Job ID = 10608874 sra ファイルのダウンロード中... Completed: 561078K bytes transferred in 22 seconds (206772K 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 12618035 spots for /home/okishinya/chipatlas/results/rn6/SRX2727609/SRR5437672.sra Written 12618035 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: 00:19:38 12618035 reads; of these: 12618035 (100.00%) were unpaired; of these: 347303 (2.75%) aligned 0 times 10042768 (79.59%) aligned exactly 1 time 2227964 (17.66%) aligned >1 times 97.25% overall alignment rate Time searching: 00:19:41 Overall time: 00:19:41 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_sort_core] merging from 8 files... [bam_rmdupse_core] 807580 / 12270732 = 0.0658 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 22:41:17: # Command line: callpeak -t SRX2727609.bam -f BAM -g 2.15e9 -n SRX2727609.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2727609.05 # format = BAM # ChIP-seq file = ['SRX2727609.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 22:41:17: #1 read tag files... INFO @ Thu, 03 May 2018 22:41:17: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:41:17: # Command line: callpeak -t SRX2727609.bam -f BAM -g 2.15e9 -n SRX2727609.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2727609.20 # format = BAM # ChIP-seq file = ['SRX2727609.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 22:41:17: #1 read tag files... INFO @ Thu, 03 May 2018 22:41:17: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:41:17: # Command line: callpeak -t SRX2727609.bam -f BAM -g 2.15e9 -n SRX2727609.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2727609.10 # format = BAM # ChIP-seq file = ['SRX2727609.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 22:41:17: #1 read tag files... INFO @ Thu, 03 May 2018 22:41:17: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:41:26: 1000000 INFO @ Thu, 03 May 2018 22:41:27: 1000000 INFO @ Thu, 03 May 2018 22:41:27: 1000000 INFO @ Thu, 03 May 2018 22:41:34: 2000000 INFO @ Thu, 03 May 2018 22:41:36: 2000000 INFO @ Thu, 03 May 2018 22:41:36: 2000000 INFO @ Thu, 03 May 2018 22:41:43: 3000000 INFO @ Thu, 03 May 2018 22:41:45: 3000000 INFO @ Thu, 03 May 2018 22:41:45: 3000000 INFO @ Thu, 03 May 2018 22:41:51: 4000000 INFO @ Thu, 03 May 2018 22:41:54: 4000000 INFO @ Thu, 03 May 2018 22:41:55: 4000000 INFO @ Thu, 03 May 2018 22:42:01: 5000000 INFO @ Thu, 03 May 2018 22:42:03: 5000000 INFO @ Thu, 03 May 2018 22:42:05: 5000000 INFO @ Thu, 03 May 2018 22:42:11: 6000000 INFO @ Thu, 03 May 2018 22:42:12: 6000000 INFO @ Thu, 03 May 2018 22:42:15: 6000000 INFO @ Thu, 03 May 2018 22:42:19: 7000000 INFO @ Thu, 03 May 2018 22:42:22: 7000000 INFO @ Thu, 03 May 2018 22:42:25: 7000000 INFO @ Thu, 03 May 2018 22:42:28: 8000000 INFO @ Thu, 03 May 2018 22:42:33: 8000000 INFO @ Thu, 03 May 2018 22:42:35: 8000000 INFO @ Thu, 03 May 2018 22:42:36: 9000000 INFO @ Thu, 03 May 2018 22:42:43: 9000000 INFO @ Thu, 03 May 2018 22:42:44: 10000000 INFO @ Thu, 03 May 2018 22:42:45: 9000000 INFO @ Thu, 03 May 2018 22:42:53: 11000000 INFO @ Thu, 03 May 2018 22:42:54: 10000000 INFO @ Thu, 03 May 2018 22:42:55: 10000000 INFO @ Thu, 03 May 2018 22:42:57: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:42:57: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:42:57: #1 total tags in treatment: 11463152 INFO @ Thu, 03 May 2018 22:42:57: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:42:57: #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 22:42:57: #1 tags after filtering in treatment: 11462924 INFO @ Thu, 03 May 2018 22:42:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:42:57: #1 finished! INFO @ Thu, 03 May 2018 22:42:57: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:42:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:43:00: #2 number of paired peaks: 56997 INFO @ Thu, 03 May 2018 22:43:00: start model_add_line... INFO @ Thu, 03 May 2018 22:43:01: start X-correlation... INFO @ Thu, 03 May 2018 22:43:01: end of X-cor INFO @ Thu, 03 May 2018 22:43:01: #2 finished! INFO @ Thu, 03 May 2018 22:43:01: #2 predicted fragment length is 192 bps INFO @ Thu, 03 May 2018 22:43:01: #2 alternative fragment length(s) may be 192 bps INFO @ Thu, 03 May 2018 22:43:01: #2.2 Generate R script for model : SRX2727609.20_model.r WARNING @ Thu, 03 May 2018 22:43:01: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:43:01: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Thu, 03 May 2018 22:43:01: #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 22:43:01: #3 Call peaks... INFO @ Thu, 