Job ID = 10194726 sra ファイルのダウンロード中... Completed: 6435254K bytes transferred in 88 seconds (595786K 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 107811340 spots for /home/okishinya/chipatlas/results/rn6/SRX1037561/SRR2039165.sra Written 107811340 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 07:18:56 107811340 reads; of these: 107811340 (100.00%) were unpaired; of these: 3242607 (3.01%) aligned 0 times 80698228 (74.85%) aligned exactly 1 time 23870505 (22.14%) aligned >1 times 96.99% overall alignment rate Time searching: 07:19:01 Overall time: 07:19:01 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 44 files... [bam_rmdupse_core] 99677653 / 104568733 = 0.9532 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 @ Sat, 11 Nov 2017 03:29:45: # Command line: callpeak -t SRX1037561.bam -f BAM -g 2.15e9 -n SRX1037561.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1037561.20 # format = BAM # ChIP-seq file = ['SRX1037561.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 @ Sat, 11 Nov 2017 03:29:45: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:29:45: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:29:45: # Command line: callpeak -t SRX1037561.bam -f BAM -g 2.15e9 -n SRX1037561.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1037561.05 # format = BAM # ChIP-seq file = ['SRX1037561.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 @ Sat, 11 Nov 2017 03:29:45: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:29:45: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:29:45: # Command line: callpeak -t SRX1037561.bam -f BAM -g 2.15e9 -n SRX1037561.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1037561.10 # format = BAM # ChIP-seq file = ['SRX1037561.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 @ Sat, 11 Nov 2017 03:29:45: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:29:45: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:30:10: 1000000 INFO @ Sat, 11 Nov 2017 03:30:26: 1000000 INFO @ Sat, 11 Nov 2017 03:30:27: 1000000 INFO @ Sat, 11 Nov 2017 03:30:28: 2000000 INFO @ Sat, 11 Nov 2017 03:30:49: 3000000 INFO @ Sat, 11 Nov 2017 03:30:52: 2000000 INFO @ Sat, 11 Nov 2017 03:30:56: 2000000 INFO @ Sat, 11 Nov 2017 03:31:11: 4000000 INFO @ Sat, 11 Nov 2017 03:31:15: 3000000 INFO @ Sat, 11 Nov 2017 03:31:23: 3000000 INFO @ Sat, 11 Nov 2017 03:31:31: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 03:31:31: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 03:31:31: #1 total tags in treatment: 4891080 INFO @ Sat, 11 Nov 2017 03:31:31: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:31:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 03:31:32: #1 tags after filtering in treatment: 4890780 INFO @ Sat, 11 Nov 2017 03:31:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:31:32: #1 finished! INFO @ Sat, 11 Nov 2017 03:31:32: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:31:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:31:37: #2 number of paired peaks: 86994 INFO @ Sat, 11 Nov 2017 03:31:37: start model_add_line... INFO @ Sat, 11 Nov 2017 03:31:37: start X-correlation... INFO @ Sat, 11 Nov 2017 03:31:37: end of X-cor INFO @ Sat, 11 Nov 2017 03:31:37: #2 finished! INFO @ Sat, 11 Nov 2017 03:31:37: #2 predicted fragment length is 110 bps INFO @ Sat, 11 Nov 2017 03:31:37: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 11 Nov 2017 03:31:37: #2.2 Generate R script for model : SRX1037561.10_model.r WARNING @ Sat, 11 Nov 2017 03:31:37: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 03:31:37: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Sat, 11 Nov 2017 03:31:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 03:31:37: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:31:40: 4000000 INFO @ Sat, 11 Nov 2017 03:31:50: 4000000 INFO @ Sat, 11 Nov 2017 03:32:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:32:02: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 03:32:02: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 03:32:02: #1 total tags in treatment: 4891080 INFO @ Sat, 11 Nov 2017 03:32:02: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:32:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 03:32:02: #1 tags after filtering in treatment: 4890780 INFO @ Sat, 11 Nov 2017 03:32:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:32:02: #1 finished! INFO @ Sat, 11 Nov 2017 03:32:02: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:32:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:32:09: #2 number of paired peaks: 86994 INFO @ Sat, 11 Nov 2017 03:32:09: start model_add_line... INFO @ Sat, 11 Nov 2017 03:32:10: start X-correlation... INFO @ Sat, 11 Nov 2017 03:32:10: end of X-cor INFO @ Sat, 11 Nov 2017 03:32:10: #2 finished! INFO @ Sat, 11 Nov 2017 03:32:10: #2 predicted fragment length is 110 bps INFO @ Sat, 11 Nov 2017 03:32:10: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 11 Nov 2017 03:32:10: #2.2 Generate R script for model : SRX1037561.05_model.r WARNING @ Sat, 11 Nov 2017 03:32:10: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 03:32:10: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Sat, 11 Nov 2017 03:32:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 03:32:10: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:32:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:32:12: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 03:32:12: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 03:32:12: #1 total tags in treatment: 4891080 INFO @ Sat, 11 Nov 2017 03:32:12: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:32:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 03:32:13: #1 tags after filtering in treatment: 4890780 INFO @ Sat, 11 Nov 2017 03:32:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:32:13: #1 finished! INFO @ Sat, 11 Nov 2017 03:32:13: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:32:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:32:19: #2 number of paired peaks: 86994 INFO @ Sat, 11 Nov 2017 03:32:19: start model_add_line... INFO @ Sat, 11 Nov 2017 03:32:19: start X-correlation... INFO @ Sat, 11 Nov 2017 03:32:19: end of X-cor INFO @ Sat, 11 Nov 2017 03:32:19: #2 finished! INFO @ Sat, 11 Nov 2017 03:32:19: #2 predicted fragment length is 110 bps INFO @ Sat, 11 Nov 2017 03:32:19: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 11 Nov 2017 03:32:19: #2.2 Generate R script for model : SRX1037561.20_model.r WARNING @ Sat, 11 Nov 2017 03:32:19: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 03:32:19: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Sat, 11 Nov 2017 03:32:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 03:32:19: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:32:19: #4 Write output xls file... SRX1037561.10_peaks.xls INFO @ Sat, 11 Nov 2017 03:32:19: #4 Write peak in narrowPeak format file... SRX1037561.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:32:19: #4 Write summits bed file... SRX1037561.10_summits.bed INFO @ Sat, 11 Nov 2017 03:32:19: Done! pass1 - making usageList (40 chroms): 3 millis pass2 - checking and writing primary data (1150 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:32:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:32:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:32:52: #4 Write output xls file... SRX1037561.20_peaks.xls INFO @ Sat, 11 Nov 2017 03:32:52: #4 Write peak in narrowPeak format file... SRX1037561.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:32:52: #4 Write summits bed file... SRX1037561.20_summits.bed INFO @ Sat, 11 Nov 2017 03:32:52: Done! pass1 - making usageList (24 chroms): 2 millis pass2 - checking and writing primary data (166 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:33:02: #4 Write output xls file... SRX1037561.05_peaks.xls INFO @ Sat, 11 Nov 2017 03:33:02: #4 Write peak in narrowPeak format file... SRX1037561.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:33:03: #4 Write summits bed file... SRX1037561.05_summits.bed INFO @ Sat, 11 Nov 2017 03:33:03: Done! pass1 - making usageList (86 chroms): 5 millis pass2 - checking and writing primary data (11789 records, 4 fields): 46 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。