Job ID = 9297530 sra ファイルのダウンロード中... Completed: 307927K bytes transferred in 6 seconds (393842K bits/sec), in 1 file, 2 directories. 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 19307979 spots for /home/okishinya/chipatlas/results/dm3/SRX2745585/SRR5457522.sra Written 19307979 spots total 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: 00:07:19 19307979 reads; of these: 19307979 (100.00%) were unpaired; of these: 963884 (4.99%) aligned 0 times 13836086 (71.66%) aligned exactly 1 time 4508009 (23.35%) aligned >1 times 95.01% overall alignment rate Time searching: 00:07:19 Overall time: 00:07:19 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] 4172315 / 18344095 = 0.2274 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 @ Thu, 27 Jul 2017 15:39:19: # Command line: callpeak -t SRX2745585.bam -f BAM -g dm -n SRX2745585.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2745585.20 # format = BAM # ChIP-seq file = ['SRX2745585.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 @ Thu, 27 Jul 2017 15:39:19: # Command line: callpeak -t SRX2745585.bam -f BAM -g dm -n SRX2745585.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2745585.05 # format = BAM # ChIP-seq file = ['SRX2745585.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 @ Thu, 27 Jul 2017 15:39:19: # Command line: callpeak -t SRX2745585.bam -f BAM -g dm -n SRX2745585.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2745585.10 # format = BAM # ChIP-seq file = ['SRX2745585.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 @ Thu, 27 Jul 2017 15:39:19: #1 read tag files... INFO @ Thu, 27 Jul 2017 15:39:19: #1 read tag files... INFO @ Thu, 27 Jul 2017 15:39:19: #1 read tag files... INFO @ Thu, 27 Jul 2017 15:39:19: #1 read treatment tags... INFO @ Thu, 27 Jul 2017 15:39:19: #1 read treatment tags... INFO @ Thu, 27 Jul 2017 15:39:19: #1 read treatment tags... INFO @ Thu, 27 Jul 2017 15:39:27: 1000000 INFO @ Thu, 27 Jul 2017 15:39:27: 1000000 INFO @ Thu, 27 Jul 2017 15:39:27: 1000000 INFO @ Thu, 27 Jul 2017 15:39:34: 2000000 INFO @ Thu, 27 Jul 2017 15:39:34: 2000000 INFO @ Thu, 27 Jul 2017 15:39:35: 2000000 INFO @ Thu, 27 Jul 2017 15:39:43: 3000000 INFO @ Thu, 27 Jul 2017 15:39:43: 3000000 INFO @ Thu, 27 Jul 2017 15:39:43: 3000000 INFO @ Thu, 27 Jul 2017 15:39:51: 4000000 INFO @ Thu, 27 Jul 2017 15:39:51: 4000000 INFO @ Thu, 27 Jul 2017 15:39:53: 4000000 INFO @ Thu, 27 Jul 2017 15:40:00: 5000000 INFO @ Thu, 27 Jul 2017 15:40:00: 5000000 INFO @ Thu, 27 Jul 2017 15:40:02: 5000000 INFO @ Thu, 27 Jul 2017 15:40:09: 6000000 INFO @ Thu, 27 Jul 2017 15:40:09: 6000000 INFO @ Thu, 27 Jul 2017 15:40:11: 6000000 INFO @ Thu, 27 Jul 2017 15:40:17: 7000000 INFO @ Thu, 27 Jul 2017 15:40:17: 7000000 INFO @ Thu, 27 Jul 2017 15:40:21: 7000000 INFO @ Thu, 27 Jul 2017 15:40:26: 8000000 INFO @ Thu, 27 Jul 2017 15:40:26: 8000000 INFO @ Thu, 27 Jul 2017 15:40:30: 8000000 INFO @ Thu, 27 Jul 2017 15:40:34: 9000000 INFO @ Thu, 27 Jul 2017 15:40:35: 9000000 INFO @ Thu, 27 Jul 2017 15:40:39: 9000000 INFO @ Thu, 27 Jul 2017 15:40:43: 10000000 INFO @ Thu, 27 Jul 2017 15:40:43: 10000000 INFO @ Thu, 27 Jul 2017 15:40:49: 10000000 INFO @ Thu, 27 Jul 2017 15:40:52: 11000000 INFO @ Thu, 27 Jul 2017 15:40:52: 11000000 INFO @ Thu, 27 Jul 2017 15:40:58: 11000000 INFO @ Thu, 27 Jul 2017 15:41:01: 12000000 INFO @ Thu, 27 Jul 2017 15:41:01: 12000000 INFO @ Thu, 27 Jul 2017 15:41:07: 12000000 INFO @ Thu, 27 Jul 2017 15:41:09: 13000000 INFO @ Thu, 27 Jul 2017 15:41:10: 13000000 INFO @ Thu, 27 Jul 2017 15:41:17: 13000000 INFO @ Thu, 27 Jul 2017 15:41:18: 14000000 INFO @ Thu, 27 Jul 2017 15:41:18: 14000000 INFO @ Thu, 27 Jul 2017 15:41:20: #1 tag size is determined as 50 bps INFO @ Thu, 27 Jul 2017 15:41:20: #1 tag size = 50 INFO @ Thu, 27 Jul 2017 15:41:20: #1 total tags in treatment: 14171780 INFO @ Thu, 27 Jul 2017 15:41:20: #1 user defined the maximum tags... INFO @ Thu, 27 Jul 2017 15:41:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 27 Jul 2017 15:41:20: #1 tag size is determined as 50 bps INFO @ Thu, 27 Jul 2017 15:41:20: #1 tag size = 50 INFO @ Thu, 27 Jul 2017 15:41:20: #1 total tags in treatment: 14171780 INFO @ Thu, 27 Jul 2017 15:41:20: #1 user defined the maximum tags... INFO @ Thu, 27 Jul 2017 15:41:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 27 Jul 2017 15:41:20: #1 tags after filtering in treatment: 14171780 INFO @ Thu, 27 Jul 2017 15:41:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 27 Jul 2017 15:41:20: #1 finished! INFO @ Thu, 27 Jul 2017 15:41:20: #2 Build Peak Model... INFO @ Thu, 27 Jul 2017 15:41:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 27 Jul 2017 15:41:20: #1 tags after filtering in treatment: 14171780 INFO @ Thu, 27 Jul 2017 15:41:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 27 Jul 2017 15:41:20: #1 finished! INFO @ Thu, 27 Jul 2017 15:41:20: #2 Build Peak Model... INFO @ Thu, 27 Jul 2017 15:41:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 27 Jul 2017 15:41:21: #2 number of paired peaks: 266 WARNING @ Thu, 27 Jul 2017 15:41:21: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Thu, 27 Jul 2017 15:41:21: start model_add_line... INFO @ Thu, 27 Jul 2017 15:41:21: #2 number of paired peaks: 266 WARNING @ Thu, 27 Jul 2017 15:41:21: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Thu, 27 Jul 2017 15:41:21: start model_add_line... INFO @ Thu, 27 Jul 2017 15:41:21: start X-correlation... INFO @ Thu, 27 Jul 2017 15:41:21: start X-correlation... INFO @ Thu, 27 Jul 2017 15:41:21: end of X-cor INFO @ Thu, 27 Jul 2017 15:41:21: end of X-cor INFO @ Thu, 27 Jul 2017 15:41:21: #2 finished! INFO @ Thu, 27 Jul 2017 15:41:21: #2 finished! INFO @ Thu, 27 Jul 2017 15:41:21: #2 predicted fragment length is 92 bps INFO @ Thu, 27 Jul 2017 15:41:21: #2 predicted fragment length is 92 bps INFO @ Thu, 27 Jul 2017 15:41:21: #2 alternative fragment length(s) may be 92 bps INFO @ Thu, 27 Jul 2017 15:41:21: #2 alternative fragment length(s) may be 92 bps INFO @ Thu, 27 Jul 2017 15:41:21: #2.2 Generate R script for model : SRX2745585.20_model.r INFO @ Thu, 27 Jul 2017 15:41:21: #2.2 Generate R script for model : SRX2745585.10_model.r WARNING @ Thu, 27 Jul 2017 15:41:21: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 27 Jul 2017 15:41:21: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 27 Jul 2017 15:41:21: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Thu, 27 Jul 2017 15:41:21: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Thu, 27 Jul 2017 15:41:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Thu, 27 Jul 2017 15:41:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 27 Jul 2017 15:41:21: #3 Call