Job ID = 10450761 sra ファイルのダウンロード中... Completed: 60903K bytes transferred in 3 seconds (130026K 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 3029004 spots for /home/okishinya/chipatlas/results/dm3/SRX3404024/SRR6303501.sra Written 3029004 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:03:24 3029004 reads; of these: 3029004 (100.00%) were unpaired; of these: 399844 (13.20%) aligned 0 times 1095252 (36.16%) aligned exactly 1 time 1533908 (50.64%) aligned >1 times 86.80% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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] 939245 / 2629160 = 0.3572 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 @ Wed, 07 Feb 2018 12:21:04: # Command line: callpeak -t SRX3404024.bam -f BAM -g dm -n SRX3404024.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404024.05 # format = BAM # ChIP-seq file = ['SRX3404024.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 @ Wed, 07 Feb 2018 12:21:04: # Command line: callpeak -t SRX3404024.bam -f BAM -g dm -n SRX3404024.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404024.20 # format = BAM # ChIP-seq file = ['SRX3404024.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 @ Wed, 07 Feb 2018 12:21:04: # Command line: callpeak -t SRX3404024.bam -f BAM -g dm -n SRX3404024.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404024.10 # format = BAM # ChIP-seq file = ['SRX3404024.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 @ Wed, 07 Feb 2018 12:21:04: #1 read tag files... INFO @ Wed, 07 Feb 2018 12:21:04: #1 read tag files... INFO @ Wed, 07 Feb 2018 12:21:04: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 12:21:04: #1 read tag files... INFO @ Wed, 07 Feb 2018 12:21:04: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 12:21:04: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 12:21:14: 1000000 INFO @ Wed, 07 Feb 2018 12:21:21: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 12:21:21: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 12:21:21: #1 total tags in treatment: 1689915 INFO @ Wed, 07 Feb 2018 12:21:21: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 12:21:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 12:21:21: #1 tags after filtering in treatment: 1689915 INFO @ Wed, 07 Feb 2018 12:21:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 12:21:21: #1 finished! INFO @ Wed, 07 Feb 2018 12:21:21: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 12:21:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 12:21:21: #2 number of paired peaks: 1979 INFO @ Wed, 07 Feb 2018 12:21:21: start model_add_line... INFO @ Wed, 07 Feb 2018 12:21:21: start X-correlation... INFO @ Wed, 07 Feb 2018 12:21:21: end of X-cor INFO @ Wed, 07 Feb 2018 12:21:21: #2 finished! INFO @ Wed, 07 Feb 2018 12:21:21: #2 predicted fragment length is 51 bps INFO @ Wed, 07 Feb 2018 12:21:21: #2 alternative fragment length(s) may be 51 bps INFO @ Wed, 07 Feb 2018 12:21:21: #2.2 Generate R script for model : SRX3404024.05_model.r WARNING @ Wed, 07 Feb 2018 12:21:21: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 12:21:21: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Wed, 07 Feb 2018 12:21:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 12:21:21: #3 Call peaks... INFO @ Wed, 07 Feb 2018 12:21:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 12:21:24: 1000000 INFO @ Wed, 07 Feb 2018 12:21:25: 1000000 INFO @ Wed, 07 Feb 2018 12:21:26: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 12:21:29: #4 Write output xls file... SRX3404024.05_peaks.xls INFO @ Wed, 07 Feb 2018 12:21:29: #4 Write peak in narrowPeak format file... SRX3404024.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 12:21:29: #4 Write summits bed file... SRX3404024.05_summits.bed INFO @ Wed, 07 Feb 2018 12:21:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1937 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 12:21:35: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 12:21:35: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 12:21:35: #1 total tags in treatment: 1689915 INFO @ Wed, 07 Feb 2018 12:21:35: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 12:21:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 12:21:35: #1 tags after filtering in treatment: 1689915 INFO @ Wed, 07 Feb 2018 12:21:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 12:21:35: #1 finished! INFO @ Wed, 07 Feb 2018 12:21:35: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 12:21:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 12:21:35: #2 number of paired peaks: 1979 INFO @ Wed, 07 Feb 2018 12:21:35: start model_add_line... INFO @ Wed, 07 Feb 2018 12:21:35: start X-correlation... INFO @ Wed, 07 Feb 2018 12:21:35: end of X-cor INFO @ Wed, 07 Feb 2018 12:21:35: #2 finished! INFO @ Wed, 07 Feb 2018 12:21:35: #2 predicted fragment length is 51 bps INFO @ Wed, 07 Feb 2018 12:21:35: #2 alternative fragment length(s) may be 51 bps INFO @ Wed, 07 Feb 2018 12:21:35: #2.2 Generate R script for model : SRX3404024.20_model.r WARNING @ Wed, 07 Feb 2018 12:21:35: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 12:21:35: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Wed, 07 Feb 2018 12:21:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 12:21:35: #3 Call peaks... INFO @ Wed, 07 Feb 2018 12:21:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 12:21:38: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 12:21:38: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 12:21:38: #1 total tags in treatment: 1689915 INFO @ Wed, 07 Feb 2018 12:21:38: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 12:21:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 12:21:38: #1 tags after filtering in treatment: 1689915 INFO @ Wed, 07 Feb 2018 12:21:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 12:21:38: #1 finished! INFO @ Wed, 07 Feb 2018 12:21:38: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 12:21:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 12:21:38: #2 number of paired peaks: 1979 INFO @ Wed, 07 Feb 2018 12:21:38: start model_add_line... INFO @ Wed, 07 Feb 2018 12:21:38: start X-correlation... INFO @ Wed, 07 Feb 2018 12:21:38: end of X-cor INFO @ Wed, 07 Feb 2018 12:21:38: #2 finished! INFO @ Wed, 07 Feb 2018 12:21:38: #2 predicted fragment length is 51 bps INFO @ Wed, 07 Feb 2018 12:21:38: #2 alternative fragment length(s) may be 51 bps INFO @ Wed, 07 Feb 2018 12:21:38: #2.2 Generate R script for model : SRX3404024.10_model.r WARNING @ Wed, 07 Feb 2018 12:21:38: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 12:21:38: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Wed, 07 Feb 2018 12:21:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 12:21:38: #3 Call peaks... INFO @ Wed, 07 Feb 2018 12:21:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 12:21:41: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 12:21:44: #4 Write output xls file... SRX3404024.20_peaks.xls INFO @ Wed, 07 Feb 2018 12:21:44: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 12:21:44: #4 Write peak in narrowPeak format file... SRX3404024.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 12:21:44: #4 Write summits bed file... SRX3404024.20_summits.bed INFO @ Wed, 07 Feb 2018 12:21:44: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (817 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 12:21:47: #4 Write output xls file... SRX3404024.10_peaks.xls INFO @ Wed, 07 Feb 2018 12:21:47: #4 Write peak in narrowPeak format file... SRX3404024.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 12:21:47: #4 Write summits bed file... SRX3404024.10_summits.bed INFO @ Wed, 07 Feb 2018 12:21:47: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1358 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。