Job ID = 10714361 sra ファイルのダウンロード中... Completed: 1232280K bytes transferred in 61 seconds (165440K 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 22743849 spots for /home/okishinya/chipatlas/results/ce10/SRX2965742/SRR5766327.sra Written 22743849 spots for /home/okishinya/chipatlas/results/ce10/SRX2965742/SRR5766327.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: 00:08:29 22743849 reads; of these: 22743849 (100.00%) were unpaired; of these: 9630015 (42.34%) aligned 0 times 11177542 (49.15%) aligned exactly 1 time 1936292 (8.51%) aligned >1 times 57.66% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 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 8 files... [bam_rmdupse_core] 1849855 / 13113834 = 0.1411 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 12:42:36: # Command line: callpeak -t SRX2965742.bam -f BAM -g ce -n SRX2965742.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2965742.05 # format = BAM # ChIP-seq file = ['SRX2965742.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 12:42:36: # Command line: callpeak -t SRX2965742.bam -f BAM -g ce -n SRX2965742.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2965742.20 # format = BAM # ChIP-seq file = ['SRX2965742.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 12:42:36: # Command line: callpeak -t SRX2965742.bam -f BAM -g ce -n SRX2965742.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2965742.10 # format = BAM # ChIP-seq file = ['SRX2965742.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 12:42:36: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:42:36: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:42:36: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:42:36: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:42:36: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:42:36: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:42:44: 1000000 INFO @ Sun, 03 Jun 2018 12:42:45: 1000000 INFO @ Sun, 03 Jun 2018 12:42:45: 1000000 INFO @ Sun, 03 Jun 2018 12:42:53: 2000000 INFO @ Sun, 03 Jun 2018 12:42:54: 2000000 INFO @ Sun, 03 Jun 2018 12:42:54: 2000000 INFO @ Sun, 03 Jun 2018 12:43:01: 3000000 INFO @ Sun, 03 Jun 2018 12:43:03: 3000000 INFO @ Sun, 03 Jun 2018 12:43:03: 3000000 INFO @ Sun, 03 Jun 2018 12:43:10: 4000000 INFO @ Sun, 03 Jun 2018 12:43:12: 4000000 INFO @ Sun, 03 Jun 2018 12:43:12: 4000000 INFO @ Sun, 03 Jun 2018 12:43:18: 5000000 INFO @ Sun, 03 Jun 2018 12:43:20: 5000000 INFO @ Sun, 03 Jun 2018 12:43:20: 5000000 INFO @ Sun, 03 Jun 2018 12:43:27: 6000000 INFO @ Sun, 03 Jun 2018 12:43:29: 6000000 INFO @ Sun, 03 Jun 2018 12:43:29: 6000000 INFO @ Sun, 03 Jun 2018 12:43:35: 7000000 INFO @ Sun, 03 Jun 2018 12:43:38: 7000000 INFO @ Sun, 03 Jun 2018 12:43:38: 7000000 INFO @ Sun, 03 Jun 2018 12:43:44: 8000000 INFO @ Sun, 03 Jun 2018 12:43:47: 8000000 INFO @ Sun, 03 Jun 2018 12:43:47: 8000000 INFO @ Sun, 03 Jun 2018 12:43:52: 9000000 INFO @ Sun, 03 Jun 2018 12:43:56: 9000000 INFO @ Sun, 03 Jun 2018 12:43:56: 9000000 INFO @ Sun, 03 Jun 2018 12:44:01: 10000000 INFO @ Sun, 03 Jun 2018 12:44:05: 10000000 INFO @ Sun, 03 Jun 2018 12:44:05: 10000000 INFO @ Sun, 03 Jun 2018 12:44:09: 11000000 INFO @ Sun, 03 Jun 2018 12:44:12: #1 tag size is determined as 101 bps INFO @ Sun, 03 Jun 2018 12:44:12: #1 tag size = 101 INFO @ Sun, 03 Jun 2018 12:44:12: #1 total tags in treatment: 11263979 INFO @ Sun, 03 Jun 2018 12:44:12: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:44:12: #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 12:44:12: #1 tags after filtering in treatment: 11263979 INFO @ Sun, 03 Jun 2018 12:44:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:44:12: #1 finished! INFO @ Sun, 03 Jun 2018 12:44:12: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:44:13: #2 number of paired peaks: 865 WARNING @ Sun, 03 Jun 2018 12:44:13: Fewer paired peaks (865) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 865 pairs to build model! INFO @ Sun, 03 Jun 2018 12:44:13: start model_add_line... INFO @ Sun, 03 Jun 2018 12:44:13: start X-correlation... INFO @ Sun, 03 Jun 2018 12:44:13: end of X-cor INFO @ Sun, 03 Jun 2018 12:44:13: #2 finished! INFO @ Sun, 03 Jun 2018 12:44:13: #2 predicted fragment length is 146 bps INFO @ Sun, 03 Jun 2018 12:44:13: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 03 Jun 2018 12:44:13: #2.2 Generate R script for model : SRX2965742.10_model.r WARNING @ Sun, 03 Jun 2018 12:44:13: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:44:13: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sun, 03 Jun 2018 12:44:13: #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 