Job ID = 10450730 sra ファイルのダウンロード中... Completed: 141557K bytes transferred in 8 seconds (129149K 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 6702486 spots for /home/okishinya/chipatlas/results/dm3/SRX3404017/SRR6303494.sra Written 6702486 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:46 6702486 reads; of these: 6702486 (100.00%) were unpaired; of these: 813572 (12.14%) aligned 0 times 2099853 (31.33%) aligned exactly 1 time 3789061 (56.53%) aligned >1 times 87.86% overall alignment rate Time searching: 00:09:47 Overall time: 00:09:47 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] 2677671 / 5888914 = 0.4547 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 10:59:30: # Command line: callpeak -t SRX3404017.bam -f BAM -g dm -n SRX3404017.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404017.20 # format = BAM # ChIP-seq file = ['SRX3404017.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 10:59:30: # Command line: callpeak -t SRX3404017.bam -f BAM -g dm -n SRX3404017.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404017.10 # format = BAM # ChIP-seq file = ['SRX3404017.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 10:59:30: # Command line: callpeak -t SRX3404017.bam -f BAM -g dm -n SRX3404017.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404017.05 # format = BAM # ChIP-seq file = ['SRX3404017.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 10:59:30: #1 read tag files... INFO @ Wed, 07 Feb 2018 10:59:30: #1 read tag files... INFO @ Wed, 07 Feb 2018 10:59:30: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 10:59:30: #1 read tag files... INFO @ Wed, 07 Feb 2018 10:59:30: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 10:59:30: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 10:59:38: 1000000 INFO @ Wed, 07 Feb 2018 10:59:38: 1000000 INFO @ Wed, 07 Feb 2018 10:59:38: 1000000 INFO @ Wed, 07 Feb 2018 10:59:46: 2000000 INFO @ Wed, 07 Feb 2018 10:59:46: 2000000 INFO @ Wed, 07 Feb 2018 10:59:47: 2000000 INFO @ Wed, 07 Feb 2018 10:59:54: 3000000 INFO @ Wed, 07 Feb 2018 10:59:54: 3000000 INFO @ Wed, 07 Feb 2018 10:59:55: 3000000 INFO @ Wed, 07 Feb 2018 10:59:55: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 10:59:55: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 10:59:55: #1 total tags in treatment: 3211243 INFO @ Wed, 07 Feb 2018 10:59:55: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 10:59:55: #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 10:59:55: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 10:59:55: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 10:59:55: #1 total tags in treatment: 3211243 INFO @ Wed, 07 Feb 2018 10:59:55: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 10:59:55: #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 10:59:55: #1 tags after filtering in treatment: 3211243 INFO @ Wed, 07 Feb 2018 10:59:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 10:59:55: #1 finished! INFO @ Wed, 07 Feb 2018 10:59:55: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 10:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 10:59:55: #1 tags after filtering in treatment: 3211243 INFO @ Wed, 07 Feb 2018 10:59:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 10:59:55: #1 finished! INFO @ Wed, 07 Feb 2018 10:59:55: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 10:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 10:59:56: #2 number of paired peaks: 1707 INFO @ Wed, 07 Feb 2018 10:59:56: start model_add_line... INFO @ Wed, 07 Feb 2018 10:59:56: start X-correlation... INFO @ Wed, 07 Feb 2018 10:59:56: #2 number of paired peaks: 1707 INFO @ Wed, 07 Feb 2018 10:59:56: start model_add_line... INFO @ Wed, 07 Feb 2018 10:59:56: end of X-cor INFO @ Wed, 07 Feb 2018 10:59:56: #2 finished! INFO @ Wed, 07 Feb 2018 10:59:56: #2 predicted fragment length is 51 bps INFO @ Wed, 07 Feb 2018 10:59:56: #2 alternative fragment length(s) may be 51 bps INFO @ Wed, 07 Feb 2018 10:59:56: #2.2 Generate R script for model : SRX3404017.10_model.r WARNING @ Wed, 07 Feb 2018 10:59:56: #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 10:59:56: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Wed, 07 Feb 2018 10:59:56: #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 10:59:56: #3 Call peaks... INFO @ Wed, 07 Feb 2018 10:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 10:59:56: start X-correlation... INFO @ Wed, 07 Feb 2018 10:59:56: end of X-cor INFO @ Wed, 07 Feb 2018 10:59:56: #2 finished! INFO @ Wed, 07 Feb 2018 10:59:56: #2 predicted fragment length is 51 bps INFO @ Wed, 07 Feb 2018 10:59:56: #2 alternative fragment length(s) may be 51 bps INFO @ Wed, 07 Feb 2018 10:59:56: #2.2 Generate R script for model : SRX3404017.20_model.r WARNING @ Wed, 07 Feb 2018 10:59:56: #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 10:59:56: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Wed, 07 Feb 2018 10:59:56: #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 10:59:56: #3 Call peaks... INFO @ Wed, 07 Feb 2018 10:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 10:59:57: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 10:59:57: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 10:59:57: #1 total tags in treatment: 3211243 INFO @ Wed, 07 Feb 2018 10:59:57: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 10:59:57: #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 10:59:57: #1 tags after filtering in treatment: 3211243 INFO @ Wed, 07 Feb 2018 10:59:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 10:59:57: #1 finished! INFO @ Wed, 07 Feb 2018 10:59:57: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 10:59:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 10:59:57: #2 number of paired peaks: 1707 INFO @ Wed, 07 Feb 2018 10:59:57: start model_add_line... INFO @ Wed, 07 Feb 2018 10:59:58: start X-correlation... INFO @ Wed, 07 Feb 2018 10:59:58: end of X-cor INFO @ Wed, 07 Feb 2018 10:59:58: #2 finished! INFO @ Wed, 07 Feb 2018 10:59:58: #2 predicted fragment length is 51 bps INFO @ Wed, 07 Feb 2018 10:59:58: #2 alternative fragment length(s) may be 51 bps INFO @ Wed, 07 Feb 2018 10:59:58: #2.2 Generate R script for model : SRX3404017.05_model.r WARNING @ Wed, 07 Feb 2018 10:59:58: #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 10:59:58: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Wed, 07 Feb 2018 10:59:58: #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 10:59:58: #3 Call peaks... INFO @ Wed, 07 Feb 2018 10:59:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:00:06: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:00:06: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:00:08: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:00:11: #4 Write output xls file... SRX3404017.10_peaks.xls INFO @ Wed, 07 Feb 2018 11:00:11: #4 Write peak in narrowPeak format file... SRX3404017.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:00:12: #4 Write summits bed file... SRX3404017.10_summits.bed INFO @ Wed, 07 Feb 2018 11:00:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1658 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 11:00:12: #4 Write output xls file... SRX3404017.20_peaks.xls INFO @ Wed, 07 Feb 2018 11:00:12: #4 Write peak in narrowPeak format file... SRX3404017.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:00:12: #4 Write summits bed file... SRX3404017.20_summits.bed INFO @ Wed, 07 Feb 2018 11:00:12: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1169 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 11:00:13: #4 Write output xls file... SRX3404017.05_peaks.xls INFO @ Wed, 07 Feb 2018 11:00:13: #4 Write peak in narrowPeak format file... SRX3404017.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:00:13: #4 Write summits bed file... SRX3404017.05_summits.bed INFO @ Wed, 07 Feb 2018 11:00:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2271 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。