Job ID = 11240747 sra ファイルのダウンロード中... Completed: 397925K bytes transferred in 8 seconds (390037K 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 23723488 spots for /home/okishinya/chipatlas/results/dm3/SRX4669031/SRR7817556.sra Written 23723488 spots for /home/okishinya/chipatlas/results/dm3/SRX4669031/SRR7817556.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: 00:10:48 23723488 reads; of these: 23723488 (100.00%) were unpaired; of these: 664288 (2.80%) aligned 0 times 13725381 (57.86%) aligned exactly 1 time 9333819 (39.34%) aligned >1 times 97.20% overall alignment rate Time searching: 00:10:48 Overall time: 00:10:48 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 12 files... [bam_rmdupse_core] 8928674 / 23059200 = 0.3872 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, 07 Oct 2018 20:45:50: # Command line: callpeak -t SRX4669031.bam -f BAM -g dm -n SRX4669031.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669031.20 # format = BAM # ChIP-seq file = ['SRX4669031.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, 07 Oct 2018 20:45:50: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:50: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:50: # Command line: callpeak -t SRX4669031.bam -f BAM -g dm -n SRX4669031.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669031.10 # format = BAM # ChIP-seq file = ['SRX4669031.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, 07 Oct 2018 20:45:50: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:50: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:50: # Command line: callpeak -t SRX4669031.bam -f BAM -g dm -n SRX4669031.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669031.05 # format = BAM # ChIP-seq file = ['SRX4669031.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, 07 Oct 2018 20:45:50: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:50: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:58: 1000000 INFO @ Sun, 07 Oct 2018 20:45:59: 1000000 INFO @ Sun, 07 Oct 2018 20:45:59: 1000000 INFO @ Sun, 07 Oct 2018 20:46:06: 2000000 INFO @ Sun, 07 Oct 2018 20:46:06: 2000000 INFO @ Sun, 07 Oct 2018 20:46:07: 2000000 INFO @ Sun, 07 Oct 2018 20:46:14: 3000000 INFO @ Sun, 07 Oct 2018 20:46:14: 3000000 INFO @ Sun, 07 Oct 2018 20:46:15: 3000000 INFO @ Sun, 07 Oct 2018 20:46:21: 4000000 INFO @ Sun, 07 Oct 2018 20:46:21: 4000000 INFO @ Sun, 07 Oct 2018 20:46:23: 4000000 INFO @ Sun, 07 Oct 2018 20:46:28: 5000000 INFO @ Sun, 07 Oct 2018 20:46:29: 5000000 INFO @ Sun, 07 Oct 2018 20:46:31: 5000000 INFO @ Sun, 07 Oct 2018 20:46:35: 6000000 INFO @ Sun, 07 Oct 2018 20:46:37: 6000000 INFO @ Sun, 07 Oct 2018 20:46:39: 6000000 INFO @ Sun, 07 Oct 2018 20:46:42: 7000000 INFO @ Sun, 07 Oct 2018 20:46:44: 7000000 INFO @ Sun, 07 Oct 2018 20:46:47: 7000000 INFO @ Sun, 07 Oct 2018 20:46:49: 8000000 INFO @ Sun, 07 Oct 2018 20:46:52: 8000000 INFO @ Sun, 07 Oct 2018 20:46:55: 8000000 INFO @ Sun, 07 Oct 2018 20:46:56: 9000000 INFO @ Sun, 07 Oct 2018 20:47:00: 9000000 INFO @ Sun, 07 Oct 2018 20:47:03: 9000000 INFO @ Sun, 07 Oct 2018 20:47:03: 10000000 INFO @ Sun, 07 Oct 2018 20:47:08: 10000000 INFO @ Sun, 07 Oct 2018 20:47:11: 11000000 INFO @ Sun, 07 Oct 2018 20:47:11: 10000000 INFO @ Sun, 07 Oct 2018 20:47:15: 11000000 INFO @ Sun, 07 Oct 2018 20:47:18: 12000000 INFO @ Sun, 07 Oct 2018 20:47:19: 11000000 INFO @ Sun, 07 Oct 2018 20:47:22: 12000000 INFO @ Sun, 07 Oct 2018 20:47:25: 13000000 INFO @ Sun, 07 Oct 2018 20:47:27: 12000000 INFO @ Sun, 07 Oct 2018 20:47:30: 13000000 INFO @ Sun, 07 Oct 2018 20:47:32: 14000000 INFO @ Sun, 07 Oct 2018 20:47:32: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:47:32: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:47:32: #1 total tags in treatment: 14130526 INFO @ Sun, 07 Oct 2018 20:47:32: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:47:33: #1 tags after filtering in treatment: 14130526 INFO @ Sun, 07 Oct 2018 20:47:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:33: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:33: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:34: #2 number of paired peaks: 197 WARNING @ Sun, 07 Oct 2018 20:47:34: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Sun, 07 Oct 2018 20:47:34: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:34: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:34: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:34: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:34: #2 predicted fragment length is 51 bps INFO @ Sun, 07 Oct 2018 20:47:34: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 07 Oct 2018 20:47:34: #2.2 Generate R script for model : SRX4669031.10_model.r WARNING @ Sun, 07 Oct 2018 20:47:34: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:47:34: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 07 Oct 2018 20:47:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:47:34: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:35: 13000000 INFO @ Sun, 07 Oct 2018 20:47:37: 14000000 INFO @ Sun, 07 Oct 2018 20:47:38: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:47:38: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:47:38: #1 total tags in treatment: 14130526 INFO @ Sun, 07 Oct 2018 20:47:38: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:47:38: #1 tags after filtering in treatment: 14130526 INFO @ Sun, 07 Oct 2018 20:47:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:38: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:38: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:39: #2 number of paired peaks: 197 WARNING @ Sun, 07 Oct 2018 20:47:39: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Sun, 07 Oct 2018 20:47:39: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:40: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:40: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:40: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:40: #2 predicted fragment length is 51 bps INFO @ Sun, 07 Oct 2018 20:47:40: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 07 Oct 2018 20:47:40: #2.2 Generate R script for model : SRX4669031.20_model.r WARNING @ Sun, 07 Oct 2018 20:47:40: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:47:40: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 07 Oct 2018 20:47:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:47:40: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:42: 14000000 INFO @ Sun, 07 Oct 2018 20:47:43: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:47:43: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:47:43: #1 total tags in treatment: 14130526 INFO @ Sun, 07 Oct 2018 20:47:43: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:47:43: #1 tags after filtering in treatment: 14130526 INFO @ Sun, 07 Oct 2018 20:47:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:43: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:43: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:44: #2 number of paired peaks: 197 WARNING @ Sun, 07 Oct 2018 20:47:44: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Sun, 07 Oct 2018 20:47:44: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:44: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:44: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:44: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:44: #2 predicted fragment length is 51 bps INFO @ Sun, 07 Oct 2018 20:47:44: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 07 Oct 2018 20:47:44: #2.2 Generate R script for model : SRX4669031.05_model.r WARNING @ Sun, 07 Oct 2018 20:47:44: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:47:44: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 07 Oct 2018 20:47:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:47:44: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:48:06: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:11: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:15: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:23: #4 Write output xls file... SRX4669031.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:23: #4 Write peak in narrowPeak format file... SRX4669031.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:23: #4 Write summits bed file... SRX4669031.10_summits.bed INFO @ Sun, 07 Oct 2018 20:48:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1600 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:48:30: #4 Write output xls file... SRX4669031.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:30: #4 Write peak in narrowPeak format file... SRX4669031.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:30: #4 Write summits bed file... SRX4669031.20_summits.bed INFO @ Sun, 07 Oct 2018 20:48:30: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (789 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:48:32: #4 Write output xls file... SRX4669031.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:32: #4 Write peak in narrowPeak format file... SRX4669031.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:32: #4 Write summits bed file... SRX4669031.05_summits.bed INFO @ Sun, 07 Oct 2018 20:48:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3987 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。