Job ID = 10609601 sra ファイルのダウンロード中... Completed: 539029K bytes transferred in 18 seconds (242935K 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 18360537 spots for /home/okishinya/chipatlas/results/dm3/SRX3011248/SRR5834725.sra Written 18360537 spots for /home/okishinya/chipatlas/results/dm3/SRX3011248/SRR5834725.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: 00:08:16 18360537 reads; of these: 18360537 (100.00%) were unpaired; of these: 972667 (5.30%) aligned 0 times 13592794 (74.03%) aligned exactly 1 time 3795076 (20.67%) aligned >1 times 94.70% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5339627 / 17387870 = 0.3071 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 @ Mon, 07 May 2018 13:01:06: # Command line: callpeak -t SRX3011248.bam -f BAM -g dm -n SRX3011248.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011248.05 # format = BAM # ChIP-seq file = ['SRX3011248.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 07 May 2018 13:01:06: #1 read tag files... INFO @ Mon, 07 May 2018 13:01:06: #1 read treatment tags... INFO @ Mon, 07 May 2018 13:01:06: # Command line: callpeak -t SRX3011248.bam -f BAM -g dm -n SRX3011248.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011248.10 # format = BAM # ChIP-seq file = ['SRX3011248.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 07 May 2018 13:01:06: #1 read tag files... INFO @ Mon, 07 May 2018 13:01:06: #1 read treatment tags... INFO @ Mon, 07 May 2018 13:01:06: # Command line: callpeak -t SRX3011248.bam -f BAM -g dm -n SRX3011248.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011248.20 # format = BAM # ChIP-seq file = ['SRX3011248.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 07 May 2018 13:01:06: #1 read tag files... INFO @ Mon, 07 May 2018 13:01:06: #1 read treatment tags... INFO @ Mon, 07 May 2018 13:01:13: 1000000 INFO @ Mon, 07 May 2018 13:01:13: 1000000 INFO @ Mon, 07 May 2018 13:01:13: 1000000 INFO @ Mon, 07 May 2018 13:01:20: 2000000 INFO @ Mon, 07 May 2018 13:01:20: 2000000 INFO @ Mon, 07 May 2018 13:01:21: 2000000 INFO @ Mon, 07 May 2018 13:01:26: 3000000 INFO @ Mon, 07 May 2018 13:01:27: 3000000 INFO @ Mon, 07 May 2018 13:01:28: 3000000 INFO @ Mon, 07 May 2018 13:01:33: 4000000 INFO @ Mon, 07 May 2018 13:01:35: 4000000 INFO @ Mon, 07 May 2018 13:01:35: 4000000 INFO @ Mon, 07 May 2018 13:01:40: 5000000 INFO @ Mon, 07 May 2018 13:01:42: 5000000 INFO @ Mon, 07 May 2018 13:01:42: 5000000 INFO @ Mon, 07 May 2018 13:01:47: 6000000 INFO @ Mon, 07 May 2018 13:01:49: 6000000 INFO @ Mon, 07 May 2018 13:01:50: 6000000 INFO @ Mon, 07 May 2018 13:01:54: 7000000 INFO @ Mon, 07 May 2018 13:01:56: 7000000 INFO @ Mon, 07 May 2018 13:01:57: 7000000 INFO @ Mon, 07 May 2018 13:02:00: 8000000 INFO @ Mon, 07 May 2018 13:02:04: 8000000 INFO @ Mon, 07 May 2018 13:02:05: 8000000 INFO @ Mon, 07 May 2018 13:02:07: 9000000 INFO @ Mon, 07 May 2018 13:02:11: 9000000 INFO @ Mon, 07 May 2018 13:02:12: 9000000 INFO @ Mon, 07 May 2018 13:02:14: 10000000 INFO @ Mon, 07 May 2018 13:02:19: 10000000 INFO @ Mon, 07 May 2018 13:02:20: 10000000 INFO @ Mon, 07 May 2018 13:02:21: 11000000 INFO @ Mon, 07 May 2018 13:02:26: 11000000 INFO @ Mon, 07 May 2018 13:02:27: 11000000 INFO @ Mon, 07 May 2018 13:02:28: 12000000 INFO @ Mon, 07 May 2018 13:02:29: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 13:02:29: #1 tag size = 80 INFO @ Mon, 07 May 2018 13:02:29: #1 total tags in treatment: 12048243 INFO @ Mon, 07 May 2018 13:02:29: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 13:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 13:02:29: #1 tags after filtering in treatment: 12048243 INFO @ Mon, 07 May 2018 13:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 13:02:29: #1 finished! INFO @ Mon, 07 May 2018 13:02:29: #2 Build Peak Model... INFO @ Mon, 07 May 2018 13:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 13:02:30: #2 number of paired peaks: 1078 INFO @ Mon, 07 May 2018 13:02:30: start model_add_line... INFO @ Mon, 07 May 2018 13:02:30: start X-correlation... INFO @ Mon, 07 May 2018 13:02:30: end of X-cor INFO @ Mon, 07 May 2018 13:02:30: #2 finished! INFO @ Mon, 07 May 2018 13:02:30: #2 predicted fragment length is 152 bps INFO @ Mon, 07 May 2018 13:02:30: #2 alternative fragment length(s) may be 152 bps INFO @ Mon, 07 May 2018 13:02:30: #2.2 Generate R script for model : SRX3011248.05_model.r WARNING @ Mon, 07 May 2018 13:02:30: #2 Since the d (152) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 May 2018 13:02:30: #2 You may need to consider one of the other alternative d(s): 152 WARNING @ Mon, 07 May 2018 13:02:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 