Job ID = 11632735 sra ファイルのダウンロード中... Completed: 1077178K bytes transferred in 13 seconds (655736K 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 64182850 spots for /home/okishinya/chipatlas/results/rn6/SRX4497205/SRR7633475.sra Written 64182850 spots for /home/okishinya/chipatlas/results/rn6/SRX4497205/SRR7633475.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: 00:00:02 Multiseed full-index search: 00:42:12 64182850 reads; of these: 64182850 (100.00%) were unpaired; of these: 33140394 (51.63%) aligned 0 times 20942083 (32.63%) aligned exactly 1 time 10100373 (15.74%) aligned >1 times 48.37% overall alignment rate Time searching: 00:42:15 Overall time: 00:42:16 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 16 files... [bam_rmdupse_core] 18963844 / 31042456 = 0.6109 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 08:15:15: # Command line: callpeak -t SRX4497205.bam -f BAM -g 2.15e9 -n SRX4497205.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4497205.05 # format = BAM # ChIP-seq file = ['SRX4497205.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 08:15:15: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:15:15: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:15:15: # Command line: callpeak -t SRX4497205.bam -f BAM -g 2.15e9 -n SRX4497205.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4497205.20 # format = BAM # ChIP-seq file = ['SRX4497205.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 08:15:15: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:15:15: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:15:15: # Command line: callpeak -t SRX4497205.bam -f BAM -g 2.15e9 -n SRX4497205.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4497205.10 # format = BAM # ChIP-seq file = ['SRX4497205.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 08:15:15: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:15:15: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:15:22: 1000000 INFO @ Fri, 15 Feb 2019 08:15:22: 1000000 INFO @ Fri, 15 Feb 2019 08:15:22: 1000000 INFO @ Fri, 15 Feb 2019 08:15:29: 2000000 INFO @ Fri, 15 Feb 2019 08:15:29: 2000000 INFO @ Fri, 15 Feb 2019 08:15:29: 2000000 INFO @ Fri, 15 Feb 2019 08:15:36: 3000000 INFO @ Fri, 15 Feb 2019 08:15:36: 3000000 INFO @ Fri, 15 Feb 2019 08:15:36: 3000000 INFO @ Fri, 15 Feb 2019 08:15:43: 4000000 INFO @ Fri, 15 Feb 2019 08:15:43: 4000000 INFO @ Fri, 15 Feb 2019 08:15:43: 4000000 INFO @ Fri, 15 Feb 2019 08:15:50: 5000000 INFO @ Fri, 15 Feb 2019 08:15:51: 5000000 INFO @ Fri, 15 Feb 2019 08:15:51: 5000000 INFO @ Fri, 15 Feb 2019 08:15:57: 6000000 INFO @ Fri, 15 Feb 2019 08:15:58: 6000000 INFO @ Fri, 15 Feb 2019 08:15:58: 6000000 INFO @ Fri, 15 Feb 2019 08:16:04: 7000000 INFO @ Fri, 15 Feb 2019 08:16:05: 7000000 INFO @ Fri, 15 Feb 2019 08:16:05: 7000000 INFO @ Fri, 15 Feb 2019 08:16:11: 8000000 INFO @ Fri, 15 Feb 2019 08:16:12: 8000000 INFO @ Fri, 15 Feb 2019 08:16:12: 8000000 INFO @ Fri, 15 Feb 2019 08:16:20: 9000000 INFO @ Fri, 15 Feb 2019 08:16:20: 9000000 INFO @ Fri, 15 Feb 2019 08:16:21: 9000000 INFO @ Fri, 15 Feb 2019 08:16:28: 10000000 INFO @ Fri, 15 Feb 2019 08:16:28: 10000000 INFO @ Fri, 15 Feb 2019 08:16:30: 10000000 INFO @ Fri, 15 Feb 2019 08:16:36: 11000000 INFO @ Fri, 15 Feb 2019 08:16:37: 11000000 INFO @ Fri, 15 Feb 2019 08:16:38: 11000000 INFO @ Fri, 15 Feb 2019 08:16:44: 12000000 INFO @ Fri, 15 Feb 2019 08:16:45: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:16:45: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:16:45: #1 total tags in treatment: 12078612 INFO @ Fri, 15 Feb 2019 08:16:45: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:16:45: #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 08:16:45: #1 tags after filtering in treatment: 12078462 INFO @ Fri, 15 Feb 2019 08:16:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:16:45: #1 finished! INFO @ Fri, 15 Feb 2019 08:16:45: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:16:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:16:46: 12000000 INFO @ Fri, 15 Feb 2019 08:16:46: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:16:46: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:16:46: #1 total tags in treatment: 12078612 INFO @ Fri, 15 Feb 2019 08:16:46: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:16:46: #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 08:16:47: #1 tags after filtering in treatment: 12078462 INFO @ Fri, 15 Feb 2019 08:16:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:16:47: #1 finished! INFO @ Fri, 15 Feb 2019 08:16:47: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:16:47: 12000000 INFO @ Fri, 15 Feb 2019 08:16:47: #2 number of paired peaks: 27118 INFO @ Fri, 15 Feb 2019 08:16:47: start model_add_line... INFO @ Fri, 15 Feb 2019 08:16:48: start X-correlation... INFO @ Fri, 15 Feb 2019 08:16:48: end of X-cor INFO @ Fri, 15 Feb 2019 08:16:48: #2 finished! INFO @ Fri, 15 Feb 2019 08:16:48: #2 predicted fragment length is 50 bps INFO @ Fri, 15 Feb 2019 08:16:48: #2 alternative fragment length(s) may be 50,409,523 bps INFO @ Fri, 15 Feb 2019 08:16:48: #2.2 Generate R script for model : SRX4497205.10_model.r WARNING @ Fri, 15 Feb 2019 08:16:48: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 08:16:48: #2 You may need to consider one of the other alternative d(s): 50,409,523 WARNING @ Fri, 15 Feb 2019 08:16:48: #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 08:16:48: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:16:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:16:48: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:16:48: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:16:48: #1 total tags in treatment: 12078612 INFO @ Fri, 15 Feb 2019 08:16:48: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:16:48: #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 08:16:48: #1 tags after filtering in treatment: 12078462 INFO @ Fri, 15 Feb 2019 08:16:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:16:48: #1 finished! INFO @ Fri, 15 Feb 2019 08:16:48: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:16:49: #2 number of paired peaks: 27118 INFO @ Fri, 15 Feb 2019 08:16:49: start model_add_line... INFO @ Fri, 15 Feb 2019 08:16:49: start X-correlation... INFO @ Fri, 15 Feb 2019 08:16:49: end of X-cor INFO @ Fri, 15 Feb 2019 08:16:49: #2 finished! INFO @ Fri, 15 Feb 2019 08:16:49: #2 predicted fragment length is 50 bps INFO @ Fri, 15 Feb 2019 08:16:49: #2 alternative fragment length(s) may be 50,409,523 bps INFO @ Fri, 15 Feb 2019 08:16:49: #2.2 Generate R script for model : SRX4497205.05_model.r WARNING @ Fri, 15 Feb 2019 08:16:49: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 08:16:49: #2 You may need to consider one of the other alternative d(s): 50,409,523 WARNING @ Fri, 15 Feb 2019 08:16:49: #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 08:16:49: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:16:51: #2 number of paired peaks: 27118 INFO @ Fri, 15 Feb 2019 08:16:51: start model_add_line... INFO @ Fri, 15 Feb 2019 08:16:51: start X-correlation... INFO @ Fri, 15 Feb 2019 08:16:51: end of X-cor INFO @ Fri, 15 Feb 2019 08:16:51: #2 finished! INFO @ Fri, 15 Feb 2019 08:16:51: #2 predicted fragment length is 50 bps INFO @ Fri, 15 Feb 2019 08:16:51: #2 alternative fragment length(s) may be 50,409,523 bps INFO @ Fri, 15 Feb 2019 08:16:51: #2.2 Generate R script for model : SRX4497205.20_model.r WARNING @ Fri, 15 Feb 2019 08:16:51: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 08:16:51: #2 You may need to consider one of the other alternative d(s): 50,409,523 WARNING @ Fri, 15 Feb 2019 08:16:51: #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 08:16:51: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:16:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:17:15: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:17:19: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:17:20: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:17:33: #4 Write output xls file... SRX4497205.10_peaks.xls INFO @ Fri, 15 Feb 2019 08:17:33: #4 Write peak in narrowPeak format file... SRX4497205.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:17:33: #4 Write summits bed file... SRX4497205.10_summits.bed INFO @ Fri, 15 Feb 2019 08:17:33: Done! pass1 - making usageList (58 chroms): 3 millis pass2 - checking and writing primary data (4937 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:17:36: #4 Write output xls file... SRX4497205.05_peaks.xls INFO @ Fri, 15 Feb 2019 08:17:36: #4 Write peak in narrowPeak format file... SRX4497205.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:17:36: #4 Write summits bed file... SRX4497205.05_summits.bed INFO @ Fri, 15 Feb 2019 08:17:36: Done! pass1 - making usageList (84 chroms): 4 millis pass2 - checking and writing primary data (10603 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:17:36: #4 Write output xls file... SRX4497205.20_peaks.xls INFO @ Fri, 15 Feb 2019 08:17:36: #4 Write peak in narrowPeak format file... SRX4497205.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:17:36: #4 Write summits bed file... SRX4497205.20_summits.bed INFO @ Fri, 15 Feb 2019 08:17:36: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (1699 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。