Job ID = 11632734 sra ファイルのダウンロード中... Completed: 591046K bytes transferred in 8 seconds (596911K 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... Read 34823334 spots for /home/okishinya/chipatlas/results/rn6/SRX4497204/SRR7633474.sra Written 34823334 spots for /home/okishinya/chipatlas/results/rn6/SRX4497204/SRR7633474.sra 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:28:26 34823334 reads; of these: 34823334 (100.00%) were unpaired; of these: 7161147 (20.56%) aligned 0 times 19560912 (56.17%) aligned exactly 1 time 8101275 (23.26%) aligned >1 times 79.44% overall alignment rate Time searching: 00:28:29 Overall time: 00:28:29 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 12 files... [bam_rmdupse_core] 14511349 / 27662187 = 0.5246 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 @ Fri, 15 Feb 2019 07:57:20: # Command line: callpeak -t SRX4497204.bam -f BAM -g 2.15e9 -n SRX4497204.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4497204.20 # format = BAM # ChIP-seq file = ['SRX4497204.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 @ Fri, 15 Feb 2019 07:57:20: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:57:20: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:57:20: # Command line: callpeak -t SRX4497204.bam -f BAM -g 2.15e9 -n SRX4497204.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4497204.10 # format = BAM # ChIP-seq file = ['SRX4497204.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 @ Fri, 15 Feb 2019 07:57:20: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:57:20: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:57:20: # Command line: callpeak -t SRX4497204.bam -f BAM -g 2.15e9 -n SRX4497204.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4497204.05 # format = BAM # ChIP-seq file = ['SRX4497204.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 @ Fri, 15 Feb 2019 07:57:20: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:57:20: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:57:27: 1000000 INFO @ Fri, 15 Feb 2019 07:57:27: 1000000 INFO @ Fri, 15 Feb 2019 07:57:27: 1000000 INFO @ Fri, 15 Feb 2019 07:57:34: 2000000 INFO @ Fri, 15 Feb 2019 07:57:34: 2000000 INFO @ Fri, 15 Feb 2019 07:57:34: 2000000 INFO @ Fri, 15 Feb 2019 07:57:42: 3000000 INFO @ Fri, 15 Feb 2019 07:57:42: 3000000 INFO @ Fri, 15 Feb 2019 07:57:42: 3000000 INFO @ Fri, 15 Feb 2019 07:57:49: 4000000 INFO @ Fri, 15 Feb 2019 07:57:49: 4000000 INFO @ Fri, 15 Feb 2019 07:57:49: 4000000 INFO @ Fri, 15 Feb 2019 07:57:56: 5000000 INFO @ Fri, 15 Feb 2019 07:57:56: 5000000 INFO @ Fri, 15 Feb 2019 07:57:56: 5000000 INFO @ Fri, 15 Feb 2019 07:58:03: 6000000 INFO @ Fri, 15 Feb 2019 07:58:03: 6000000 INFO @ Fri, 15 Feb 2019 07:58:03: 6000000 INFO @ Fri, 15 Feb 2019 07:58:10: 7000000 INFO @ Fri, 15 Feb 2019 07:58:10: 7000000 INFO @ Fri, 15 Feb 2019 07:58:10: 7000000 INFO @ Fri, 15 Feb 2019 07:58:17: 8000000 INFO @ Fri, 15 Feb 2019 07:58:17: 8000000 INFO @ Fri, 15 Feb 2019 07:58:18: 8000000 INFO @ Fri, 15 Feb 2019 07:58:25: 9000000 INFO @ Fri, 15 Feb 2019 07:58:25: 9000000 INFO @ Fri, 15 Feb 2019 07:58:25: 9000000 INFO @ Fri, 15 Feb 2019 07:58:32: 10000000 INFO @ Fri, 15 Feb 2019 07:58:32: 10000000 INFO @ Fri, 15 Feb 2019 07:58:32: 10000000 INFO @ Fri, 15 Feb 2019 07:58:39: 11000000 INFO @ Fri, 15 Feb 2019 07:58:39: 11000000 INFO @ Fri, 15 Feb 2019 07:58:40: 11000000 INFO @ Fri, 15 Feb 2019 07:58:47: 12000000 INFO @ Fri, 15 Feb 2019 07:58:47: 12000000 INFO @ Fri, 15 Feb 2019 07:58:47: 12000000 INFO @ Fri, 15 Feb 2019 07:58:55: 13000000 INFO @ Fri, 15 Feb 2019 07:58:55: 13000000 INFO @ Fri, 15 Feb 2019 07:58:55: 13000000 INFO @ Fri, 15 Feb 2019 07:58:56: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:58:56: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:58:56: #1 total tags in treatment: 13150838 INFO @ Fri, 15 Feb 2019 07:58:56: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:58:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:58:56: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:58:56: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:58:56: #1 total tags in treatment: 13150838 INFO @ Fri, 15 Feb 2019 07:58:56: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:58:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:58:57: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:58:57: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:58:57: #1 total tags in treatment: 13150838 INFO @ Fri, 15 Feb 2019 07:58:57: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:58:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:58:57: #1 tags after filtering in treatment: 