Job ID = 10714411 sra ファイルのダウンロード中... Completed: 125540K bytes transferred in 6 seconds (162523K 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 11730132 spots for /home/okishinya/chipatlas/results/ce10/SRX4082371/SRR7164189.sra Written 11730132 spots for /home/okishinya/chipatlas/results/ce10/SRX4082371/SRR7164189.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:36 11730132 reads; of these: 11730132 (100.00%) were unpaired; of these: 4517560 (38.51%) aligned 0 times 5543116 (47.26%) aligned exactly 1 time 1669456 (14.23%) aligned >1 times 61.49% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 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_rmdupse_core] 1110167 / 7212572 = 0.1539 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 12:32:08: # Command line: callpeak -t SRX4082371.bam -f BAM -g ce -n SRX4082371.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082371.05 # format = BAM # ChIP-seq file = ['SRX4082371.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 12:32:08: # Command line: callpeak -t SRX4082371.bam -f BAM -g ce -n SRX4082371.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082371.10 # format = BAM # ChIP-seq file = ['SRX4082371.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 12:32:08: # Command line: callpeak -t SRX4082371.bam -f BAM -g ce -n SRX4082371.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082371.20 # format = BAM # ChIP-seq file = ['SRX4082371.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 12:32:08: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:32:08: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:32:08: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:32:08: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:32:08: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:32:08: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:32:15: 1000000 INFO @ Sun, 03 Jun 2018 12:32:15: 1000000 INFO @ Sun, 03 Jun 2018 12:32:15: 1000000 INFO @ Sun, 03 Jun 2018 12:32:21: 2000000 INFO @ Sun, 03 Jun 2018 12:32:22: 2000000 INFO @ Sun, 03 Jun 2018 12:32:22: 2000000 INFO @ Sun, 03 Jun 2018 12:32:28: 3000000 INFO @ Sun, 03 Jun 2018 12:32:29: 3000000 INFO @ Sun, 03 Jun 2018 12:32:30: 3000000 INFO @ Sun, 03 Jun 2018 12:32:35: 4000000 INFO @ Sun, 03 Jun 2018 12:32:37: 4000000 INFO @ Sun, 03 Jun 2018 12:32:37: 4000000 INFO @ Sun, 03 Jun 2018 12:32:42: 5000000 INFO @ Sun, 03 Jun 2018 12:32:45: 5000000 INFO @ Sun, 03 Jun 2018 12:32:45: 5000000 INFO @ Sun, 03 Jun 2018 12:32:50: 6000000 INFO @ Sun, 03 Jun 2018 12:32:50: #1 tag size is determined as 32 bps INFO @ Sun, 03 Jun 2018 12:32:50: #1 tag size = 32 INFO @ Sun, 03 Jun 2018 12:32:50: #1 total tags in treatment: 6102405 INFO @ Sun, 03 Jun 2018 12:32:50: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:32:50: #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 12:32:50: #1 tags after filtering in treatment: 6102405 INFO @ Sun, 03 Jun 2018 12:32:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:32:50: #1 finished! INFO @ Sun, 03 Jun 2018 12:32:50: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:32:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:32:51: #2 number of paired peaks: 291 WARNING @ Sun, 03 Jun 2018 12:32:51: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Sun, 03 Jun 2018 12:32:51: start model_add_line... INFO @ Sun, 03 Jun 2018 12:32:51: start X-correlation... INFO @ Sun, 03 Jun 2018 12:32:51: end of X-cor INFO @ Sun, 03 Jun 2018 12:32:51: #2 finished! INFO @ Sun, 03 Jun 2018 12:32:51: #2 predicted fragment length is 30 bps INFO @ Sun, 03 Jun 2018 12:32:51: #2 alternative fragment length(s) may be 1,30,69,91,117,546,572 bps INFO @ Sun, 03 Jun 2018 12:32:51: #2.2 Generate R script for model : SRX4082371.20_model.r WARNING @ Sun, 03 Jun 2018 12:32:51: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:32:51: #2 You may need to consider one of the other alternative d(s): 1,30,69,91,117,546,572 WARNING @ Sun, 03 Jun 2018 12:32:51: #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 12:32:51: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:32:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:32:53: 6000000 INFO @ Sun, 03 Jun 2018 12:32:53: 6000000 INFO @ Sun, 03 Jun 2018 12:32:54: #1 tag size is determined as 32 bps INFO @ Sun, 03 Jun 2018 