Job ID = 10608881 sra ファイルのダウンロード中... Completed: 293066K bytes transferred in 13 seconds (175217K 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 9573086 spots for /home/okishinya/chipatlas/results/rn6/SRX3145019/SRR5989260.sra Written 9573086 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: 00:06:37 9573086 reads; of these: 9573086 (100.00%) were unpaired; of these: 261123 (2.73%) aligned 0 times 6590835 (68.85%) aligned exactly 1 time 2721128 (28.42%) aligned >1 times 97.27% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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_rmdupse_core] 2501467 / 9311963 = 0.2686 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 22:28:20: # Command line: callpeak -t SRX3145019.bam -f BAM -g 2.15e9 -n SRX3145019.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3145019.20 # format = BAM # ChIP-seq file = ['SRX3145019.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 22:28:20: #1 read tag files... INFO @ Thu, 03 May 2018 22:28:20: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:28:20: # Command line: callpeak -t SRX3145019.bam -f BAM -g 2.15e9 -n SRX3145019.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3145019.05 # format = BAM # ChIP-seq file = ['SRX3145019.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 22:28:20: #1 read tag files... INFO @ Thu, 03 May 2018 22:28:20: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:28:20: # Command line: callpeak -t SRX3145019.bam -f BAM -g 2.15e9 -n SRX3145019.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3145019.10 # format = BAM # ChIP-seq file = ['SRX3145019.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 22:28:20: #1 read tag files... INFO @ Thu, 03 May 2018 22:28:20: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:28:27: 1000000 INFO @ Thu, 03 May 2018 22:28:27: 1000000 INFO @ Thu, 03 May 2018 22:28:27: 1000000 INFO @ Thu, 03 May 2018 22:28:34: 2000000 INFO @ Thu, 03 May 2018 22:28:34: 2000000 INFO @ Thu, 03 May 2018 22:28:35: 2000000 INFO @ Thu, 03 May 2018 22:28:41: 3000000 INFO @ Thu, 03 May 2018 22:28:42: 3000000 INFO @ Thu, 03 May 2018 22:28:42: 3000000 INFO @ Thu, 03 May 2018 22:28:48: 4000000 INFO @ Thu, 03 May 2018 22:28:49: 4000000 INFO @ Thu, 03 May 2018 22:28:49: 4000000 INFO @ Thu, 03 May 2018 22:28:55: 5000000 INFO @ Thu, 03 May 2018 22:28:56: 5000000 INFO @ Thu, 03 May 2018 22:28:57: 5000000 INFO @ Thu, 03 May 2018 22:29:02: 6000000 INFO @ Thu, 03 May 2018 22:29:03: 6000000 INFO @ Thu, 03 May 2018 22:29:04: 6000000 INFO @ Thu, 03 May 2018 22:29:08: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:29:08: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:29:08: #1 total tags in treatment: 6810496 INFO @ Thu, 03 May 2018 22:29:08: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:29:08: #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 22:29:08: #1 tags after filtering in treatment: 6810243 INFO @ Thu, 03 May 2018 22:29:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:29:08: #1 finished! INFO @ Thu, 03 May 2018 22:29:08: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:29:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:29:09: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:29:09: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:29:09: #1 total tags in treatment: 6810496 INFO @ Thu, 03 May 2018 22:29:09: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:29:09: #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 22:29:09: #2 number of paired peaks: 7301 INFO @ Thu, 03 May 2018 22:29:09: start model_add_line... INFO @ Thu, 03 May 2018 22:29:09: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:29:09: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:29:09: #1 total tags in treatment: 6810496 INFO @ Thu, 03 May 2018 22:29:09: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:29:09: #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 22:29:09: start X-correlation... INFO @ Thu, 03 May 2018 22:29:09: end of X-cor INFO @ Thu, 03 May 2018 22:29:09: #2 finished! INFO @ Thu, 03 May 2018 22:29:09: #2 predicted fragment length is 51 bps INFO @ Thu, 03 May 2018 22:29:09: #2 alternative fragment length(s) may be 51,136,234,597 bps INFO @ Thu, 03 May 2018 22:29:09: #2.2 