12:44:13: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:44:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:44:14: 11000000 INFO @ Sun, 03 Jun 2018 12:44:14: 11000000 INFO @ Sun, 03 Jun 2018 12:44:16: #1 tag size is determined as 101 bps INFO @ Sun, 03 Jun 2018 12:44:16: #1 tag size = 101 INFO @ Sun, 03 Jun 2018 12:44:16: #1 total tags in treatment: 11263979 INFO @ Sun, 03 Jun 2018 12:44:16: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:44:16: #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 12:44:16: #1 tag size is determined as 101 bps INFO @ Sun, 03 Jun 2018 12:44:16: #1 tag size = 101 INFO @ Sun, 03 Jun 2018 12:44:16: #1 total tags in treatment: 11263979 INFO @ Sun, 03 Jun 2018 12:44:16: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:44:16: #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 12:44:17: #1 tags after filtering in treatment: 11263979 INFO @ Sun, 03 Jun 2018 12:44:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:44:17: #1 finished! INFO @ Sun, 03 Jun 2018 12:44:17: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:44:17: #1 tags after filtering in treatment: 11263979 INFO @ Sun, 03 Jun 2018 12:44:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:44:17: #1 finished! INFO @ Sun, 03 Jun 2018 12:44:17: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:44:18: #2 number of paired peaks: 865 WARNING @ Sun, 03 Jun 2018 12:44:18: Fewer paired peaks (865) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 865 pairs to build model! INFO @ Sun, 03 Jun 2018 12:44:18: start model_add_line... INFO @ Sun, 03 Jun 2018 12:44:18: #2 number of paired peaks: 865 WARNING @ Sun, 03 Jun 2018 12:44:18: Fewer paired peaks (865) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 865 pairs to build model! INFO @ Sun, 03 Jun 2018 12:44:18: start model_add_line... INFO @ Sun, 03 Jun 2018 12:44:18: start X-correlation... INFO @ Sun, 03 Jun 2018 12:44:18: end of X-cor INFO @ Sun, 03 Jun 2018 12:44:18: #2 finished! INFO @ Sun, 03 Jun 2018 12:44:18: #2 predicted fragment length is 146 bps INFO @ Sun, 03 Jun 2018 12:44:18: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 03 Jun 2018 12:44:18: #2.2 Generate R script for model : SRX2965742.20_model.r WARNING @ Sun, 03 Jun 2018 12:44:18: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:44:18: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sun, 03 Jun 2018 12:44:18: #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 12:44:18: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:44:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:44:18: start X-correlation... INFO @ Sun, 03 Jun 2018 12:44:18: end of X-cor INFO @ Sun, 03 Jun 2018 12:44:18: #2 finished! INFO @ Sun, 03 Jun 2018 12:44:18: #2 predicted fragment length is 146 bps INFO @ Sun, 03 Jun 2018 12:44:18: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 03 Jun 2018 12:44:18: #2.2 Generate R script for model : SRX2965742.05_model.r WARNING @ Sun, 03 Jun 2018 12:44:18: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:44:18: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sun, 03 Jun 2018 12:44:18: #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 12:44:18: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:44:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:44:40: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:44:42: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:44:45: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:44:55: #4 Write output xls file... SRX2965742.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:44:55: #4 Write peak in narrowPeak format file... SRX2965742.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:44:55: #4 Write summits bed file... SRX2965742.10_summits.bed INFO @ Sun, 03 Jun 2018 12:44:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2812 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:44:56: #4 Write output xls file... SRX2965742.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:44:56: #4 Write peak in narrowPeak format file... SRX2965742.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:44:56: #4 Write summits bed file... SRX2965742.05_summits.bed INFO @ Sun, 03 Jun 2018 12:44:57: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3870 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:44:59: #4 Write output xls file... SRX2965742.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:44:59: #4 Write peak in narrowPeak format file... SRX2965742.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:44:59: #4 Write summits bed file... SRX2965742.20_summits.bed INFO @ Sun, 03 Jun 2018 12:44:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1742 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。