45:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:45:31: #3 Call peaks... INFO @ Thu, 03 May 2018 22:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:45:31: start X-correlation... INFO @ Thu, 03 May 2018 22:45:31: end of X-cor INFO @ Thu, 03 May 2018 22:45:31: #2 finished! INFO @ Thu, 03 May 2018 22:45:31: #2 predicted fragment length is 100 bps INFO @ Thu, 03 May 2018 22:45:31: #2 alternative fragment length(s) may be 100 bps INFO @ Thu, 03 May 2018 22:45:31: #2.2 Generate R script for model : SRX2727601.10_model.r WARNING @ Thu, 03 May 2018 22:45:31: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:45:31: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Thu, 03 May 2018 22:45:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:45:31: #3 Call peaks... INFO @ Thu, 03 May 2018 22:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:45:57: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:46:00: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:46:01: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:46:14: #4 Write output xls file... SRX2727601.05_peaks.xls INFO @ Thu, 03 May 2018 22:46:14: #4 Write peak in narrowPeak format file... SRX2727601.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:46:14: #4 Write summits bed file... SRX2727601.05_summits.bed INFO @ Thu, 03 May 2018 22:46:14: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (718 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:46:17: #4 Write output xls file... SRX2727601.10_peaks.xls INFO @ Thu, 03 May 2018 22:46:17: #4 Write peak in narrowPeak format file... SRX2727601.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:46:17: #4 Write summits bed file... SRX2727601.10_summits.bed INFO @ Thu, 03 May 2018 22:46:17: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (420 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:46:19: #4 Write output xls file... SRX2727601.20_peaks.xls INFO @ Thu, 03 May 2018 22:46:19: #4 Write peak in narrowPeak format file... SRX2727601.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:46:19: #4 Write summits bed file... SRX2727601.20_summits.bed INFO @ Thu, 03 May 2018 22:46:19: Done! pass1 - making usageList (20 chroms): 1 millis pass2 - checking and writing primary data (233 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。