Generate R script for model : SRX3145019.10_model.r WARNING @ Thu, 03 May 2018 22:29:09: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:29:09: #2 You may need to consider one of the other alternative d(s): 51,136,234,597 WARNING @ Thu, 03 May 2018 22:29:09: #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 22:29:09: #3 Call peaks... INFO @ Thu, 03 May 2018 22:29:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:29:10: #1 tags after filtering in treatment: 6810243 INFO @ Thu, 03 May 2018 22:29:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:29:10: #1 finished! INFO @ Thu, 03 May 2018 22:29:10: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:29:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:29:10: #1 tags after filtering in treatment: 6810243 INFO @ Thu, 03 May 2018 22:29:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:29:10: #1 finished! INFO @ Thu, 03 May 2018 22:29:10: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:29:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:29:11: #2 number of paired peaks: 7301 INFO @ Thu, 03 May 2018 22:29:11: start model_add_line... INFO @ Thu, 03 May 2018 22:29:11: start X-correlation... INFO @ Thu, 03 May 2018 22:29:11: end of X-cor INFO @ Thu, 03 May 2018 22:29:11: #2 finished! INFO @ Thu, 03 May 2018 22:29:11: #2 predicted fragment length is 51 bps INFO @ Thu, 03 May 2018 22:29:11: #2 alternative fragment length(s) may be 51,136,234,597 bps INFO @ Thu, 03 May 2018 22:29:11: #2.2 Generate R script for model : SRX3145019.20_model.r WARNING @ Thu, 03 May 2018 22:29:11: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:29:11: #2 You may need to consider one of the other alternative d(s): 51,136,234,597 WARNING @ Thu, 03 May 2018 22:29:11: #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 22:29:11: #3 Call peaks... INFO @ Thu, 03 May 2018 22:29:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:29:11: #2 number of paired peaks: 7301 INFO @ Thu, 03 May 2018 22:29:11: start model_add_line... INFO @ Thu, 03 May 2018 22:29:11: start X-correlation... INFO @ Thu, 03 May 2018 22:29:11: end of X-cor INFO @ Thu, 03 May 2018 22:29:11: #2 finished! INFO @ Thu, 03 May 2018 22:29:11: #2 predicted fragment length is 51 bps INFO @ Thu, 03 May 2018 22:29:11: #2 alternative fragment length(s) may be 51,136,234,597 bps INFO @ Thu, 03 May 2018 22:29:11: #2.2 Generate R script for model : SRX3145019.05_model.r WARNING @ Thu, 03 May 2018 22:29:11: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:29:11: #2 You may need to consider one of the other alternative d(s): 51,136,234,597 WARNING @ Thu, 03 May 2018 22:29:11: #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 22:29:11: #3 Call peaks... INFO @ Thu, 03 May 2018 22:29:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:29:26: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:29:28: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:29:29: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:29:36: #4 Write output xls file... SRX3145019.10_peaks.xls INFO @ Thu, 03 May 2018 22:29:36: #4 Write peak in narrowPeak format file... SRX3145019.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:29:36: #4 Write summits bed file... SRX3145019.10_summits.bed INFO @ Thu, 03 May 2018 22:29:36: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (490 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:29:38: #4 Write output xls file... SRX3145019.20_peaks.xls INFO @ Thu, 03 May 2018 22:29:38: #4 Write peak in narrowPeak format file... SRX3145019.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:29:38: #4 Write summits bed file... SRX3145019.20_summits.bed INFO @ Thu, 03 May 2018 22:29:38: Done! pass1 - making usageList (20 chroms): 0 millis pass2 - checking and writing primary data (212 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:29:38: #4 Write output xls file... SRX3145019.05_peaks.xls INFO @ Thu, 03 May 2018 22:29:38: #4 Write peak in narrowPeak format file... SRX3145019.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:29:38: #4 Write summits bed file... SRX3145019.05_summits.bed INFO @ Thu, 03 May 2018 22:29:38: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (845 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。