Job ID = 11240726 sra ファイルのダウンロード中... Completed: 1496645K bytes transferred in 35 seconds (341882K 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 45471418 spots for /home/okishinya/chipatlas/results/dm3/SRX4639145/SRR7784126.sra Written 45471418 spots for /home/okishinya/chipatlas/results/dm3/SRX4639145/SRR7784126.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: 00:10:50 45471418 reads; of these: 45471418 (100.00%) were unpaired; of these: 26278305 (57.79%) aligned 0 times 13749846 (30.24%) aligned exactly 1 time 5443267 (11.97%) aligned >1 times 42.21% overall alignment rate Time searching: 00:10:50 Overall time: 00:10:50 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] 15119706 / 19193113 = 0.7878 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, 07 Oct 2018 20:45:48: # Command line: callpeak -t SRX4639145.bam -f BAM -g dm -n SRX4639145.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4639145.10 # format = BAM # ChIP-seq file = ['SRX4639145.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 @ Sun, 07 Oct 2018 20:45:48: # Command line: callpeak -t SRX4639145.bam -f BAM -g dm -n SRX4639145.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4639145.05 # format = BAM # ChIP-seq file = ['SRX4639145.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 @ Sun, 07 Oct 2018 20:45:48: # Command line: callpeak -t SRX4639145.bam -f BAM -g dm -n SRX4639145.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4639145.20 # format = BAM # ChIP-seq file = ['SRX4639145.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 @ Sun, 07 Oct 2018 20:45:48: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:48: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:48: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:48: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:48: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:48: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:55: 1000000 INFO @ Sun, 07 Oct 2018 20:45:55: 1000000 INFO @ Sun, 07 Oct 2018 20:45:55: 1000000 INFO @ Sun, 07 Oct 2018 20:46:01: 2000000 INFO @ Sun, 07 Oct 2018 20:46:01: 2000000 INFO @ Sun, 07 Oct 2018 20:46:01: 2000000 INFO @ Sun, 07 Oct 2018 20:46:08: 3000000 INFO @ Sun, 07 Oct 2018 20:46:08: 3000000 INFO @ Sun, 07 Oct 2018 20:46:08: 3000000 INFO @ Sun, 07 Oct 2018 20:46:14: 4000000 INFO @ Sun, 07 Oct 2018 20:46:14: 4000000 INFO @ Sun, 07 Oct 2018 20:46:14: 4000000 INFO @ Sun, 07 Oct 2018 20:46:14: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:46:14: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:46:14: #1 total tags in treatment: 4073407 INFO @ Sun, 07 Oct 2018 20:46:14: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:46:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:46:15: #1 tags after filtering in treatment: 4073407 INFO @ Sun, 07 Oct 2018 20:46:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:46:15: #1 finished! INFO @ Sun, 07 Oct 2018 20:46:15: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:46:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:46:15: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:46:15: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:46:15: #1 total tags in treatment: 4073407 INFO @ Sun, 07 Oct 2018 20:46:15: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:46:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:46:15: #1 tags after filtering in treatment: 4073407 INFO @ Sun, 07 Oct 2018 20:46:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:46:15: #1 finished! INFO @ Sun, 07 Oct 2018 20:46:15: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:46:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:46:15: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:46:15: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:46:15: #1 total tags in treatment: 4073407 INFO @ Sun, 07 Oct 2018 20:46:15: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:46:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:46:15: #1 tags after filtering in treatment: 4073407 INFO @ Sun, 07 Oct 2018 20:46:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:46:15: #1 finished! INFO @ Sun, 07 Oct 2018 20:46:15: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:46:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:46:15: #2 number of paired peaks: 3962 INFO @ Sun, 07 Oct 2018 20:46:15: start model_add_line... INFO @ Sun, 07 Oct 2018 20:46:15: start X-correlation... INFO @ Sun, 07 Oct 2018 20:46:15: #2 number of paired peaks: 3962 INFO @ Sun, 07 Oct 2018 20:46:15: start model_add_line... INFO @ Sun, 07 Oct 2018 20:46:15: start X-correlation... INFO @ Sun, 07 Oct 2018 20:46:15: end of X-cor INFO @ Sun, 07 Oct 2018 20:46:15: end of X-cor INFO @ Sun, 07 Oct 2018 20:46:15: #2 finished! INFO @ Sun, 07 Oct 2018 20:46:15: #2 finished! INFO @ Sun, 07 Oct 2018 20:46:15: #2 predicted fragment length is 71 bps INFO @ Sun, 07 Oct 2018 20:46:15: #2 predicted fragment length is 71 bps INFO @ Sun, 07 Oct 2018 20:46:15: #2 alternative fragment length(s) may be 71 bps INFO @ Sun, 07 Oct 2018 20:46:15: #2 alternative fragment length(s) may be 71 bps INFO @ Sun, 07 Oct 2018 20:46:15: #2.2 Generate R script for model : SRX4639145.20_model.r INFO @ Sun, 07 Oct 2018 20:46:15: #2.2 Generate R script for model : SRX4639145.05_model.r WARNING @ Sun, 07 Oct 2018 20:46:15: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:46:15: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sun, 07 Oct 2018 20:46:15: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:46:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Sun, 07 Oct 2018 20:46:15: #2 You may need to consider one of the other alternative d(s): 71 INFO @ Sun, 07 Oct 2018 20:46:15: #3 Call peaks... WARNING @ Sun, 07 Oct 2018 20:46:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:46:15: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:46:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:46:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:46:16: #2 number of paired peaks: 3962 INFO @ Sun, 07 Oct 2018 20:46:16: start model_add_line... INFO @ Sun, 07 Oct 2018 20:46:16: start X-correlation... INFO @ Sun, 07 Oct 2018 20:46:16: end of X-cor INFO @ Sun, 07 Oct 2018 20:46:16: #2 finished! INFO @ Sun, 07 Oct 2018 20:46:16: #2 predicted fragment length is 71 bps INFO @ Sun, 07 Oct 2018 20:46:16: #2 alternative fragment length(s) may be 71 bps INFO @ Sun, 07 Oct 2018 20:46:16: #2.2 Generate R script for model : SRX4639145.10_model.r WARNING @ Sun, 07 Oct 2018 20:46:16: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:46:16: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sun, 07 Oct 2018 20:46:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:46:16: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:46:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:46:25: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:46:26: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:46:26: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:46:31: #4 Write output xls file... SRX4639145.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:46:31: #4 Write peak in narrowPeak format file... SRX4639145.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:46:31: #4 Write summits bed file... SRX4639145.20_summits.bed INFO @ Sun, 07 Oct 2018 20:46:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1323 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:46:31: #4 Write output xls file... SRX4639145.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:46:31: #4 Write peak in narrowPeak format file... SRX4639145.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:46:31: #4 Write summits bed file... SRX4639145.10_summits.bed INFO @ Sun, 07 Oct 2018 20:46:32: Done! INFO @ Sun, 07 Oct 2018 20:46:32: #4 Write output xls file... SRX4639145.05_peaks.xls pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3685 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:46:32: #4 Write peak in narrowPeak format file... SRX4639145.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:46:32: #4 Write summits bed file... SRX4639145.05_summits.bed INFO @ Sun, 07 Oct 2018 20:46:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7872 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。