Job ID = 10609112 sra ファイルのダウンロード中... Completed: 499186K bytes transferred in 66 seconds (61590K 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 17522354 spots for /home/okishinya/chipatlas/results/dm3/SRX3011250/SRR5834727.sra Written 17522354 spots for /home/okishinya/chipatlas/results/dm3/SRX3011250/SRR5834727.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: 00:07:30 17522354 reads; of these: 17522354 (100.00%) were unpaired; of these: 243212 (1.39%) aligned 0 times 13322750 (76.03%) aligned exactly 1 time 3956392 (22.58%) aligned >1 times 98.61% overall alignment rate Time searching: 00:07:30 Overall time: 00:07:30 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] 5705087 / 17279142 = 0.3302 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, 04 May 2018 07:16:00: # Command line: callpeak -t SRX3011250.bam -f BAM -g dm -n SRX3011250.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011250.20 # format = BAM # ChIP-seq file = ['SRX3011250.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 @ Fri, 04 May 2018 07:16:00: #1 read tag files... INFO @ Fri, 04 May 2018 07:16:00: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:16:00: # Command line: callpeak -t SRX3011250.bam -f BAM -g dm -n SRX3011250.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011250.05 # format = BAM # ChIP-seq file = ['SRX3011250.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 @ Fri, 04 May 2018 07:16:00: #1 read tag files... INFO @ Fri, 04 May 2018 07:16:00: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:16:00: # Command line: callpeak -t SRX3011250.bam -f BAM -g dm -n SRX3011250.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011250.10 # format = BAM # ChIP-seq file = ['SRX3011250.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 @ Fri, 04 May 2018 07:16:00: #1 read tag files... INFO @ Fri, 04 May 2018 07:16:00: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:16:09: 1000000 INFO @ Fri, 04 May 2018 07:16:09: 1000000 INFO @ Fri, 04 May 2018 07:16:09: 1000000 INFO @ Fri, 04 May 2018 07:16:17: 2000000 INFO @ Fri, 04 May 2018 07:16:17: 2000000 INFO @ Fri, 04 May 2018 07:16:17: 2000000 INFO @ Fri, 04 May 2018 07:16:26: 3000000 INFO @ Fri, 04 May 2018 07:16:26: 3000000 INFO @ Fri, 04 May 2018 07:16:26: 3000000 INFO @ Fri, 04 May 2018 07:16:34: 4000000 INFO @ Fri, 04 May 2018 07:16:34: 4000000 INFO @ Fri, 04 May 2018 07:16:35: 4000000 INFO @ Fri, 04 May 2018 07:16:43: 5000000 INFO @ Fri, 04 May 2018 07:16:43: 5000000 INFO @ Fri, 04 May 2018 07:16:43: 5000000 INFO @ Fri, 04 May 2018 07:16:52: 6000000 INFO @ Fri, 04 May 2018 07:16:52: 6000000 INFO @ Fri, 04 May 2018 07:16:52: 6000000 INFO @ Fri, 04 May 2018 07:17:01: 7000000 INFO @ Fri, 04 May 2018 07:17:01: 7000000 INFO @ Fri, 04 May 2018 07:17:01: 7000000 INFO @ Fri, 04 May 2018 07:17:09: 8000000 INFO @ Fri, 04 May 2018 07:17:10: 8000000 INFO @ Fri, 04 May 2018 07:17:10: 8000000 INFO @ Fri, 04 May 2018 07:17:18: 9000000 INFO @ Fri, 04 May 2018 07:17:18: 9000000 INFO @ Fri, 04 May 2018 07:17:19: 9000000 INFO @ Fri, 04 May 2018 07:17:27: 10000000 INFO @ Fri, 04 May 2018 07:17:27: 10000000 INFO @ Fri, 04 May 2018 07:17:27: 10000000 INFO @ Fri, 04 May 2018 07:17:35: 11000000 INFO @ Fri, 04 May 2018 07:17:36: 11000000 INFO @ Fri, 04 May 2018 07:17:36: 11000000 INFO @ Fri, 04 May 2018 07:17:41: #1 tag size is determined as 80 bps INFO @ Fri, 04 May 2018 07:17:41: #1 tag size = 80 INFO @ Fri, 04 May 2018 07:17:41: #1 total tags in treatment: 11574055 INFO @ Fri, 04 May 2018 07:17:41: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:17:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:17:41: #1 tag size is determined as 80 bps INFO @ Fri, 04 May 2018 07:17:41: #1 tag size = 80 INFO @ Fri, 04 May 2018 07:17:41: #1 total tags in treatment: 11574055 INFO @ Fri, 04 May 2018 07:17:41: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:17:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:17:41: #1 tags after filtering in treatment: 11574055 INFO @ Fri, 04 May 2018 07:17:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:17:41: #1 finished! INFO @ Fri, 04 May 2018 07:17:41: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:17:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:17:41: #1 tag size is determined as 80 bps INFO @ Fri, 04 May 2018 07:17:41: #1 tag size = 80 INFO @ Fri, 04 May 2018 07:17:41: #1 total tags in treatment: 11574055 INFO @ Fri, 04 May 2018 07:17:41: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:17:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:17:41: #1 tags after filtering in treatment: 11574055 INFO @ Fri, 04 May 2018 07:17:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:17:41: #1 finished! INFO @ Fri, 04 May 2018 07:17:41: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:17:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:17:41: #1 tags after filtering in treatment: 11574055 INFO @ Fri, 04 May 2018 07:17:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:17:41: #1 finished! INFO @ Fri, 04 May 2018 07:17:41: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:17:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:17:42: #2 number of paired peaks: 1479 INFO @ Fri, 04 May 2018 07:17:42: start model_add_line... INFO @ Fri, 04 May 2018 07:17:42: #2 number of paired peaks: 1479 INFO @ Fri, 04 May 2018 07:17:42: start model_add_line... INFO @ Fri, 04 May 2018 07:17:42: start X-correlation... INFO @ Fri, 04 May 2018 07:17:42: end of X-cor INFO @ Fri, 04 May 2018 07:17:42: #2 finished! INFO @ Fri, 04 May 2018 07:17:42: #2 predicted fragment length is 136 bps INFO @ Fri, 04 May 2018 07:17:42: #2 alternative fragment length(s) may be 136 bps INFO @ Fri, 04 May 2018 07:17:42: #2.2 Generate R script for model : SRX3011250.20_model.r WARNING @ Fri, 04 May 2018 07:17:42: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:17:42: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Fri, 04 May 2018 07:17:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 May 2018 07:17:42: #3 Call peaks... INFO @ Fri, 04 May 2018 07:17:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:17:42: #2 number of paired peaks: 1479 INFO @ Fri, 04 May 2018 07:17:42: start model_add_line... INFO @ Fri, 04 May 2018 07:17:42: start X-correlation... INFO @ Fri, 04 May 2018 07:17:42: end of X-cor INFO @ Fri, 04 May 2018 07:17:42: #2 finished! INFO @ Fri, 04 May 2018 07:17:42: #2 predicted fragment length is 136 bps INFO @ Fri, 04 May 2018 07:17:42: #2 alternative fragment length(s) may be 136 bps INFO @ Fri, 04 May 2018 07:17:42: #2.2 Generate R script for model : SRX3011250.10_model.r WARNING @ Fri, 04 May 2018 07:17:42: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:17:42: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Fri, 04 May 2018 07:17:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 May 2018 07:17:42: #3 Call peaks... INFO @ Fri, 04 May 2018 07:17:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:17:42: start X-correlation... INFO @ Fri, 04 May 2018 07:17:42: end of X-cor INFO @ Fri, 04 May 2018 07:17:42: #2 finished! INFO @ Fri, 04 May 2018 07:17:42: #2 predicted fragment length is 136 bps INFO @ Fri, 04 May 2018 07:17:42: #2 alternative fragment length(s) may be 136 bps INFO @ Fri, 04 May 2018 07:17:42: #2.2 Generate R script for model : SRX3011250.05_model.r WARNING @ Fri, 04 May 2018 07:17:42: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:17:42: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Fri, 04 May 2018 07:17:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 May 2018 07:17:42: #3 Call peaks... INFO @ Fri, 04 May 2018 07:17:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:18:10: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:18:11: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:18:13: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:18:24: #4 Write output xls file... SRX3011250.20_peaks.xls INFO @ Fri, 04 May 2018 07:18:24: #4 Write peak in narrowPeak format file... SRX3011250.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:18:24: #4 Write summits bed file... SRX3011250.20_summits.bed INFO @ Fri, 04 May 2018 07:18:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2955 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:18:26: #4 Write output xls file... SRX3011250.05_peaks.xls INFO @ Fri, 04 May 2018 07:18:26: #4 Write peak in narrowPeak format file... SRX3011250.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:18:26: #4 Write summits bed file... SRX3011250.05_summits.bed INFO @ Fri, 04 May 2018 07:18:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10290 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:18:28: #4 Write output xls file... SRX3011250.10_peaks.xls INFO @ Fri, 04 May 2018 07:18:28: #4 Write peak in narrowPeak format file... SRX3011250.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:18:28: #4 Write summits bed file... SRX3011250.10_summits.bed INFO @ Fri, 04 May 2018 07:18:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6204 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。