Job ID = 10714570 sra ファイルのダウンロード中... Completed: 214867K bytes transferred in 22 seconds (78358K 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 13491391 spots for /home/okishinya/chipatlas/results/dm3/SRX4053304/SRR7132409.sra Written 13491391 spots for /home/okishinya/chipatlas/results/dm3/SRX4053304/SRR7132409.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: 00:07:20 13491391 reads; of these: 13491391 (100.00%) were unpaired; of these: 2226234 (16.50%) aligned 0 times 6039197 (44.76%) aligned exactly 1 time 5225960 (38.74%) aligned >1 times 83.50% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 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] 3739713 / 11265157 = 0.3320 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, 03 Jun 2018 13:40:05: # Command line: callpeak -t SRX4053304.bam -f BAM -g dm -n SRX4053304.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053304.05 # format = BAM # ChIP-seq file = ['SRX4053304.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, 03 Jun 2018 13:40:05: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:40:05: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:40:05: # Command line: callpeak -t SRX4053304.bam -f BAM -g dm -n SRX4053304.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053304.20 # format = BAM # ChIP-seq file = ['SRX4053304.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, 03 Jun 2018 13:40:05: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:40:05: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:40:05: # Command line: callpeak -t SRX4053304.bam -f BAM -g dm -n SRX4053304.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053304.10 # format = BAM # ChIP-seq file = ['SRX4053304.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, 03 Jun 2018 13:40:05: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:40:05: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:40:12: 1000000 INFO @ Sun, 03 Jun 2018 13:40:12: 1000000 INFO @ Sun, 03 Jun 2018 13:40:12: 1000000 INFO @ Sun, 03 Jun 2018 13:40:18: 2000000 INFO @ Sun, 03 Jun 2018 13:40:18: 2000000 INFO @ Sun, 03 Jun 2018 13:40:18: 2000000 INFO @ Sun, 03 Jun 2018 13:40:25: 3000000 INFO @ Sun, 03 Jun 2018 13:40:25: 3000000 INFO @ Sun, 03 Jun 2018 13:40:25: 3000000 INFO @ Sun, 03 Jun 2018 13:40:31: 4000000 INFO @ Sun, 03 Jun 2018 13:40:32: 4000000 INFO @ Sun, 03 Jun 2018 13:40:32: 4000000 INFO @ Sun, 03 Jun 2018 13:40:38: 5000000 INFO @ Sun, 03 Jun 2018 13:40:38: 5000000 INFO @ Sun, 03 Jun 2018 13:40:39: 5000000 INFO @ Sun, 03 Jun 2018 13:40:45: 6000000 INFO @ Sun, 03 Jun 2018 13:40:45: 6000000 INFO @ Sun, 03 Jun 2018 13:40:47: 6000000 INFO @ Sun, 03 Jun 2018 13:40:52: 7000000 INFO @ Sun, 03 Jun 2018 13:40:52: 7000000 INFO @ Sun, 03 Jun 2018 13:40:54: 7000000 INFO @ Sun, 03 Jun 2018 13:40:56: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:40:56: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:40:56: #1 total tags in treatment: 7525444 INFO @ Sun, 03 Jun 2018 13:40:56: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:40:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:40:56: #1 tags after filtering in treatment: 7525444 INFO @ Sun, 03 Jun 2018 13:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:40:56: #1 finished! INFO @ Sun, 03 Jun 2018 13:40:56: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:40:56: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:40:56: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:40:56: #1 total tags in treatment: 7525444 INFO @ Sun, 03 Jun 2018 13:40:56: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:40:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:40:56: #1 tags after filtering in treatment: 7525444 INFO @ Sun, 03 Jun 2018 13:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:40:56: #1 finished! INFO @ Sun, 03 Jun 2018 13:40:56: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:40:57: #2 number of paired peaks: 587 WARNING @ Sun, 03 Jun 2018 13:40:57: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Sun, 03 Jun 2018 13:40:57: start model_add_line... INFO @ Sun, 03 Jun 2018 13:40:57: start X-correlation... INFO @ Sun, 03 Jun 2018 13:40:57: end of X-cor INFO @ Sun, 03 Jun 2018 13:40:57: #2 finished! INFO @ Sun, 03 Jun 2018 13:40:57: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:40:57: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 03 Jun 2018 13:40:57: #2.2 Generate R script for model : SRX4053304.05_model.r WARNING @ Sun, 03 Jun 2018 13:40:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:40:57: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 03 Jun 2018 13:40:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:40:57: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:40:57: #2 number of paired peaks: 587 WARNING @ Sun, 03 Jun 2018 13:40:57: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Sun, 03 Jun 2018 13:40:57: start model_add_line... INFO @ Sun, 03 Jun 2018 13:40:57: start X-correlation... INFO @ Sun, 03 Jun 2018 13:40:57: end of X-cor INFO @ Sun, 03 Jun 2018 13:40:57: #2 finished! INFO @ Sun, 03 Jun 2018 13:40:57: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:40:57: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 03 Jun 2018 13:40:57: #2.2 Generate R script for model : SRX4053304.10_model.r WARNING @ Sun, 03 Jun 2018 13:40:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:40:57: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 03 Jun 2018 13:40:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:40:57: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:40:58: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:40:58: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:40:58: #1 total tags in treatment: 7525444 INFO @ Sun, 03 Jun 2018 13:40:58: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:40:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:40:58: #1 tags after filtering in treatment: 7525444 INFO @ Sun, 03 Jun 2018 13:40:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:40:58: #1 finished! INFO @ Sun, 03 Jun 2018 13:40:58: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:40:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:40:59: #2 number of paired peaks: 587 WARNING @ Sun, 03 Jun 2018 13:40:59: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Sun, 03 Jun 2018 13:40:59: start model_add_line... INFO @ Sun, 03 Jun 2018 13:40:59: start X-correlation... INFO @ Sun, 03 Jun 2018 13:40:59: end of X-cor INFO @ Sun, 03 Jun 2018 13:40:59: #2 finished! INFO @ Sun, 03 Jun 2018 13:40:59: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:40:59: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 03 Jun 2018 13:40:59: #2.2 Generate R script for model : SRX4053304.20_model.r WARNING @ Sun, 03 Jun 2018 13:40:59: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:40:59: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 03 Jun 2018 13:40:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:40:59: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:40:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:41:14: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:41:14: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:41:17: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:41:23: #4 Write output xls file... SRX4053304.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:41:23: #4 Write peak in narrowPeak format file... SRX4053304.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:41:23: #4 Write summits bed file... SRX4053304.10_summits.bed INFO @ Sun, 03 Jun 2018 13:41:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1614 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:41:24: #4 Write output xls file... SRX4053304.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:41:24: #4 Write peak in narrowPeak format file... SRX4053304.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:41:24: #4 Write summits bed file... SRX4053304.05_summits.bed INFO @ Sun, 03 Jun 2018 13:41:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2226 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:41:26: #4 Write output xls file... SRX4053304.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:41:26: #4 Write peak in narrowPeak format file... SRX4053304.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:41:26: #4 Write summits bed file... SRX4053304.20_summits.bed INFO @ Sun, 03 Jun 2018 13:41:26: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1116 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。