03 May 2018 22:43:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:43:04: 11000000 INFO @ Thu, 03 May 2018 22:43:05: 11000000 INFO @ Thu, 03 May 2018 22:43:09: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:43:09: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:43:09: #1 total tags in treatment: 11463152 INFO @ Thu, 03 May 2018 22:43:09: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:43:09: #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 22:43:09: #1 tags after filtering in treatment: 11462924 INFO @ Thu, 03 May 2018 22:43:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:43:09: #1 finished! INFO @ Thu, 03 May 2018 22:43:09: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:43:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:43:10: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:43:10: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:43:10: #1 total tags in treatment: 11463152 INFO @ Thu, 03 May 2018 22:43:10: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:43:10: #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 22:43:10: #1 tags after filtering in treatment: 11462924 INFO @ Thu, 03 May 2018 22:43:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:43:10: #1 finished! INFO @ Thu, 03 May 2018 22:43:10: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:43:12: #2 number of paired peaks: 56997 INFO @ Thu, 03 May 2018 22:43:12: start model_add_line... INFO @ Thu, 03 May 2018 22:43:13: start X-correlation... INFO @ Thu, 03 May 2018 22:43:13: end of X-cor INFO @ Thu, 03 May 2018 22:43:13: #2 finished! INFO @ Thu, 03 May 2018 22:43:13: #2 predicted fragment length is 192 bps INFO @ Thu, 03 May 2018 22:43:13: #2 alternative fragment length(s) may be 192 bps INFO @ Thu, 03 May 2018 22:43:13: #2.2 Generate R script for model : SRX2727609.05_model.r WARNING @ Thu, 03 May 2018 22:43:13: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:43:13: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Thu, 03 May 2018 22:43:13: #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 22:43:13: #3 Call peaks... INFO @ Thu, 03 May 2018 22:43:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:43:13: #2 number of paired peaks: 56997 INFO @ Thu, 03 May 2018 22:43:13: start model_add_line... INFO @ Thu, 03 May 2018 22:43:13: start X-correlation... INFO @ Thu, 03 May 2018 22:43:13: end of X-cor INFO @ Thu, 03 May 2018 22:43:13: #2 finished! INFO @ Thu, 03 May 2018 22:43:13: #2 predicted fragment length is 192 bps INFO @ Thu, 03 May 2018 22:43:13: #2 alternative fragment length(s) may be 192 bps INFO @ Thu, 03 May 2018 22:43:13: #2.2 Generate R script for model : SRX2727609.10_model.r WARNING @ Thu, 03 May 2018 22:43:13: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:43:13: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Thu, 03 May 2018 22:43:13: #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 22:43:13: #3 Call peaks... INFO @ Thu, 03 May 2018 22:43:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:43:32: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:43:42: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:43:43: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:43:49: #4 Write output xls file... SRX2727609.20_peaks.xls INFO @ Thu, 03 May 2018 22:43:49: #4 Write peak in narrowPeak format file... SRX2727609.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:43:49: #4 Write summits bed file... SRX2727609.20_summits.bed INFO @ Thu, 03 May 2018 22:43:49: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (5158 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:44:00: #4 Write output xls file... SRX2727609.05_peaks.xls INFO @ Thu, 03 May 2018 22:44:00: #4 Write output xls file... SRX2727609.10_peaks.xls INFO @ Thu, 03 May 2018 22:44:00: #4 Write peak in narrowPeak format file... SRX2727609.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:44:00: #4 Write peak in narrowPeak format file... SRX2727609.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:44:01: #4 Write summits bed file... SRX2727609.10_summits.bed INFO @ Thu, 03 May 2018 22:44:01: #4 Write summits bed file... SRX2727609.05_summits.bed INFO @ Thu, 03 May 2018 22:44:01: Done! INFO @ Thu, 03 May 2018 22:44:01: Done! pass1 - making usageList (67 chroms): 3 millis pass2 - checking and writing primary data (13063 records, 4 fields): 18 millis CompletedMACS2peakCalling pass1 - making usageList (91 chroms): 5 millis pass2 - checking and writing primary data (22374 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。