Job ID = 11597967 sra ファイルのダウンロード中... Completed: 393111K bytes transferred in 7 seconds (454387K 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 9619195 spots for /home/okishinya/chipatlas/results/dm3/SRX4520672/SRR7659070.sra Written 9619195 spots for /home/okishinya/chipatlas/results/dm3/SRX4520672/SRR7659070.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: 00:04:52 9619195 reads; of these: 9619195 (100.00%) were unpaired; of these: 485464 (5.05%) aligned 0 times 5963329 (61.99%) aligned exactly 1 time 3170402 (32.96%) aligned >1 times 94.95% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 704802 / 9133731 = 0.0772 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, 30 Jan 2019 16:40:22: # Command line: callpeak -t SRX4520672.bam -f BAM -g dm -n SRX4520672.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4520672.05 # format = BAM # ChIP-seq file = ['SRX4520672.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, 30 Jan 2019 16:40:22: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:40:22: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:40:22: # Command line: callpeak -t SRX4520672.bam -f BAM -g dm -n SRX4520672.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4520672.10 # format = BAM # ChIP-seq file = ['SRX4520672.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, 30 Jan 2019 16:40:22: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:40:22: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:40:22: # Command line: callpeak -t SRX4520672.bam -f BAM -g dm -n SRX4520672.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4520672.20 # format = BAM # ChIP-seq file = ['SRX4520672.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, 30 Jan 2019 16:40:22: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:40:22: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:40:30: 1000000 INFO @ Wed, 30 Jan 2019 16:40:31: 1000000 INFO @ Wed, 30 Jan 2019 16:40:31: 1000000 INFO @ Wed, 30 Jan 2019 16:40:38: 2000000 INFO @ Wed, 30 Jan 2019 16:40:39: 2000000 INFO @ Wed, 30 Jan 2019 16:40:39: 2000000 INFO @ Wed, 30 Jan 2019 16:40:45: 3000000 INFO @ Wed, 30 Jan 2019 16:40:46: 3000000 INFO @ Wed, 30 Jan 2019 16:40:47: 3000000 INFO @ Wed, 30 Jan 2019 16:40:52: 4000000 INFO @ Wed, 30 Jan 2019 16:40:53: 4000000 INFO @ Wed, 30 Jan 2019 16:40:56: 4000000 INFO @ Wed, 30 Jan 2019 16:40:59: 5000000 INFO @ Wed, 30 Jan 2019 16:41:01: 5000000 INFO @ Wed, 30 Jan 2019 16:41:05: 5000000 INFO @ Wed, 30 Jan 2019 16:41:06: 6000000 INFO @ Wed, 30 Jan 2019 16:41:10: 6000000 INFO @ Wed, 30 Jan 2019 16:41:12: 6000000 INFO @ Wed, 30 Jan 2019 16:41:13: 7000000 INFO @ Wed, 30 Jan 2019 16:41:17: 7000000 INFO @ Wed, 30 Jan 2019 16:41:19: 7000000 INFO @ Wed, 30 Jan 2019 16:41:22: 8000000 INFO @ Wed, 30 Jan 2019 16:41:25: 8000000 INFO @ Wed, 30 Jan 2019 16:41:26: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:41:26: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:41:26: #1 total tags in treatment: 8428929 INFO @ Wed, 30 Jan 2019 16:41:26: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:41:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:41:26: #1 tags after filtering in treatment: 8428929 INFO @ Wed, 30 Jan 2019 16:41:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:41:26: #1 finished! INFO @ Wed, 30 Jan 2019 16:41:26: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:41:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:41:26: #2 number of paired peaks: 778 WARNING @ Wed, 30 Jan 2019 16:41:26: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Wed, 30 Jan 2019 16:41:26: start model_add_line... INFO @ Wed, 30 Jan 2019 16:41:27: start X-correlation... INFO @ Wed, 30 Jan 2019 16:41:27: end of X-cor INFO @ Wed, 30 Jan 2019 16:41:27: #2 finished! INFO @ Wed, 30 Jan 2019 16:41:27: #2 predicted fragment length is 52 bps INFO @ Wed, 30 Jan 2019 16:41:27: #2 alternative fragment length(s) may be 4,52,553 bps INFO @ Wed, 30 Jan 2019 16:41:27: #2.2 Generate R script for model : SRX4520672.20_model.r WARNING @ Wed, 30 Jan 2019 16:41:27: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:41:27: #2 You may need to consider one of the other alternative d(s): 4,52,553 WARNING @ Wed, 30 Jan 2019 16:41:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:41:27: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:41:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:41:27: 8000000 INFO @ Wed, 30 Jan 2019 