Job ID = 10175229 sra ファイルのダウンロード中... Completed: 158399K bytes transferred in 6 seconds (209943K 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... Written 9611221 spots for /home/okishinya/chipatlas/results/dm3/SRX2458932/SRR5140281.sra Written 9611221 spots total 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: 00:04:06 9611221 reads; of these: 9611221 (100.00%) were unpaired; of these: 491673 (5.12%) aligned 0 times 6933452 (72.14%) aligned exactly 1 time 2186096 (22.75%) aligned >1 times 94.88% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:07 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] 5564386 / 9119548 = 0.6102 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 @ Mon, 06 Nov 2017 11:47:46: # Command line: callpeak -t SRX2458932.bam -f BAM -g dm -n SRX2458932.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2458932.20 # format = BAM # ChIP-seq file = ['SRX2458932.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 @ Mon, 06 Nov 2017 11:47:46: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:47:46: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:47:46: # Command line: callpeak -t SRX2458932.bam -f BAM -g dm -n SRX2458932.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2458932.05 # format = BAM # ChIP-seq file = ['SRX2458932.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 @ Mon, 06 Nov 2017 11:47:46: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:47:46: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:47:46: # Command line: callpeak -t SRX2458932.bam -f BAM -g dm -n SRX2458932.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2458932.10 # format = BAM # ChIP-seq file = ['SRX2458932.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 @ Mon, 06 Nov 2017 11:47:46: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:47:46: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:47:54: 1000000 INFO @ Mon, 06 Nov 2017 11:47:54: 1000000 INFO @ Mon, 06 Nov 2017 11:47:55: 1000000 INFO @ Mon, 06 Nov 2017 11:48:02: 2000000 INFO @ Mon, 06 Nov 2017 11:48:02: 2000000 INFO @ Mon, 06 Nov 2017 11:48:04: 2000000 INFO @ Mon, 06 Nov 2017 11:48:10: 3000000 INFO @ Mon, 06 Nov 2017 11:48:11: 3000000 INFO @ Mon, 06 Nov 2017 11:48:11: 3000000 INFO @ Mon, 06 Nov 2017 11:48:15: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:48:15: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:48:15: #1 total tags in treatment: 3555162 INFO @ Mon, 06 Nov 2017 11:48:15: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:48:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:48:15: #1 tags after filtering in treatment: 3555162 INFO @ Mon, 06 Nov 2017 11:48:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:48:15: #1 finished! INFO @ Mon, 06 Nov 2017 11:48:15: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:48:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:48:15: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:48:15: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:48:15: #1 total tags in treatment: 3555162 INFO @ Mon, 06 Nov 2017 11:48:15: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:48:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:48:15: #1 tags after filtering in treatment: 3555162 INFO @ Mon, 06 Nov 2017 11:48:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:48:15: #1 finished! INFO @ Mon, 06 Nov 2017 11:48:15: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:48:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:48:15: #2 number of paired peaks: 2488 INFO @ Mon, 06 Nov 2017 11:48:15: start model_add_line... INFO @ Mon, 06 Nov 2017 11:48:15: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:48:15: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:48:15: #1 total tags in treatment: 3555162 INFO @ Mon, 06 Nov 2017 11:48:15: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:48:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:48:15: start X-correlation... INFO @ Mon, 06 Nov 2017 11:48:15: #1 tags after filtering in treatment: 3555162 INFO @ Mon, 06 Nov 2017 11:48:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:48:15: #1 finished! INFO @ Mon, 06 Nov 2017 11:48:15: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:48:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:48:15: #2 number of paired peaks: 2488 INFO @ Mon, 06 Nov 2017 11:48:15: start model_add_line... INFO @ Mon, 06 Nov 2017 11:48:15: end of X-cor INFO @ Mon, 06 Nov 2017 11:48:15: #2 finished! INFO @ Mon, 06 Nov 2017 11:48:15: #2 predicted fragment length is 69 bps INFO @ Mon, 06 Nov 2017 11:48:15: #2 alternative fragment length(s) may be 69 bps INFO @ Mon, 06 Nov 2017 11:48:15: #2.2 Generate R script for model : SRX2458932.05_model.r WARNING @ Mon, 06 Nov 2017 11:48:15: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:48:15: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Mon, 06 Nov 2017 11:48:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:48:15: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:48:15: start X-correlation... INFO @ Mon, 06 Nov 2017 11:48:15: end of X-cor INFO @ Mon, 06 Nov 2017 11:48:15: #2 finished! INFO @ Mon, 06 Nov 2017 11:48:15: #2 predicted fragment length is 69 bps INFO @ Mon, 06 Nov 2017 11:48:15: #2 alternative fragment length(s) may be 69 bps INFO @ Mon, 06 Nov 2017 11:48:15: #2.2 Generate R script for model : SRX2458932.10_model.r WARNING @ Mon, 06 Nov 2017 11:48:15: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:48:15: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Mon, 06 Nov 2017 11:48:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:48:15: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:48:16: #2 number of paired peaks: 2488 INFO @ Mon, 06 Nov 2017 11:48:16: start model_add_line... INFO @ Mon, 06 Nov 2017 11:48:16: start X-correlation... INFO @ Mon, 06 Nov 2017 11:48:16: end of X-cor INFO @ Mon, 06 Nov 2017 11:48:16: #2 finished! INFO @ Mon, 06 Nov 2017 11:48:16: #2 predicted fragment length is 69 bps INFO @ Mon, 06 Nov 2017 11:48:16: #2 alternative fragment length(s) may be 69 bps INFO @ Mon, 06 Nov 2017 11:48:16: #2.2 Generate R script for model : SRX2458932.20_model.r WARNING @ Mon, 06 Nov 2017 11:48:16: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:48:16: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Mon, 06 Nov 2017 11:48:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:48:16: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:48:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:48:24: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:48:25: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:48:25: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:48:29: #4 Write output xls file... SRX2458932.10_peaks.xls INFO @ Mon, 06 Nov 2017 11:48:29: #4 Write peak in narrowPeak format file... SRX2458932.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:48:29: #4 Write summits bed file... SRX2458932.10_summits.bed INFO @ Mon, 06 Nov 2017 11:48:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1218 records, 4 fields): 115 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:48:30: #4 Write output xls file... SRX2458932.05_peaks.xls INFO @ Mon, 06 Nov 2017 11:48:30: #4 Write peak in narrowPeak format file... SRX2458932.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:48:30: #4 Write summits bed file... SRX2458932.05_summits.bed INFO @ Mon, 06 Nov 2017 11:48:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2073 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:48:30: #4 Write output xls file... SRX2458932.20_peaks.xls INFO @ Mon, 06 Nov 2017 11:48:30: #4 Write peak in narrowPeak format file... SRX2458932.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:48:30: #4 Write summits bed file... SRX2458932.20_summits.bed INFO @ Mon, 06 Nov 2017 11:48:30: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (618 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。