Job ID = 11240750 sra ファイルのダウンロード中... Completed: 141629K bytes transferred in 5 seconds (194271K 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 9436862 spots for /home/okishinya/chipatlas/results/dm3/SRX4669034/SRR7817559.sra Written 9436862 spots for /home/okishinya/chipatlas/results/dm3/SRX4669034/SRR7817559.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: 00:02:09 9436862 reads; of these: 9436862 (100.00%) were unpaired; of these: 5970651 (63.27%) aligned 0 times 2177188 (23.07%) aligned exactly 1 time 1289023 (13.66%) aligned >1 times 36.73% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 674204 / 3466211 = 0.1945 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 20:32:27: # Command line: callpeak -t SRX4669034.bam -f BAM -g dm -n SRX4669034.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669034.20 # format = BAM # ChIP-seq file = ['SRX4669034.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 20:32:27: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:32:27: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:32:27: # Command line: callpeak -t SRX4669034.bam -f BAM -g dm -n SRX4669034.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669034.05 # format = BAM # ChIP-seq file = ['SRX4669034.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 20:32:27: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:32:27: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:32:27: # Command line: callpeak -t SRX4669034.bam -f BAM -g dm -n SRX4669034.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669034.10 # format = BAM # ChIP-seq file = ['SRX4669034.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 20:32:27: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:32:27: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:32:35: 1000000 INFO @ Sun, 07 Oct 2018 20:32:35: 1000000 INFO @ Sun, 07 Oct 2018 20:32:36: 1000000 INFO @ Sun, 07 Oct 2018 20:32:43: 2000000 INFO @ Sun, 07 Oct 2018 20:32:44: 2000000 INFO @ Sun, 07 Oct 2018 20:32:44: 2000000 INFO @ Sun, 07 Oct 2018 20:32:49: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:32:49: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:32:49: #1 total tags in treatment: 2792007 INFO @ Sun, 07 Oct 2018 20:32:49: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:32:49: #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 20:32:49: #1 tags after filtering in treatment: 2792007 INFO @ Sun, 07 Oct 2018 20:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:32:49: #1 finished! INFO @ Sun, 07 Oct 2018 20:32:49: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:32:49: #2 number of paired peaks: 1081 INFO @ Sun, 07 Oct 2018 20:32:49: start model_add_line... INFO @ Sun, 07 Oct 2018 20:32:49: start X-correlation... INFO @ Sun, 07 Oct 2018 20:32:49: end of X-cor INFO @ Sun, 07 Oct 2018 20:32:49: #2 finished! INFO @ Sun, 07 Oct 2018 20:32:49: #2 predicted fragment length is 73 bps INFO @ Sun, 07 Oct 2018 20:32:49: #2 alternative fragment length(s) may be 73 bps INFO @ Sun, 07 Oct 2018 20:32:49: #2.2 Generate R script for model : SRX4669034.10_model.r WARNING @ Sun, 07 Oct 2018 20:32:49: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:32:49: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sun, 07 Oct 2018 20:32:49: #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 20:32:49: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:32:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:32:50: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:32:50: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:32:50: #1 total tags in treatment: 2792007 INFO @ Sun, 07 Oct 2018 20:32:50: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:32:50: #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 20:32:50: #1 tags after filtering in treatment: 2792007 INFO @ Sun, 07 Oct 2018 20:32:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:32:50: #1 finished! INFO @ Sun, 07 Oct 2018 20:32:50: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:32:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:32:50: #2 number of paired peaks: 1081 INFO @ Sun, 07 Oct 2018 20:32:50: start model_add_line... INFO @ Sun, 07 Oct 2018 20:32:50: start X-correlation... INFO @ Sun, 07 Oct 2018 20:32:50: end of X-cor INFO @ Sun, 07 Oct 2018 20:32:50: #2 finished! INFO @ Sun, 07 Oct 2018 20:32:50: #2 predicted fragment length is 73 bps INFO @ Sun, 07 Oct 2018 20:32:50: #2 alternative fragment length(s) may be 73 bps INFO @ Sun, 07 Oct 2018 20:32:50: #2.2 Generate R script for model : SRX4669034.05_model.r WARNING @ Sun, 07 Oct 2018 20:32:50: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:32:50: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sun, 07 Oct 2018 20:32:50: #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 20:32:50: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:32:51: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:32:51: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:32:51: #1 total tags in treatment: 2792007 INFO @ Sun, 07 Oct 2018 20:32:51: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:32:51: #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 20:32:51: #1 tags after filtering in treatment: 2792007 INFO @ Sun, 07 Oct 2018 20:32:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:32:51: #1 finished! INFO @ Sun, 07 Oct 2018 20:32:51: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:32:51: #2 number of paired peaks: 1081 INFO @ Sun, 07 Oct 2018 20:32:51: start model_add_line... INFO @ Sun, 07 Oct 2018 20:32:51: start X-correlation... INFO @ Sun, 07 Oct 2018 20:32:51: end of X-cor INFO @ Sun, 07 Oct 2018 20:32:51: #2 finished! INFO @ Sun, 07 Oct 2018 20:32:51: #2 predicted fragment length is 73 bps INFO @ Sun, 07 Oct 2018 20:32:51: #2 alternative fragment length(s) may be 73 bps INFO @ Sun, 07 Oct 2018 20:32:51: #2.2 Generate R script for model : SRX4669034.20_model.r WARNING @ Sun, 07 Oct 2018 20:32:51: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:32:51: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sun, 07 Oct 2018 20:32:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:32:51: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:32:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:32:56: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:32:58: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:32:58: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:33:00: #4 Write output xls file... SRX4669034.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:33:00: #4 Write peak in narrowPeak format file... SRX4669034.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:33:00: #4 Write summits bed file... SRX4669034.10_summits.bed INFO @ Sun, 07 Oct 2018 20:33:00: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (186 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:33:02: #4 Write output xls file... SRX4669034.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:33:02: #4 Write peak in narrowPeak format file... SRX4669034.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:33:02: #4 Write summits bed file... SRX4669034.20_summits.bed INFO @ Sun, 07 Oct 2018 20:33:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (83 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:33:02: #4 Write output xls file... SRX4669034.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:33:02: #4 Write peak in narrowPeak format file... SRX4669034.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:33:02: #4 Write summits bed file... SRX4669034.05_summits.bed INFO @ Sun, 07 Oct 2018 20:33:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (714 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。