Job ID = 10480715 sra ファイルのダウンロード中... Completed: 447208K bytes transferred in 15 seconds (230605K 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 14875190 spots for /home/okishinya/chipatlas/results/dm3/SRX3068986/SRR5907462.sra Written 14875190 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: 00:05:00 14875190 reads; of these: 14875190 (100.00%) were unpaired; of these: 1339652 (9.01%) aligned 0 times 10749516 (72.26%) aligned exactly 1 time 2786022 (18.73%) aligned >1 times 90.99% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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] 4100401 / 13535538 = 0.3029 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 07:51:08: # Command line: callpeak -t SRX3068986.bam -f BAM -g dm -n SRX3068986.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068986.10 # format = BAM # ChIP-seq file = ['SRX3068986.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 07:51:08: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:51:08: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:51:08: # Command line: callpeak -t SRX3068986.bam -f BAM -g dm -n SRX3068986.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068986.05 # format = BAM # ChIP-seq file = ['SRX3068986.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 07:51:08: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:51:08: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:51:08: # Command line: callpeak -t SRX3068986.bam -f BAM -g dm -n SRX3068986.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068986.20 # format = BAM # ChIP-seq file = ['SRX3068986.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 07:51:08: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:51:08: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:51:14: 1000000 INFO @ Fri, 16 Mar 2018 07:51:15: 1000000 INFO @ Fri, 16 Mar 2018 07:51:15: 1000000 INFO @ Fri, 16 Mar 2018 07:51:22: 2000000 INFO @ Fri, 16 Mar 2018 07:51:22: 2000000 INFO @ Fri, 16 Mar 2018 07:51:22: 2000000 INFO @ Fri, 16 Mar 2018 07:51:29: 3000000 INFO @ Fri, 16 Mar 2018 07:51:29: 3000000 INFO @ Fri, 16 Mar 2018 07:51:30: 3000000 INFO @ Fri, 16 Mar 2018 07:51:36: 4000000 INFO @ Fri, 16 Mar 2018 07:51:36: 4000000 INFO @ Fri, 16 Mar 2018 07:51:37: 4000000 INFO @ Fri, 16 Mar 2018 07:51:43: 5000000 INFO @ Fri, 16 Mar 2018 07:51:43: 5000000 INFO @ Fri, 16 Mar 2018 07:51:44: 5000000 INFO @ Fri, 16 Mar 2018 07:51:50: 6000000 INFO @ Fri, 16 Mar 2018 07:51:51: 6000000 INFO @ Fri, 16 Mar 2018 07:51:52: 6000000 INFO @ Fri, 16 Mar 2018 07:51:57: 7000000 INFO @ Fri, 16 Mar 2018 07:51:58: 7000000 INFO @ Fri, 16 Mar 2018 07:51:59: 7000000 INFO @ Fri, 16 Mar 2018 07:52:04: 8000000 INFO @ Fri, 16 Mar 2018 07:52:05: 8000000 INFO @ Fri, 16 Mar 2018 07:52:07: 8000000 INFO @ Fri, 16 Mar 2018 07:52:13: 9000000 INFO @ Fri, 16 Mar 2018 07:52:14: 9000000 INFO @ Fri, 16 Mar 2018 07:52:14: 9000000 INFO @ Fri, 16 Mar 2018 07:52:16: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:52:16: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:52:16: #1 total tags in treatment: 9435137 INFO @ Fri, 16 Mar 2018 07:52:16: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:52:16: #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 07:52:16: #1 tags after filtering in treatment: 9435137 INFO @ Fri, 16 Mar 2018 07:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:52:16: #1 finished! INFO @ Fri, 16 Mar 2018 07:52:16: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:52:17: #2 number of paired peaks: 166 WARNING @ Fri, 16 Mar 2018 07:52:17: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Fri, 16 Mar 2018 07:52:17: start model_add_line... INFO @ Fri, 16 Mar 2018 07:52:17: start X-correlation... INFO @ Fri, 16 Mar 2018 07:52:17: end of X-cor INFO @ Fri, 16 Mar 2018 07:52:17: #2 finished! INFO @ Fri, 16 Mar 2018 07:52:17: #2 predicted fragment length is 53 bps INFO @ Fri, 16 Mar 2018 07:52:17: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 16 Mar 2018 07:52:17: #2.2 Generate R script for model : SRX3068986.10_model.r WARNING @ Fri, 16 Mar 2018 07:52:17: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:52:17: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 16 Mar 2018 07:52:17: #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 