May 2018 13:02:30: #3 Call peaks... INFO @ Mon, 07 May 2018 13:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 13:02:33: 12000000 INFO @ Mon, 07 May 2018 13:02:34: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 13:02:34: #1 tag size = 80 INFO @ Mon, 07 May 2018 13:02:34: #1 total tags in treatment: 12048243 INFO @ Mon, 07 May 2018 13:02:34: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 13:02:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 13:02:34: #1 tags after filtering in treatment: 12048243 INFO @ Mon, 07 May 2018 13:02:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 13:02:34: #1 finished! INFO @ Mon, 07 May 2018 13:02:34: #2 Build Peak Model... INFO @ Mon, 07 May 2018 13:02:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 13:02:34: 12000000 INFO @ Mon, 07 May 2018 13:02:35: #2 number of paired peaks: 1078 INFO @ Mon, 07 May 2018 13:02:35: start model_add_line... INFO @ Mon, 07 May 2018 13:02:35: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 13:02:35: #1 tag size = 80 INFO @ Mon, 07 May 2018 13:02:35: #1 total tags in treatment: 12048243 INFO @ Mon, 07 May 2018 13:02:35: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 13:02:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 13:02:35: start X-correlation... INFO @ Mon, 07 May 2018 13:02:35: end of X-cor INFO @ Mon, 07 May 2018 13:02:35: #2 finished! INFO @ Mon, 07 May 2018 13:02:35: #2 predicted fragment length is 152 bps INFO @ Mon, 07 May 2018 13:02:35: #2 alternative fragment length(s) may be 152 bps INFO @ Mon, 07 May 2018 13:02:35: #2.2 Generate R script for model : SRX3011248.10_model.r WARNING @ Mon, 07 May 2018 13:02:35: #2 Since the d (152) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 May 2018 13:02:35: #2 You may need to consider one of the other alternative d(s): 152 WARNING @ Mon, 07 May 2018 13:02:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 May 2018 13:02:35: #3 Call peaks... INFO @ Mon, 07 May 2018 13:02:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 13:02:35: #1 tags after filtering in treatment: 12048243 INFO @ Mon, 07 May 2018 13:02:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 13:02:35: #1 finished! INFO @ Mon, 07 May 2018 13:02:35: #2 Build Peak Model... INFO @ Mon, 07 May 2018 13:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 13:02:36: #2 number of paired peaks: 1078 INFO @ Mon, 07 May 2018 13:02:36: start model_add_line... INFO @ Mon, 07 May 2018 13:02:36: start X-correlation... INFO @ Mon, 07 May 2018 13:02:36: end of X-cor INFO @ Mon, 07 May 2018 13:02:36: #2 finished! INFO @ Mon, 07 May 2018 13:02:36: #2 predicted fragment length is 152 bps INFO @ Mon, 07 May 2018 13:02:36: #2 alternative fragment length(s) may be 152 bps INFO @ Mon, 07 May 2018 13:02:36: #2.2 Generate R script for model : SRX3011248.20_model.r WARNING @ Mon, 07 May 2018 13:02:36: #2 Since the d (152) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 May 2018 13:02:36: #2 You may need to consider one of the other alternative d(s): 152 WARNING @ Mon, 07 May 2018 13:02:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 May 2018 13:02:36: #3 Call peaks... INFO @ Mon, 07 May 2018 13:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 13:03:01: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 13:03:05: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 13:03:06: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 13:03:20: #4 Write output xls file... SRX3011248.05_peaks.xls INFO @ Mon, 07 May 2018 13:03:20: #4 Write peak in narrowPeak format file... SRX3011248.05_peaks.narrowPeak INFO @ Mon, 07 May 2018 13:03:20: #4 Write summits bed file... SRX3011248.05_summits.bed INFO @ Mon, 07 May 2018 13:03:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8191 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 13:03:21: #4 Write output xls file... SRX3011248.20_peaks.xls INFO @ Mon, 07 May 2018 13:03:21: #4 Write peak in narrowPeak format file... SRX3011248.20_peaks.narrowPeak INFO @ Mon, 07 May 2018 13:03:21: #4 Write summits bed file... SRX3011248.20_summits.bed INFO @ Mon, 07 May 2018 13:03:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2185 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 13:03:21: #4 Write output xls file... SRX3011248.10_peaks.xls INFO @ Mon, 07 May 2018 13:03:21: #4 Write peak in narrowPeak format file... SRX3011248.10_peaks.narrowPeak INFO @ Mon, 07 May 2018 13:03:21: #4 Write summits bed file... SRX3011248.10_summits.bed INFO @ Mon, 07 May 2018 13:03:21: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4590 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。