Job ID = 10608864 sra ファイルのダウンロード中... Completed: 699566K bytes transferred in 25 seconds (227750K 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 15398857 spots for /home/okishinya/chipatlas/results/rn6/SRX2727598/SRR5437662.sra Written 15398857 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: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:29:11 15398857 reads; of these: 15398857 (100.00%) were unpaired; of these: 445963 (2.90%) aligned 0 times 11549307 (75.00%) aligned exactly 1 time 3403587 (22.10%) aligned >1 times 97.10% overall alignment rate Time searching: 00:29:17 Overall time: 00:29:18 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] 682264 / 14952894 = 0.0456 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 22:48:12: # Command line: callpeak -t SRX2727598.bam -f BAM -g 2.15e9 -n SRX2727598.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2727598.05 # format = BAM # ChIP-seq file = ['SRX2727598.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 22:48:12: #1 read tag files... INFO @ Thu, 03 May 2018 22:48:12: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:48:12: # Command line: callpeak -t SRX2727598.bam -f BAM -g 2.15e9 -n SRX2727598.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2727598.10 # format = BAM # ChIP-seq file = ['SRX2727598.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 22:48:12: #1 read tag files... INFO @ Thu, 03 May 2018 22:48:12: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:48:12: # Command line: callpeak -t SRX2727598.bam -f BAM -g 2.15e9 -n SRX2727598.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2727598.20 # format = BAM # ChIP-seq file = ['SRX2727598.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 22:48:12: #1 read tag files... INFO @ Thu, 03 May 2018 22:48:12: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:48:20: 1000000 INFO @ Thu, 03 May 2018 22:48:20: 1000000 INFO @ Thu, 03 May 2018 22:48:20: 1000000 INFO @ Thu, 03 May 2018 22:48:28: 2000000 INFO @ Thu, 03 May 2018 22:48:28: 2000000 INFO @ Thu, 03 May 2018 22:48:29: 2000000 INFO @ Thu, 03 May 2018 22:48:36: 3000000 INFO @ Thu, 03 May 2018 22:48:37: 3000000 INFO @ Thu, 03 May 2018 22:48:37: 3000000 INFO @ Thu, 03 May 2018 22:48:43: 4000000 INFO @ Thu, 03 May 2018 22:48:45: 4000000 INFO @ Thu, 03 May 2018 22:48:46: 4000000 INFO @ Thu, 03 May 2018 22:48:51: 5000000 INFO @ Thu, 03 May 2018 22:48:53: 5000000 INFO @ Thu, 03 May 2018 22:48:55: 5000000 INFO @ Thu, 03 May 2018 22:48:59: 6000000 INFO @ Thu, 03 May 2018 22:49:02: 6000000 INFO @ Thu, 03 May 2018 22:49:04: 6000000 INFO @ Thu, 03 May 2018 22:49:07: 7000000 INFO @ Thu, 03 May 2018 22:49:11: 7000000 INFO @ Thu, 03 May 2018 22:49:13: 7000000 INFO @ Thu, 03 May 2018 22:49:14: 8000000 INFO @ Thu, 03 May 2018 22:49:19: 8000000 INFO @ Thu, 03 May 2018 22:49:22: 8000000 INFO @ Thu, 03 May 2018 22:49:22: 9000000 INFO @ Thu, 03 May 2018 22:49:28: 9000000 INFO @ Thu, 03 May 2018 22:49:30: 10000000 INFO @ Thu, 03 May 2018 22:49:31: 9000000 INFO @ Thu, 03 May 2018 22:49:37: 10000000 INFO @ Thu, 03 May 2018 22:49:38: 11000000 INFO @ Thu, 03 May 2018 22:49:41: 10000000 INFO @ Thu, 03 May 2018 22:49:46: 12000000 INFO @ Thu, 03 May 2018 22:49:46: 11000000 INFO @ Thu, 03 May 2018 22:49:50: 11000000 INFO @ Thu, 03 May 2018 22:49:54: 13000000 INFO @ Thu, 03 May 2018 22:49:55: 12000000 INFO @ Thu, 03 May 2018 22:49:59: 12000000 INFO @ Thu, 03 May 2018 22:50:02: 14000000 INFO @ Thu, 03 May 2018 22:50:04: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:50:04: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:50:04: #1 total tags in treatment: 14270630 INFO @ Thu, 03 May 2018 22:50:04: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:50:04: #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 22:50:04: 13000000 INFO @ Thu, 03 May 2018 22:50:04: #1 tags after filtering in treatment: 14270456 INFO @ Thu, 03 May 2018 22:50:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:50:04: #1 finished! INFO @ Thu, 03 May 2018 22:50:04: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:50:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:50:06: #2 number of paired peaks: 4603 INFO @ Thu, 03 May 2018 22:50:06: start model_add_line... INFO @ Thu, 03 May 2018 22:50:06: start X-correlation... INFO @ Thu, 03 May 2018 22:50:06: end of X-cor INFO @ Thu, 03 May 2018 22:50:06: #2 finished! INFO @ Thu, 03 May 2018 22:50:06: #2 predicted fragment length is 99 bps INFO @ Thu, 03 May 2018 22:50:06: #2 alternative fragment length(s) may be 99 bps INFO @ Thu, 03 May 2018 22:50:06: #2.2 Generate R script for model : SRX2727598.20_model.r WARNING @ Thu, 03 May 2018 