Job ID = 11171368 sra ファイルのダウンロード中... Completed: 119400K bytes transferred in 4 seconds (215822K 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 6973813 spots for /home/okishinya/chipatlas/results/dm3/SRX4315041/SRR7444502.sra Written 6973813 spots for /home/okishinya/chipatlas/results/dm3/SRX4315041/SRR7444502.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: 00:03:06 6973813 reads; of these: 6973813 (100.00%) were unpaired; of these: 2094 (0.03%) aligned 0 times 5920700 (84.90%) aligned exactly 1 time 1051019 (15.07%) aligned >1 times 99.97% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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_rmdupse_core] 3712158 / 6971719 = 0.5325 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 @ Sat, 08 Sep 2018 14:13:47: # Command line: callpeak -t SRX4315041.bam -f BAM -g dm -n SRX4315041.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4315041.05 # format = BAM # ChIP-seq file = ['SRX4315041.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 @ Sat, 08 Sep 2018 14:13:47: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:13:47: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:13:47: # Command line: callpeak -t SRX4315041.bam -f BAM -g dm -n SRX4315041.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4315041.10 # format = BAM # ChIP-seq file = ['SRX4315041.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 @ Sat, 08 Sep 2018 14:13:47: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:13:47: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:13:47: # Command line: callpeak -t SRX4315041.bam -f BAM -g dm -n SRX4315041.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4315041.20 # format = BAM # ChIP-seq file = ['SRX4315041.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 @ Sat, 08 Sep 2018 14:13:47: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:13:47: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:13:54: 1000000 INFO @ Sat, 08 Sep 2018 14:13:54: 1000000 INFO @ Sat, 08 Sep 2018 14:13:54: 1000000 INFO @ Sat, 08 Sep 2018 14:14:01: 2000000 INFO @ Sat, 08 Sep 2018 14:14:01: 2000000 INFO @ Sat, 08 Sep 2018 14:14:01: 2000000 INFO @ Sat, 08 Sep 2018 14:14:08: 3000000 INFO @ Sat, 08 Sep 2018 14:14:08: 3000000 INFO @ Sat, 08 Sep 2018 14:14:08: 3000000 INFO @ Sat, 08 Sep 2018 14:14:09: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:14:09: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:14:09: #1 total tags in treatment: 3259561 INFO @ Sat, 08 Sep 2018 14:14:09: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:14:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:14:10: #1 tags after filtering in treatment: 3259561 INFO @ Sat, 08 Sep 2018 14:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:14:10: #1 finished! INFO @ Sat, 08 Sep 2018 14:14:10: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:14:10: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:14:10: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:14:10: #1 total tags in treatment: 3259561 INFO @ Sat, 08 Sep 2018 14:14:10: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:14:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:14:10: #1 tags after filtering in treatment: 3259561 INFO @ Sat, 08 Sep 2018 14:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:14:10: #1 finished! INFO @ Sat, 08 Sep 2018 14:14:10: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:14:10: #2 number of paired peaks: 384 WARNING @ Sat, 08 Sep 2018 14:14:10: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Sat, 08 Sep 2018 14:14:10: start model_add_line... INFO @ Sat, 08 Sep 2018 14:14:10: start X-correlation... INFO @ Sat, 08 Sep 2018 14:14:10: end of X-cor INFO @ Sat, 08 Sep 2018 14:14:10: #2 finished! INFO @ Sat, 08 Sep 2018 14:14:10: #2 predicted fragment length is 79 bps INFO @ Sat, 08 Sep 2018 14:14:10: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 08 Sep 2018 14:14:10: #2.2 Generate R script for model : SRX4315041.20_model.r INFO @ Sat, 08 Sep 2018 14:14:10: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:14:10: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:14:10: #1 total tags in treatment: 3259561 INFO @ Sat, 08 Sep 2018 14:14:10: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:14:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) WARNING @ Sat, 08 Sep 2018 14:14:10: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:14:10: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Sat, 08 Sep 2018 14:14:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:14:10: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:14:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:14:10: #1 tags after filtering in treatment: 3259561 INFO @ Sat, 08 Sep 2018 14:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:14:10: #1 finished! INFO @ Sat, 08 Sep 2018 14:14:10: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:14:10: #2 number of paired peaks: 384 WARNING @ Sat, 08 Sep 2018 14:14:10: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Sat, 08 Sep 2018 14:14:10: start model_add_line... INFO @ Sat, 08 Sep 2018 14:14:10: start X-correlation... INFO @ Sat, 08 Sep 2018 14:14:10: end of X-cor INFO @ Sat, 08 Sep 2018 14:14:10: #2 finished! INFO @ Sat, 08 Sep 2018 14:14:10: #2 predicted fragment length is 79 bps INFO @ Sat, 08 Sep 2018 14:14:10: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 08 Sep 2018 14:14:10: #2.2 Generate R script for model : SRX4315041.10_model.r WARNING @ Sat, 08 Sep 2018 14:14:10: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:14:10: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Sat, 08 Sep 2018 14:14:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:14:10: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:14:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:14:10: #2 number of paired peaks: 384 WARNING @ Sat, 08 Sep 2018 14:14:10: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Sat, 08 Sep 2018 14:14:10: start model_add_line... INFO @ Sat, 08 Sep 2018 14:14:10: start X-correlation... INFO @ Sat, 08 Sep 2018 14:14:10: end of X-cor INFO @ Sat, 08 Sep 2018 14:14:10: #2 finished! INFO @ Sat, 08 Sep 2018 14:14:10: #2 predicted fragment length is 79 bps INFO @ Sat, 08 Sep 2018 14:14:10: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 08 Sep 2018 14:14:10: #2.2 Generate R script for model : SRX4315041.05_model.r WARNING @ Sat, 08 Sep 2018 14:14:10: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:14:10: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Sat, 08 Sep 2018 14:14:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:14:10: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:14:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:14:17: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:14:18: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:14:19: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:14:22: #4 Write output xls file... SRX4315041.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:14:22: #4 Write peak in narrowPeak format file... SRX4315041.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:14:22: #4 Write summits bed file... SRX4315041.10_summits.bed INFO @ Sat, 08 Sep 2018 14:14:22: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (517 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:14:23: #4 Write output xls file... SRX4315041.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:14:23: #4 Write peak in narrowPeak format file... SRX4315041.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:14:23: #4 Write summits bed file... SRX4315041.20_summits.bed INFO @ Sat, 08 Sep 2018 14:14:23: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (268 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:14:23: #4 Write output xls file... SRX4315041.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:14:24: #4 Write peak in narrowPeak format file... SRX4315041.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:14:24: #4 Write summits bed file... SRX4315041.05_summits.bed INFO @ Sat, 08 Sep 2018 14:14:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (735 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。