16:41:28: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:41:28: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:41:28: #1 total tags in treatment: 8428929 INFO @ Wed, 30 Jan 2019 16:41:28: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:41:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:41:28: #1 tags after filtering in treatment: 8428929 INFO @ Wed, 30 Jan 2019 16:41:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:41:28: #1 finished! INFO @ Wed, 30 Jan 2019 16:41:28: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:41:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:41:29: #2 number of paired peaks: 778 WARNING @ Wed, 30 Jan 2019 16:41:29: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Wed, 30 Jan 2019 16:41:29: start model_add_line... INFO @ Wed, 30 Jan 2019 16:41:29: start X-correlation... INFO @ Wed, 30 Jan 2019 16:41:29: end of X-cor INFO @ Wed, 30 Jan 2019 16:41:29: #2 finished! INFO @ Wed, 30 Jan 2019 16:41:29: #2 predicted fragment length is 52 bps INFO @ Wed, 30 Jan 2019 16:41:29: #2 alternative fragment length(s) may be 4,52,553 bps INFO @ Wed, 30 Jan 2019 16:41:29: #2.2 Generate R script for model : SRX4520672.05_model.r WARNING @ Wed, 30 Jan 2019 16:41:29: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:41:29: #2 You may need to consider one of the other alternative d(s): 4,52,553 WARNING @ Wed, 30 Jan 2019 16:41:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:41:29: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:41:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:41:30: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:41:30: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:41:30: #1 total tags in treatment: 8428929 INFO @ Wed, 30 Jan 2019 16:41:30: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:41:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:41:31: #1 tags after filtering in treatment: 8428929 INFO @ Wed, 30 Jan 2019 16:41:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:41:31: #1 finished! INFO @ Wed, 30 Jan 2019 16:41:31: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:41:32: #2 number of paired peaks: 778 WARNING @ Wed, 30 Jan 2019 16:41:32: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Wed, 30 Jan 2019 16:41:32: start model_add_line... INFO @ Wed, 30 Jan 2019 16:41:32: start X-correlation... INFO @ Wed, 30 Jan 2019 16:41:32: end of X-cor INFO @ Wed, 30 Jan 2019 16:41:32: #2 finished! INFO @ Wed, 30 Jan 2019 16:41:32: #2 predicted fragment length is 52 bps INFO @ Wed, 30 Jan 2019 16:41:32: #2 alternative fragment length(s) may be 4,52,553 bps INFO @ Wed, 30 Jan 2019 16:41:32: #2.2 Generate R script for model : SRX4520672.10_model.r WARNING @ Wed, 30 Jan 2019 16:41:32: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:41:32: #2 You may need to consider one of the other alternative d(s): 4,52,553 WARNING @ Wed, 30 Jan 2019 16:41:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:41:32: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:41:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:41:47: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:41:52: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:41:53: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:41:59: #4 Write output xls file... SRX4520672.20_peaks.xls INFO @ Wed, 30 Jan 2019 16:41:59: #4 Write peak in narrowPeak format file... SRX4520672.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:41:59: #4 Write summits bed file... SRX4520672.20_summits.bed INFO @ Wed, 30 Jan 2019 16:41:59: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (513 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:42:02: #4 Write output xls file... SRX4520672.05_peaks.xls INFO @ Wed, 30 Jan 2019 16:42:02: #4 Write peak in narrowPeak format file... SRX4520672.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:42:02: #4 Write summits bed file... SRX4520672.05_summits.bed INFO @ Wed, 30 Jan 2019 16:42:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2779 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:42:05: #4 Write output xls file... SRX4520672.10_peaks.xls INFO @ Wed, 30 Jan 2019 16:42:05: #4 Write peak in narrowPeak format file... SRX4520672.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:42:05: #4 Write summits bed file... SRX4520672.10_summits.bed INFO @ Wed, 30 Jan 2019 16:42:05: Done! pass1 - making usageList (13 chroms): 8 millis pass2 - checking and writing primary data (1651 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。