22:50:06: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:50:06: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Thu, 03 May 2018 22:50:06: #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 22:50:06: #3 Call peaks... INFO @ Thu, 03 May 2018 22:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:50:08: 13000000 INFO @ Thu, 03 May 2018 22:50:13: 14000000 INFO @ Thu, 03 May 2018 22:50:15: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:50:15: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:50:15: #1 total tags in treatment: 14270630 INFO @ Thu, 03 May 2018 22:50:15: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:50:15: #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 22:50:16: #1 tags after filtering in treatment: 14270456 INFO @ Thu, 03 May 2018 22:50:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:50:16: #1 finished! INFO @ Thu, 03 May 2018 22:50:16: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:50:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:50:17: 14000000 INFO @ Thu, 03 May 2018 22:50:17: #2 number of paired peaks: 4603 INFO @ Thu, 03 May 2018 22:50:17: start model_add_line... INFO @ Thu, 03 May 2018 22:50:18: start X-correlation... INFO @ Thu, 03 May 2018 22:50:18: end of X-cor INFO @ Thu, 03 May 2018 22:50:18: #2 finished! INFO @ Thu, 03 May 2018 22:50:18: #2 predicted fragment length is 99 bps INFO @ Thu, 03 May 2018 22:50:18: #2 alternative fragment length(s) may be 99 bps INFO @ Thu, 03 May 2018 22:50:18: #2.2 Generate R script for model : SRX2727598.05_model.r WARNING @ Thu, 03 May 2018 22:50:18: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:50:18: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Thu, 03 May 2018 22:50:18: #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 22:50:18: #3 Call peaks... INFO @ Thu, 03 May 2018 22:50:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:50:20: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:50:20: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:50:20: #1 total tags in treatment: 14270630 INFO @ Thu, 03 May 2018 22:50:20: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:50:20: #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 22:50:20: #1 tags after filtering in treatment: 14270456 INFO @ Thu, 03 May 2018 22:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:50:20: #1 finished! INFO @ Thu, 03 May 2018 22:50:20: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:50:22: #2 number of paired peaks: 4603 INFO @ Thu, 03 May 2018 22:50:22: start model_add_line... INFO @ Thu, 03 May 2018 22:50:22: start X-correlation... INFO @ Thu, 03 May 2018 22:50:22: end of X-cor INFO @ Thu, 03 May 2018 22:50:22: #2 finished! INFO @ Thu, 03 May 2018 22:50:22: #2 predicted fragment length is 99 bps INFO @ Thu, 03 May 2018 22:50:22: #2 alternative fragment length(s) may be 99 bps INFO @ Thu, 03 May 2018 22:50:22: #2.2 Generate R script for model : SRX2727598.10_model.r WARNING @ Thu, 03 May 2018 22:50:22: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:50:22: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Thu, 03 May 2018 22:50:22: #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 22:50:22: #3 Call peaks... INFO @ Thu, 03 May 2018 22:50:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:50:41: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:50:56: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:50:58: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:50:59: #4 Write output xls file... SRX2727598.20_peaks.xls INFO @ Thu, 03 May 2018 22:50:59: #4 Write peak in narrowPeak format file... SRX2727598.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:50:59: #4 Write summits bed file... SRX2727598.20_summits.bed INFO @ Thu, 03 May 2018 22:50:59: Done! pass1 - making usageList (24 chroms): 0 millis pass2 - checking and writing primary data (269 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:51:16: #4 Write output xls file... SRX2727598.10_peaks.xls INFO @ Thu, 03 May 2018 22:51:16: #4 Write peak in narrowPeak format file... SRX2727598.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:51:16: #4 Write summits bed file... SRX2727598.10_summits.bed INFO @ Thu, 03 May 2018 22:51:16: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (455 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:51:16: #4 Write output xls file... SRX2727598.05_peaks.xls INFO @ Thu, 03 May 2018 22:51:16: #4 Write peak in narrowPeak format file... SRX2727598.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:51:16: #4 Write summits bed file... SRX2727598.05_summits.bed INFO @ Thu, 03 May 2018 22:51:16: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (785 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。