Job ID = 10714360 sra ファイルのダウンロード中... Completed: 1231155K bytes transferred in 64 seconds (156234K 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 24188927 spots for /home/okishinya/chipatlas/results/ce10/SRX2965741/SRR5766326.sra Written 24188927 spots for /home/okishinya/chipatlas/results/ce10/SRX2965741/SRR5766326.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:37 24188927 reads; of these: 24188927 (100.00%) were unpaired; of these: 1135617 (4.69%) aligned 0 times 19858397 (82.10%) aligned exactly 1 time 3194913 (13.21%) aligned >1 times 95.31% overall alignment rate Time searching: 00:11:37 Overall time: 00:11:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4341548 / 23053310 = 0.1883 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 @ Sun, 03 Jun 2018 12:49:14: # Command line: callpeak -t SRX2965741.bam -f BAM -g ce -n SRX2965741.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2965741.05 # format = BAM # ChIP-seq file = ['SRX2965741.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 03 Jun 2018 12:49:14: # Command line: callpeak -t SRX2965741.bam -f BAM -g ce -n SRX2965741.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2965741.10 # format = BAM # ChIP-seq file = ['SRX2965741.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 03 Jun 2018 12:49:14: # Command line: callpeak -t SRX2965741.bam -f BAM -g ce -n SRX2965741.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2965741.20 # format = BAM # ChIP-seq file = ['SRX2965741.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 03 Jun 2018 12:49:14: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:49:14: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:49:14: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:49:14: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:49:14: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:49:14: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:49:22: 1000000 INFO @ Sun, 03 Jun 2018 12:49:22: 1000000 INFO @ Sun, 03 Jun 2018 12:49:22: 1000000 INFO @ Sun, 03 Jun 2018 12:49:30: 2000000 INFO @ Sun, 03 Jun 2018 12:49:30: 2000000 INFO @ Sun, 03 Jun 2018 12:49:30: 2000000 INFO @ Sun, 03 Jun 2018 12:49:37: 3000000 INFO @ Sun, 03 Jun 2018 12:49:38: 3000000 INFO @ Sun, 03 Jun 2018 12:49:38: 3000000 INFO @ Sun, 03 Jun 2018 12:49:45: 4000000 INFO @ Sun, 03 Jun 2018 12:49:46: 4000000 INFO @ Sun, 03 Jun 2018 12:49:46: 4000000 INFO @ Sun, 03 Jun 2018 12:49:53: 5000000 INFO @ Sun, 03 Jun 2018 12:49:54: 5000000 INFO @ Sun, 03 Jun 2018 12:49:54: 5000000 INFO @ Sun, 03 Jun 2018 12:50:00: 6000000 INFO @ Sun, 03 Jun 2018 12:50:02: 6000000 INFO @ Sun, 03 Jun 2018 12:50:03: 6000000 INFO @ Sun, 03 Jun 2018 12:50:08: 7000000 INFO @ Sun, 03 Jun 2018 12:50:10: 7000000 INFO @ Sun, 03 Jun 2018 12:50:11: 7000000 INFO @ Sun, 03 Jun 2018 12:50:15: 8000000 INFO @ Sun, 03 Jun 2018 12:50:18: 8000000 INFO @ Sun, 03 Jun 2018 12:50:20: 8000000 INFO @ Sun, 03 Jun 2018 12:50:23: 9000000 INFO @ Sun, 03 Jun 2018 12:50:27: 9000000 INFO @ Sun, 03 Jun 2018 12:50:28: 9000000 INFO @ Sun, 03 Jun 2018 12:50:31: 10000000 INFO @ Sun, 03 Jun 2018 12:50:35: 10000000 INFO @ Sun, 03 Jun 2018 12:50:36: 10000000 INFO @ Sun, 03 Jun 2018 12:50:38: 11000000 INFO @ Sun, 03 Jun 2018 12:50:43: 11000000 INFO @ Sun, 03 Jun 2018 12:50:45: 11000000 INFO @ Sun, 03 Jun 2018 12:50:46: 12000000 INFO @ Sun, 03 Jun 2018 12:50:51: 12000000 INFO @ Sun, 03 Jun 2018 12:50:53: 12000000 INFO @ Sun, 03 Jun 2018 12:50:54: 13000000 INFO @ Sun, 03 Jun 2018 12:51:00: 13000000 INFO @ Sun, 03 Jun 2018 12:51:01: 13000000 INFO @ Sun, 03 Jun 2018 12:51:01: 14000000 INFO @ Sun, 03 Jun 2018 12:51:08: 14000000 INFO @ Sun, 03 Jun 2018 12:51:09: 15000000 INFO @ Sun, 03 Jun 2018 12:51:10: 14000000 INFO @ Sun, 03 Jun 2018 12:51:16: 15000000 INFO @ Sun, 03 Jun 2018 12:51:17: 16000000 INFO @ Sun, 03 Jun 2018 12:51:18: 15000000 INFO @ Sun, 03 Jun 2018 12:51:24: 16000000 INFO @ Sun, 03 Jun 2018 12:51:24: 17000000 INFO @ Sun, 03 Jun 2018 12:51:26: 16000000 INFO @ Sun, 03 Jun 2018 12:51:32: 18000000 INFO @ Sun, 03 Jun 2018 12:51:33: 17000000 INFO @ Sun, 03 Jun 2018 12:51:35: 17000000 INFO @ Sun, 03 Jun 2018 12:51:38: #1 tag size is determined as 101 bps INFO @ Sun, 03 Jun 2018 12:51:38: #1 tag size = 101 INFO @ Sun, 03 Jun 2018 12:51:38: #1 total tags in treatment: 18711762 INFO @ Sun, 03 Jun 2018 12:51:38: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:51:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:51:38: #1 tags after filtering in treatment: 18711762 INFO @ Sun, 03 Jun 2018 12:51:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:51:38: #1 finished! INFO @ Sun, 03 Jun 2018 12:51:38: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:51:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:51:39: #2 number of paired peaks: 1753 INFO @ Sun, 03 Jun 2018 12:51:39: start model_add_line... INFO @ Sun, 03 Jun 2018 12:51:40: start X-correlation... INFO @ Sun, 03 Jun 2018 12:51:40: end of X-cor INFO @ Sun, 03 Jun 