Job ID = 10714363 sra ファイルのダウンロード中... Completed: 1173908K bytes transferred in 57 seconds (166833K 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 23051447 spots for /home/okishinya/chipatlas/results/ce10/SRX2965744/SRR5766329.sra Written 23051447 spots for /home/okishinya/chipatlas/results/ce10/SRX2965744/SRR5766329.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: 00:11:18 23051447 reads; of these: 23051447 (100.00%) were unpaired; of these: 2727958 (11.83%) aligned 0 times 17726022 (76.90%) aligned exactly 1 time 2597467 (11.27%) aligned >1 times 88.17% overall alignment rate Time searching: 00:11:19 Overall time: 00:11:19 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] 3154334 / 20323489 = 0.1552 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 12:47:41: # Command line: callpeak -t SRX2965744.bam -f BAM -g ce -n SRX2965744.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2965744.20 # format = BAM # ChIP-seq file = ['SRX2965744.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 12:47:41: # Command line: callpeak -t SRX2965744.bam -f BAM -g ce -n SRX2965744.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2965744.10 # format = BAM # ChIP-seq file = ['SRX2965744.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 12:47:41: # Command line: callpeak -t SRX2965744.bam -f BAM -g ce -n SRX2965744.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2965744.05 # format = BAM # ChIP-seq file = ['SRX2965744.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 12:47:41: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:47:41: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:47:41: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:47:41: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:47:41: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:47:41: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:47:49: 1000000 INFO @ Sun, 03 Jun 2018 12:47:49: 1000000 INFO @ Sun, 03 Jun 2018 12:47:49: 1000000 INFO @ Sun, 03 Jun 2018 12:47:58: 2000000 INFO @ Sun, 03 Jun 2018 12:47:58: 2000000 INFO @ Sun, 03 Jun 2018 12:47:58: 2000000 INFO @ Sun, 03 Jun 2018 12:48:06: 3000000 INFO @ Sun, 03 Jun 2018 12:48:06: 3000000 INFO @ Sun, 03 Jun 2018 12:48:06: 3000000 INFO @ Sun, 03 Jun 2018 12:48:15: 4000000 INFO @ Sun, 03 Jun 2018 12:48:15: 4000000 INFO @ Sun, 03 Jun 2018 12:48:15: 4000000 INFO @ Sun, 03 Jun 2018 12:48:23: 5000000 INFO @ Sun, 03 Jun 2018 12:48:24: 5000000 INFO @ Sun, 03 Jun 2018 12:48:24: 5000000 INFO @ Sun, 03 Jun 2018 12:48:32: 6000000 INFO @ Sun, 03 Jun 2018 12:48:33: 6000000 INFO @ Sun, 03 Jun 2018 12:48:33: 6000000 INFO @ Sun, 03 Jun 2018 12:48:41: 7000000 INFO @ Sun, 03 Jun 2018 12:48:41: 7000000 INFO @ Sun, 03 Jun 2018 12:48:41: 7000000 INFO @ Sun, 03 Jun 2018 12:48:50: 8000000 INFO @ Sun, 03 Jun 2018 12:48:50: 8000000 INFO @ Sun, 03 Jun 2018 12:48:50: 8000000 INFO @ Sun, 03 Jun 2018 12:48:58: 9000000 INFO @ Sun, 03 Jun 2018 12:48:59: 9000000 INFO @ Sun, 03 Jun 2018 12:48:59: 9000000 INFO @ Sun, 03 Jun 2018 12:49:07: 10000000 INFO @ Sun, 03 Jun 2018 12:49:08: 10000000 INFO @ Sun, 03 Jun 2018 12:49:08: 10000000 INFO @ Sun, 03 Jun 2018 12:49:16: 11000000 INFO @ Sun, 03 Jun 2018 12:49:17: 11000000 INFO @ Sun, 03 Jun 2018 12:49:17: 11000000 INFO @ Sun, 03 Jun 2018 12:49:25: 12000000 INFO @ Sun, 03 Jun 2018 12:49:26: 12000000 INFO @ Sun, 03 Jun 2018 12:49:26: 12000000 INFO @ Sun, 03 Jun 2018 12:49:34: 13000000 INFO @ Sun, 03 Jun 2018 12:49:35: 13000000 INFO @ Sun, 03 Jun 2018 12:49:35: 13000000 INFO @ Sun, 03 Jun 2018 12:49:43: 14000000 INFO @ Sun, 03 Jun 2018 12:49:43: 14000000 INFO @ Sun, 03 Jun 2018 12:49:43: 14000000 INFO @ Sun, 03 Jun 2018 12:49:51: 15000000 INFO @ Sun, 03 Jun 2018 12:49:52: 15000000 INFO @ Sun, 03 Jun 2018 12:49:52: 15000000 INFO @ Sun, 03 Jun 2018 12:50:00: 16000000 INFO @ Sun, 03 Jun 2018 12:50:01: 16000000 INFO @ Sun, 03 Jun 2018 12:50:01: 16000000 INFO @ Sun, 03 Jun 2018 12:50:09: 17000000 INFO @ Sun, 03 Jun 2018 12:50:10: 17000000 INFO @ Sun, 03 Jun 2018 12:50:10: 17000000 INFO @ Sun, 03 Jun 2018 12:50:11: #1 tag size is determined as 101 bps INFO @ Sun, 03 Jun 2018 12:50:11: #1 tag size = 101 INFO @ Sun, 03 Jun 2018 12:50:11: #1 total tags in treatment: 17169155 INFO @ Sun, 03 Jun 2018 12:50:11: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:50:11: #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 12:50:11: #1 tags after filtering in treatment: 17169155 INFO @ Sun, 03 Jun 2018 12:50:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:50:11: #1 finished! INFO @ Sun, 03 Jun 2018 12:50:11: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:50:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:50:11: #1 tag size is determined as 101 bps INFO @ Sun, 03 Jun 2018 12:50:11: #1 tag size = 101 INFO @ Sun, 03 Jun 2018 12:50:11: #1 total tags in treatment: 17169155 INFO @ Sun, 03 Jun 2018 12:50:11: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:50:11: #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 12:50:11: #1 tag size is determined as 101 bps INFO @ Sun, 03 Jun 2018 12:50:11: #1 tag size = 101 INFO @ Sun, 03 Jun 2018 12:50:11: #1 total tags in treatment: 17169155 INFO @ Sun, 03 Jun 2018 12:50:11: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:50:11: #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 12:50:12: #1 tags after filtering in treatment: 17169155 INFO @ Sun, 03 Jun 2018 12:50:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:50:12: #1 finished! INFO @ Sun, 03 Jun 2018 12:50:12: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:50:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:50:12: #1 tags after filtering in treatment: 17169155 INFO @ Sun, 03 Jun 2018 12:50:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:50:12: #1 finished! INFO @ Sun, 03 Jun 2018 12:50:12: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:50:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:50:13: #2 number of paired peaks: 1240 INFO @ Sun, 03 Jun 2018 12:50:13: start model_add_line... INFO @ Sun, 03 Jun 2018 12:50:13: start X-correlation... INFO @ Sun, 03 Jun 2018 12:50:13: #2 number of paired peaks: 1240 INFO @ Sun, 03 Jun 2018 12:50:13: start model_add_line... INFO @ Sun, 03 Jun 2018 12:50:13: end of X-cor INFO @ Sun, 03 Jun 2018 12:50:13: #2 finished! INFO @ Sun, 03 Jun 2018 12:50:13: #2 predicted fragment length is 148 bps INFO @ Sun, 03 Jun 2018 12:50:13: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 03 Jun 2018 12:50:13: #2.2 Generate R script for model : SRX2965744.10_model.r WARNING @ Sun, 03 Jun 2018 12:50:13: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:50:13: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 03 Jun 2018 12:50:13: #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 12:50:13: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:50:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:50:13: #2 number of paired peaks: 1240 INFO @ Sun, 03 Jun 2018 12:50:13: start model_add_line... INFO @ Sun, 03 Jun 2018 12:50:13: start X-correlation... INFO @ Sun, 03 Jun 2018 12:50:13: end of X-cor INFO @ Sun, 03 Jun 2018 12:50:13: #2 finished! INFO @ Sun, 03 Jun 2018 12:50:13: #2 predicted fragment length is 148 bps INFO @ Sun, 03 Jun 2018 12:50:13: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 03 Jun 2018 12:50:13: #2.2 Generate R script for model : SRX2965744.20_model.r WARNING @ Sun, 03 Jun 2018 12:50:13: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:50:13: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 03 Jun 2018 12:50:13: #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 12:50:13: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:50:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:50:13: start X-correlation... INFO @ Sun, 03 Jun 2018 12:50:13: end of X-cor INFO @ Sun, 03 Jun 2018 12:50:13: #2 finished! INFO @ Sun, 03 Jun 2018 12:50:13: #2 predicted fragment length is 148 bps INFO @ Sun, 03 Jun 2018 12:50:13: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 03 Jun 2018 12:50:13: #2.2 Generate R script for model : SRX2965744.05_model.r WARNING @ Sun, 03 Jun 2018 12:50:13: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:50:13: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 03 Jun 2018 12:50:13: #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 12:50:13: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:50:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:50:52: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:50:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:50:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:51:13: #4 Write output xls file... SRX2965744.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:51:13: #4 Write peak in narrowPeak format file... SRX2965744.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:51:13: #4 Write summits bed file... SRX2965744.10_summits.bed INFO @ Sun, 03 Jun 2018 12:51:13: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3909 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:51:15: #4 Write output xls file... SRX2965744.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:51:15: #4 Write peak in narrowPeak format file... SRX2965744.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:51:15: #4 Write summits bed file... SRX2965744.20_summits.bed INFO @ Sun, 03 Jun 2018 12:51:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2684 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:51:15: #4 Write output xls file... SRX2965744.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:51:15: #4 Write peak in narrowPeak format file... SRX2965744.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:51:15: #4 Write summits bed file... SRX2965744.05_summits.bed INFO @ Sun, 03 Jun 2018 12:51:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5400 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。