Job ID = 10480713 sra ファイルのダウンロード中... Completed: 576547K bytes transferred in 22 seconds (205584K 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... Written 19008283 spots for /home/okishinya/chipatlas/results/dm3/SRX3068984/SRR5907460.sra Written 19008283 spots total 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: 00:06:17 19008283 reads; of these: 19008283 (100.00%) were unpaired; of these: 1615594 (8.50%) aligned 0 times 13687170 (72.01%) aligned exactly 1 time 3705519 (19.49%) aligned >1 times 91.50% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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] 3626459 / 17392689 = 0.2085 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, 16 Mar 2018 07:54:07: # Command line: callpeak -t SRX3068984.bam -f BAM -g dm -n SRX3068984.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068984.05 # format = BAM # ChIP-seq file = ['SRX3068984.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, 16 Mar 2018 07:54:07: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:54:07: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:54:07: # Command line: callpeak -t SRX3068984.bam -f BAM -g dm -n SRX3068984.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068984.20 # format = BAM # ChIP-seq file = ['SRX3068984.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, 16 Mar 2018 07:54:07: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:54:07: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:54:07: # Command line: callpeak -t SRX3068984.bam -f BAM -g dm -n SRX3068984.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068984.10 # format = BAM # ChIP-seq file = ['SRX3068984.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, 16 Mar 2018 07:54:07: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:54:07: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:54:14: 1000000 INFO @ Fri, 16 Mar 2018 07:54:14: 1000000 INFO @ Fri, 16 Mar 2018 07:54:14: 1000000 INFO @ Fri, 16 Mar 2018 07:54:20: 2000000 INFO @ Fri, 16 Mar 2018 07:54:20: 2000000 INFO @ Fri, 16 Mar 2018 07:54:21: 2000000 INFO @ Fri, 16 Mar 2018 07:54:27: 3000000 INFO @ Fri, 16 Mar 2018 07:54:27: 3000000 INFO @ Fri, 16 Mar 2018 07:54:28: 3000000 INFO @ Fri, 16 Mar 2018 07:54:33: 4000000 INFO @ Fri, 16 Mar 2018 07:54:33: 4000000 INFO @ Fri, 16 Mar 2018 07:54:35: 4000000 INFO @ Fri, 16 Mar 2018 07:54:39: 5000000 INFO @ Fri, 16 Mar 2018 07:54:40: 5000000 INFO @ Fri, 16 Mar 2018 07:54:42: 5000000 INFO @ Fri, 16 Mar 2018 07:54:46: 6000000 INFO @ Fri, 16 Mar 2018 07:54:46: 6000000 INFO @ Fri, 16 Mar 2018 07:54:49: 6000000 INFO @ Fri, 16 Mar 2018 07:54:52: 7000000 INFO @ Fri, 16 Mar 2018 07:54:52: 7000000 INFO @ Fri, 16 Mar 2018 07:54:56: 7000000 INFO @ Fri, 16 Mar 2018 07:54:59: 8000000 INFO @ Fri, 16 Mar 2018 07:54:59: 8000000 INFO @ Fri, 16 Mar 2018 07:55:02: 8000000 INFO @ Fri, 16 Mar 2018 07:55:05: 9000000 INFO @ Fri, 16 Mar 2018 07:55:05: 9000000 INFO @ Fri, 16 Mar 2018 07:55:09: 9000000 INFO @ Fri, 16 Mar 2018 07:55:11: 10000000 INFO @ Fri, 16 Mar 2018 07:55:11: 10000000 INFO @ Fri, 16 Mar 2018 07:55:15: 10000000 INFO @ Fri, 16 Mar 2018 07:55:18: 11000000 INFO @ Fri, 16 Mar 2018 07:55:18: 11000000 INFO @ Fri, 16 Mar 2018 07:55:22: 11000000 INFO @ Fri, 16 Mar 2018 07:55:24: 12000000 INFO @ Fri, 16 Mar 2018 07:55:24: 12000000 INFO @ Fri, 16 Mar 2018 07:55:29: 12000000 INFO @ Fri, 16 Mar 2018 07:55:31: 13000000 INFO @ Fri, 16 Mar 2018 07:55:31: 13000000 INFO @ Fri, 16 Mar 2018 07:55:35: 13000000 INFO @ Fri, 16 Mar 2018 07:55:36: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:55:36: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:55:36: #1 total tags in treatment: 13766230 INFO @ Fri, 16 Mar 2018 07:55:36: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:55:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:55:36: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:55:36: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:55:36: #1 total tags in treatment: 13766230 INFO @ Fri, 16 Mar 2018 07:55:36: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:55:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:55:36: #1 tags after filtering in treatment: 13766230 INFO @ Fri, 16 Mar 2018 07:55:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:55:36: #1 finished! INFO @ Fri, 16 Mar 2018 07:55:36: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:55:36: #1 tags after filtering in treatment: 13766230 INFO @ Fri, 16 Mar 2018 07:55:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:55:36: #1 finished! INFO @ Fri, 16 Mar 2018 07:55:36: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:55:37: #2 