2018 12:51:40: #2 finished! INFO @ Sun, 03 Jun 2018 12:51:40: #2 predicted fragment length is 165 bps INFO @ Sun, 03 Jun 2018 12:51:40: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 03 Jun 2018 12:51:40: #2.2 Generate R script for model : SRX2965741.05_model.r WARNING @ Sun, 03 Jun 2018 12:51:40: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:51:40: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Sun, 03 Jun 2018 12:51:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:51:40: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:51:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:51:41: 18000000 INFO @ Sun, 03 Jun 2018 12:51:43: 18000000 INFO @ Sun, 03 Jun 2018 12:51:47: #1 tag size is determined as 101 bps INFO @ Sun, 03 Jun 2018 12:51:47: #1 tag size = 101 INFO @ Sun, 03 Jun 2018 12:51:47: #1 total tags in treatment: 18711762 INFO @ Sun, 03 Jun 2018 12:51:47: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:51:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:51:47: #1 tags after filtering in treatment: 18711762 INFO @ Sun, 03 Jun 2018 12:51:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:51:47: #1 finished! INFO @ Sun, 03 Jun 2018 12:51:47: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:51:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:51:49: #2 number of paired peaks: 1753 INFO @ Sun, 03 Jun 2018 12:51:49: start model_add_line... INFO @ Sun, 03 Jun 2018 12:51:49: start X-correlation... INFO @ Sun, 03 Jun 2018 12:51:49: end of X-cor INFO @ Sun, 03 Jun 2018 12:51:49: #2 finished! INFO @ Sun, 03 Jun 2018 12:51:49: #2 predicted fragment length is 165 bps INFO @ Sun, 03 Jun 2018 12:51:49: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 03 Jun 2018 12:51:49: #2.2 Generate R script for model : SRX2965741.20_model.r WARNING @ Sun, 03 Jun 2018 12:51:49: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:51:49: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Sun, 03 Jun 2018 12:51:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:51:49: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:51:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:51:49: #1 tag size is determined as 101 bps INFO @ Sun, 03 Jun 2018 12:51:49: #1 tag size = 101 INFO @ Sun, 03 Jun 2018 12:51:49: #1 total tags in treatment: 18711762 INFO @ Sun, 03 Jun 2018 12:51:49: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:51:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:51:49: #1 tags after filtering in treatment: 18711762 INFO @ Sun, 03 Jun 2018 12:51:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:51:49: #1 finished! INFO @ Sun, 03 Jun 2018 12:51:49: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:51:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:51:51: #2 number of paired peaks: 1753 INFO @ Sun, 03 Jun 2018 12:51:51: start model_add_line... INFO @ Sun, 03 Jun 2018 12:51:52: start X-correlation... INFO @ Sun, 03 Jun 2018 12:51:52: end of X-cor INFO @ Sun, 03 Jun 2018 12:51:52: #2 finished! INFO @ Sun, 03 Jun 2018 12:51:52: #2 predicted fragment length is 165 bps INFO @ Sun, 03 Jun 2018 12:51:52: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 03 Jun 2018 12:51:52: #2.2 Generate R script for model : SRX2965741.10_model.r WARNING @ Sun, 03 Jun 2018 12:51:52: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:51:52: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Sun, 03 Jun 2018 12:51:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:51:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:52:28: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:52:34: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:52:39: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:52:50: #4 Write output xls file... SRX2965741.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:52:50: #4 Write peak in narrowPeak format file... SRX2965741.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:52:50: #4 Write summits bed file... SRX2965741.05_summits.bed INFO @ Sun, 03 Jun 2018 12:52:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5475 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:52:55: #4 Write output xls file... SRX2965741.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:52:55: #4 Write peak in narrowPeak format file... SRX2965741.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:52:55: #4 Write summits bed file... SRX2965741.20_summits.bed INFO @ Sun, 03 Jun 2018 12:52:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3128 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:52:59: #4 Write output xls file... SRX2965741.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:52:59: #4 Write peak in narrowPeak format file... SRX2965741.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:52:59: #4 Write summits bed file... SRX2965741.10_summits.bed INFO @ Sun, 03 Jun 2018 12:52:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4229 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。