12:32:54: #1 tag size = 32 INFO @ Sun, 03 Jun 2018 12:32:54: #1 total tags in treatment: 6102405 INFO @ Sun, 03 Jun 2018 12:32:54: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:32:54: #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 12:32:54: #1 tag size is determined as 32 bps INFO @ Sun, 03 Jun 2018 12:32:54: #1 tag size = 32 INFO @ Sun, 03 Jun 2018 12:32:54: #1 total tags in treatment: 6102405 INFO @ Sun, 03 Jun 2018 12:32:54: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:32:54: #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 12:32:54: #1 tags after filtering in treatment: 6102405 INFO @ Sun, 03 Jun 2018 12:32:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:32:54: #1 finished! INFO @ Sun, 03 Jun 2018 12:32:54: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:32:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:32:54: #1 tags after filtering in treatment: 6102405 INFO @ Sun, 03 Jun 2018 12:32:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:32:54: #1 finished! INFO @ Sun, 03 Jun 2018 12:32:54: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:32:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:32:54: #2 number of paired peaks: 291 WARNING @ Sun, 03 Jun 2018 12:32:54: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Sun, 03 Jun 2018 12:32:54: start model_add_line... INFO @ Sun, 03 Jun 2018 12:32:54: start X-correlation... INFO @ Sun, 03 Jun 2018 12:32:54: end of X-cor INFO @ Sun, 03 Jun 2018 12:32:54: #2 finished! INFO @ Sun, 03 Jun 2018 12:32:54: #2 predicted fragment length is 30 bps INFO @ Sun, 03 Jun 2018 12:32:54: #2 alternative fragment length(s) may be 1,30,69,91,117,546,572 bps INFO @ Sun, 03 Jun 2018 12:32:54: #2.2 Generate R script for model : SRX4082371.10_model.r WARNING @ Sun, 03 Jun 2018 12:32:54: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:32:54: #2 You may need to consider one of the other alternative d(s): 1,30,69,91,117,546,572 WARNING @ Sun, 03 Jun 2018 12:32:54: #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 12:32:54: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:32:54: #2 number of paired peaks: 291 WARNING @ Sun, 03 Jun 2018 12:32:54: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Sun, 03 Jun 2018 12:32:54: start model_add_line... INFO @ Sun, 03 Jun 2018 12:32:54: start X-correlation... INFO @ Sun, 03 Jun 2018 12:32:54: end of X-cor INFO @ Sun, 03 Jun 2018 12:32:54: #2 finished! INFO @ Sun, 03 Jun 2018 12:32:54: #2 predicted fragment length is 30 bps INFO @ Sun, 03 Jun 2018 12:32:54: #2 alternative fragment length(s) may be 1,30,69,91,117,546,572 bps INFO @ Sun, 03 Jun 2018 12:32:54: #2.2 Generate R script for model : SRX4082371.05_model.r WARNING @ Sun, 03 Jun 2018 12:32:54: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:32:54: #2 You may need to consider one of the other alternative d(s): 1,30,69,91,117,546,572 WARNING @ Sun, 03 Jun 2018 12:32:54: #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 12:32:54: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:33:05: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:33:09: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:33:09: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:33:12: #4 Write output xls file... SRX4082371.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:33:12: #4 Write peak in narrowPeak format file... SRX4082371.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:33:12: #4 Write summits bed file... SRX4082371.20_summits.bed INFO @ Sun, 03 Jun 2018 12:33:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:33:16: #4 Write output xls file... SRX4082371.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:33:16: #4 Write peak in narrowPeak format file... SRX4082371.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:33:16: #4 Write summits bed file... SRX4082371.05_summits.bed INFO @ Sun, 03 Jun 2018 12:33:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:33:17: #4 Write output xls file... SRX4082371.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:33:17: #4 Write peak in narrowPeak format file... SRX4082371.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:33:17: #4 Write summits bed file... SRX4082371.10_summits.bed INFO @ Sun, 03 Jun 2018 12:33:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。