peaks... INFO @ Thu, 27 Jul 2017 15:41:21: #3 Call peaks... INFO @ Thu, 27 Jul 2017 15:41:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 27 Jul 2017 15:41:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 27 Jul 2017 15:41:26: 14000000 INFO @ Thu, 27 Jul 2017 15:41:27: #1 tag size is determined as 50 bps INFO @ Thu, 27 Jul 2017 15:41:27: #1 tag size = 50 INFO @ Thu, 27 Jul 2017 15:41:27: #1 total tags in treatment: 14171780 INFO @ Thu, 27 Jul 2017 15:41:27: #1 user defined the maximum tags... INFO @ Thu, 27 Jul 2017 15:41:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 27 Jul 2017 15:41:28: #1 tags after filtering in treatment: 14171780 INFO @ Thu, 27 Jul 2017 15:41:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 27 Jul 2017 15:41:28: #1 finished! INFO @ Thu, 27 Jul 2017 15:41:28: #2 Build Peak Model... INFO @ Thu, 27 Jul 2017 15:41:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 27 Jul 2017 15:41:29: #2 number of paired peaks: 266 WARNING @ Thu, 27 Jul 2017 15:41:29: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Thu, 27 Jul 2017 15:41:29: start model_add_line... INFO @ Thu, 27 Jul 2017 15:41:29: start X-correlation... INFO @ Thu, 27 Jul 2017 15:41:29: end of X-cor INFO @ Thu, 27 Jul 2017 15:41:29: #2 finished! INFO @ Thu, 27 Jul 2017 15:41:29: #2 predicted fragment length is 92 bps INFO @ Thu, 27 Jul 2017 15:41:29: #2 alternative fragment length(s) may be 92 bps INFO @ Thu, 27 Jul 2017 15:41:29: #2.2 Generate R script for model : SRX2745585.05_model.r WARNING @ Thu, 27 Jul 2017 15:41:29: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 27 Jul 2017 15:41:29: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Thu, 27 Jul 2017 15:41:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 27 Jul 2017 15:41:29: #3 Call peaks... INFO @ Thu, 27 Jul 2017 15:41:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 27 Jul 2017 15:41:52: #3 Call peaks for each chromosome... INFO @ Thu, 27 Jul 2017 15:41:54: #3 Call peaks for each chromosome... INFO @ Thu, 27 Jul 2017 15:41:57: #3 Call peaks for each chromosome... INFO @ Thu, 27 Jul 2017 15:42:10: #4 Write output xls file... SRX2745585.20_peaks.xls INFO @ Thu, 27 Jul 2017 15:42:10: #4 Write peak in narrowPeak format file... SRX2745585.20_peaks.narrowPeak INFO @ Thu, 27 Jul 2017 15:42:10: #4 Write summits bed file... SRX2745585.20_summits.bed INFO @ Thu, 27 Jul 2017 15:42:10: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1348 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 27 Jul 2017 15:42:14: #4 Write output xls file... SRX2745585.10_peaks.xls INFO @ Thu, 27 Jul 2017 15:42:14: #4 Write peak in narrowPeak format file... SRX2745585.10_peaks.narrowPeak INFO @ Thu, 27 Jul 2017 15:42:14: #4 Write summits bed file... SRX2745585.10_summits.bed INFO @ Thu, 27 Jul 2017 15:42:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2859 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 27 Jul 2017 15:42:15: #4 Write output xls file... SRX2745585.05_peaks.xls INFO @ Thu, 27 Jul 2017 15:42:15: #4 Write peak in narrowPeak format file... SRX2745585.05_peaks.narrowPeak INFO @ Thu, 27 Jul 2017 15:42:15: #4 Write summits bed file... SRX2745585.05_summits.bed INFO @ Thu, 27 Jul 2017 15:42:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5067 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。