number of paired peaks: 110 WARNING @ Fri, 16 Mar 2018 07:55:37: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Fri, 16 Mar 2018 07:55:37: start model_add_line... INFO @ Fri, 16 Mar 2018 07:55:37: start X-correlation... INFO @ Fri, 16 Mar 2018 07:55:37: end of X-cor INFO @ Fri, 16 Mar 2018 07:55:37: #2 finished! INFO @ Fri, 16 Mar 2018 07:55:37: #2 predicted fragment length is 50 bps INFO @ Fri, 16 Mar 2018 07:55:37: #2 alternative fragment length(s) may be 4,50 bps INFO @ Fri, 16 Mar 2018 07:55:37: #2.2 Generate R script for model : SRX3068984.20_model.r WARNING @ Fri, 16 Mar 2018 07:55:37: #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, 16 Mar 2018 07:55:37: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Fri, 16 Mar 2018 07:55:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:55:37: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:55:37: #2 number of paired peaks: 110 WARNING @ Fri, 16 Mar 2018 07:55:37: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Fri, 16 Mar 2018 07:55:37: start model_add_line... INFO @ Fri, 16 Mar 2018 07:55:37: start X-correlation... INFO @ Fri, 16 Mar 2018 07:55:37: end of X-cor INFO @ Fri, 16 Mar 2018 07:55:37: #2 finished! INFO @ Fri, 16 Mar 2018 07:55:37: #2 predicted fragment length is 50 bps INFO @ Fri, 16 Mar 2018 07:55:37: #2 alternative fragment length(s) may be 4,50 bps INFO @ Fri, 16 Mar 2018 07:55:37: #2.2 Generate R script for model : SRX3068984.10_model.r WARNING @ Fri, 16 Mar 2018 07:55:37: #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, 16 Mar 2018 07:55:37: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Fri, 16 Mar 2018 07:55:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:55:37: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:55:40: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:55:40: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:55:40: #1 total tags in treatment: 13766230 INFO @ Fri, 16 Mar 2018 07:55:40: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:55:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:55:40: #1 tags after filtering in treatment: 13766230 INFO @ Fri, 16 Mar 2018 07:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:55:40: #1 finished! INFO @ Fri, 16 Mar 2018 07:55:40: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:55:41: #2 number of paired peaks: 110 WARNING @ Fri, 16 Mar 2018 07:55:41: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Fri, 16 Mar 2018 07:55:41: start model_add_line... INFO @ Fri, 16 Mar 2018 07:55:42: start X-correlation... INFO @ Fri, 16 Mar 2018 07:55:42: end of X-cor INFO @ Fri, 16 Mar 2018 07:55:42: #2 finished! INFO @ Fri, 16 Mar 2018 07:55:42: #2 predicted fragment length is 50 bps INFO @ Fri, 16 Mar 2018 07:55:42: #2 alternative fragment length(s) may be 4,50 bps INFO @ Fri, 16 Mar 2018 07:55:42: #2.2 Generate R script for model : SRX3068984.05_model.r WARNING @ Fri, 16 Mar 2018 07:55:42: #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, 16 Mar 2018 07:55:42: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Fri, 16 Mar 2018 07:55:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:55:42: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:56:05: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:56:07: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:56:09: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:56:21: #4 Write output xls file... SRX3068984.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:56:21: #4 Write peak in narrowPeak format file... SRX3068984.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:56:21: #4 Write summits bed file... SRX3068984.20_summits.bed INFO @ Fri, 16 Mar 2018 07:56:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (697 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:56:22: #4 Write output xls file... SRX3068984.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:56:22: #4 Write peak in narrowPeak format file... SRX3068984.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:56:22: #4 Write summits bed file... SRX3068984.10_summits.bed INFO @ Fri, 16 Mar 2018 07:56:22: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (1123 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:56:26: #4 Write output xls file... SRX3068984.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:56:26: #4 Write peak in narrowPeak format file... SRX3068984.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:56:26: #4 Write summits bed file... SRX3068984.05_summits.bed INFO @ Fri, 16 Mar 2018 07:56:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1609 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。