07:52:17: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:52:17: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:52:17: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:52:17: #1 total tags in treatment: 9435137 INFO @ Fri, 16 Mar 2018 07:52:17: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:52:17: #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 07:52:17: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:52:17: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:52:17: #1 total tags in treatment: 9435137 INFO @ Fri, 16 Mar 2018 07:52:17: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:52:17: #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 07:52:18: #1 tags after filtering in treatment: 9435137 INFO @ Fri, 16 Mar 2018 07:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:52:18: #1 finished! INFO @ Fri, 16 Mar 2018 07:52:18: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:52:18: #1 tags after filtering in treatment: 9435137 INFO @ Fri, 16 Mar 2018 07:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:52:18: #1 finished! INFO @ Fri, 16 Mar 2018 07:52:18: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:52:18: #2 number of paired peaks: 166 WARNING @ Fri, 16 Mar 2018 07:52:18: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Fri, 16 Mar 2018 07:52:18: start model_add_line... INFO @ Fri, 16 Mar 2018 07:52:18: #2 number of paired peaks: 166 WARNING @ Fri, 16 Mar 2018 07:52:18: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Fri, 16 Mar 2018 07:52:18: start model_add_line... INFO @ Fri, 16 Mar 2018 07:52:18: start X-correlation... INFO @ Fri, 16 Mar 2018 07:52:18: end of X-cor INFO @ Fri, 16 Mar 2018 07:52:18: #2 finished! INFO @ Fri, 16 Mar 2018 07:52:18: #2 predicted fragment length is 53 bps INFO @ Fri, 16 Mar 2018 07:52:18: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 16 Mar 2018 07:52:18: #2.2 Generate R script for model : SRX3068986.05_model.r WARNING @ Fri, 16 Mar 2018 07:52:18: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:52:18: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 16 Mar 2018 07:52:18: #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 07:52:18: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:52:18: start X-correlation... INFO @ Fri, 16 Mar 2018 07:52:18: end of X-cor INFO @ Fri, 16 Mar 2018 07:52:18: #2 finished! INFO @ Fri, 16 Mar 2018 07:52:18: #2 predicted fragment length is 53 bps INFO @ Fri, 16 Mar 2018 07:52:18: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 16 Mar 2018 07:52:18: #2.2 Generate R script for model : SRX3068986.20_model.r WARNING @ Fri, 16 Mar 2018 07:52:19: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:52:19: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 16 Mar 2018 07:52:19: #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 07:52:19: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:52:37: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:52:39: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:52:40: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:52:48: #4 Write output xls file... SRX3068986.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:52:48: #4 Write peak in narrowPeak format file... SRX3068986.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:52:48: #4 Write summits bed file... SRX3068986.10_summits.bed INFO @ Fri, 16 Mar 2018 07:52:48: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (984 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:52:50: #4 Write output xls file... SRX3068986.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:52:50: #4 Write peak in narrowPeak format file... SRX3068986.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:52:50: #4 Write summits bed file... SRX3068986.20_summits.bed INFO @ Fri, 16 Mar 2018 07:52:50: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (520 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:52:52: #4 Write output xls file... SRX3068986.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:52:52: #4 Write peak in narrowPeak format file... SRX3068986.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:52:52: #4 Write summits bed file... SRX3068986.05_summits.bed INFO @ Fri, 16 Mar 2018 07:52:52: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1327 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。