13150681 INFO @ Fri, 15 Feb 2019 07:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:58:57: #1 finished! INFO @ Fri, 15 Feb 2019 07:58:57: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:58:57: #1 tags after filtering in treatment: 13150681 INFO @ Fri, 15 Feb 2019 07:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:58:57: #1 finished! INFO @ Fri, 15 Feb 2019 07:58:57: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:58:57: #1 tags after filtering in treatment: 13150681 INFO @ Fri, 15 Feb 2019 07:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:58:57: #1 finished! INFO @ Fri, 15 Feb 2019 07:58:57: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:58:59: #2 number of paired peaks: 14079 INFO @ Fri, 15 Feb 2019 07:58:59: start model_add_line... INFO @ Fri, 15 Feb 2019 07:58:59: start X-correlation... INFO @ Fri, 15 Feb 2019 07:58:59: #2 number of paired peaks: 14079 INFO @ Fri, 15 Feb 2019 07:58:59: start model_add_line... INFO @ Fri, 15 Feb 2019 07:58:59: end of X-cor INFO @ Fri, 15 Feb 2019 07:58:59: #2 finished! INFO @ Fri, 15 Feb 2019 07:58:59: #2 predicted fragment length is 51 bps INFO @ Fri, 15 Feb 2019 07:58:59: #2 alternative fragment length(s) may be 51,132,212 bps INFO @ Fri, 15 Feb 2019 07:58:59: #2.2 Generate R script for model : SRX4497204.10_model.r WARNING @ Fri, 15 Feb 2019 07:58:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:58:59: #2 You may need to consider one of the other alternative d(s): 51,132,212 WARNING @ Fri, 15 Feb 2019 07:58:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:58:59: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:58:59: start X-correlation... INFO @ Fri, 15 Feb 2019 07:58:59: end of X-cor INFO @ Fri, 15 Feb 2019 07:58:59: #2 finished! INFO @ Fri, 15 Feb 2019 07:58:59: #2 predicted fragment length is 51 bps INFO @ Fri, 15 Feb 2019 07:58:59: #2 alternative fragment length(s) may be 51,132,212 bps INFO @ Fri, 15 Feb 2019 07:58:59: #2.2 Generate R script for model : SRX4497204.20_model.r WARNING @ Fri, 15 Feb 2019 07:58:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:58:59: #2 You may need to consider one of the other alternative d(s): 51,132,212 WARNING @ Fri, 15 Feb 2019 07:58:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:58:59: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:58:59: #2 number of paired peaks: 14079 INFO @ Fri, 15 Feb 2019 07:58:59: start model_add_line... INFO @ Fri, 15 Feb 2019 07:58:59: start X-correlation... INFO @ Fri, 15 Feb 2019 07:58:59: end of X-cor INFO @ Fri, 15 Feb 2019 07:58:59: #2 finished! INFO @ Fri, 15 Feb 2019 07:58:59: #2 predicted fragment length is 51 bps INFO @ Fri, 15 Feb 2019 07:58:59: #2 alternative fragment length(s) may be 51,132,212 bps INFO @ Fri, 15 Feb 2019 07:58:59: #2.2 Generate R script for model : SRX4497204.05_model.r WARNING @ Fri, 15 Feb 2019 07:58:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:58:59: #2 You may need to consider one of the other alternative d(s): 51,132,212 WARNING @ Fri, 15 Feb 2019 07:58:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:58:59: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:59:30: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:59:31: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:59:32: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:59:47: #4 Write output xls file... SRX4497204.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:59:47: #4 Write peak in narrowPeak format file... SRX4497204.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:59:47: #4 Write summits bed file... SRX4497204.20_summits.bed INFO @ Fri, 15 Feb 2019 07:59:47: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (474 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:59:49: #4 Write output xls file... SRX4497204.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:59:49: #4 Write peak in narrowPeak format file... SRX4497204.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:59:49: #4 Write summits bed file... SRX4497204.05_summits.bed INFO @ Fri, 15 Feb 2019 07:59:49: Done! pass1 - making usageList (57 chroms): 4 millis pass2 - checking and writing primary data (2309 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:59:50: #4 Write output xls file... SRX4497204.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:59:50: #4 Write peak in narrowPeak format file... SRX4497204.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:59:50: #4 Write summits bed file... SRX4497204.10_summits.bed INFO @ Fri, 15 Feb 2019 07:59:50: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (1219 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。