Job ID = 11598014 sra ファイルのダウンロード中... Completed: 581903K bytes transferred in 6 seconds (683781K 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 25972202 spots for /home/okishinya/chipatlas/results/dm3/SRX4664669/SRR7813096.sra Written 25972202 spots for /home/okishinya/chipatlas/results/dm3/SRX4664669/SRR7813096.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 25972202 reads; of these: 25972202 (100.00%) were unpaired; of these: 955189 (3.68%) aligned 0 times 17389531 (66.95%) aligned exactly 1 time 7627482 (29.37%) aligned >1 times 96.32% 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] 4003507 / 25017013 = 0.1600 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 17:15:21: # Command line: callpeak -t SRX4664669.bam -f BAM -g dm -n SRX4664669.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664669.05 # format = BAM # ChIP-seq file = ['SRX4664669.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 17:15:21: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:15:21: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:15:21: # Command line: callpeak -t SRX4664669.bam -f BAM -g dm -n SRX4664669.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664669.20 # format = BAM # ChIP-seq file = ['SRX4664669.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 17:15:21: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:15:21: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:15:21: # Command line: callpeak -t SRX4664669.bam -f BAM -g dm -n SRX4664669.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664669.10 # format = BAM # ChIP-seq file = ['SRX4664669.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 17:15:21: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:15:21: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:15:28: 1000000 INFO @ Wed, 30 Jan 2019 17:15:28: 1000000 INFO @ Wed, 30 Jan 2019 17:15:28: 1000000 INFO @ Wed, 30 Jan 2019 17:15:34: 2000000 INFO @ Wed, 30 Jan 2019 17:15:35: 2000000 INFO @ Wed, 30 Jan 2019 17:15:35: 2000000 INFO @ Wed, 30 Jan 2019 17:15:41: 3000000 INFO @ Wed, 30 Jan 2019 17:15:42: 3000000 INFO @ Wed, 30 Jan 2019 17:15:42: 3000000 INFO @ Wed, 30 Jan 2019 17:15:48: 4000000 INFO @ Wed, 30 Jan 2019 17:15:49: 4000000 INFO @ Wed, 30 Jan 2019 17:15:49: 4000000 INFO @ Wed, 30 Jan 2019 17:15:54: 5000000 INFO @ Wed, 30 Jan 2019 17:15:55: 5000000 INFO @ Wed, 30 Jan 2019 17:15:55: 5000000 INFO @ Wed, 30 Jan 2019 17:16:01: 6000000 INFO @ Wed, 30 Jan 2019 17:16:02: 6000000 INFO @ Wed, 30 Jan 2019 17:16:02: 6000000 INFO @ Wed, 30 Jan 2019 17:16:07: 7000000 INFO @ Wed, 30 Jan 2019 17:16:09: 7000000 INFO @ Wed, 30 Jan 2019 17:16:09: 7000000 INFO @ Wed, 30 Jan 2019 17:16:14: 8000000 INFO @ Wed, 30 Jan 2019 17:16:15: 8000000 INFO @ Wed, 30 Jan 2019 17:16:15: 8000000 INFO @ Wed, 30 Jan 2019 17:16:20: 9000000 INFO @ Wed, 30 Jan 2019 17:16:22: 9000000 INFO @ Wed, 30 Jan 2019 17:16:22: 9000000 INFO @ Wed, 30 Jan 2019 17:16:27: 10000000 INFO @ Wed, 30 Jan 2019 17:16:29: 10000000 INFO @ Wed, 30 Jan 2019 17:16:29: 10000000 INFO @ Wed, 30 Jan 2019 17:16:34: 11000000 INFO @ Wed, 30 Jan 2019 17:16:35: 11000000 INFO @ Wed, 30 Jan 2019 17:16:35: 11000000 INFO @ Wed, 30 Jan 2019 17:16:40: 12000000 INFO @ Wed, 30 Jan 2019 17:16:42: 12000000 INFO @ Wed, 30 Jan 2019 17:16:42: 12000000 INFO @ Wed, 30 Jan 2019 17:16:47: 13000000 INFO @ Wed, 30 Jan 2019 17:16:48: 13000000 INFO @ Wed, 30 Jan 2019 17:16:48: 13000000 INFO @ Wed, 30 Jan 2019 17:16:53: 14000000 INFO @ Wed, 30 Jan 2019 17:16:55: 14000000 INFO @ Wed, 30 Jan 2019 17:16:55: 14000000 INFO @ Wed, 30 Jan 2019 17:17:00: 15000000 INFO @ Wed, 30 Jan 2019 17:17:02: 15000000 INFO @ Wed, 30 Jan 2019 17:17:02: 15000000 INFO @ Wed, 30 Jan 2019 17:17:07: 16000000 INFO @ Wed, 30 Jan 2019 17:17:08: 16000000 INFO @ Wed, 30 Jan 2019 17:17:08: 16000000 INFO @ Wed, 30 Jan 2019 17:17:13: 17000000 INFO @ Wed, 30 Jan 2019 17:17:15: 17000000 INFO @ Wed, 30 Jan 2019 17:17:15: 17000000 INFO @ Wed, 30 Jan 2019 17:17:20: 18000000 INFO @ Wed, 30 Jan 2019 17:17:22: 18000000 INFO @ Wed, 30 Jan 2019 17:17:22: 18000000 INFO @ Wed, 30 Jan 2019 17:17:26: 19000000 INFO @ Wed, 30 Jan 2019 17:17:29: 19000000 INFO @ Wed, 30 Jan 2019 17:17:29: 19000000 INFO @ Wed, 30 Jan 2019 17:17:33: 20000000 INFO @ Wed, 30 Jan 2019 17:17:35: 20000000 INFO @ Wed, 30 Jan 2019 17:17:35: 20000000 INFO @ Wed, 30 Jan 2019 17:17:40: 21000000 INFO @ Wed, 30 Jan 2019 17:17:40: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:17:40: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:17:40: #1 total tags in treatment: 21013506 INFO @ Wed, 30 Jan 2019 17:17:40: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:17:40: #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 17:17:40: #1 tags after filtering in treatment: 21013506 INFO @ Wed, 30 Jan 2019 17:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:17:40: #1 finished! INFO @ Wed, 30 Jan 2019 17:17:40: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:17:42: 21000000 INFO @ Wed, 30 Jan 2019 17:17:42: 21000000 INFO @ Wed, 30 Jan 2019 17:17:42: #2 number of paired peaks: 855 WARNING @ Wed, 30 Jan 2019 17:17:42: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Wed, 30 Jan 2019 17:17:42: start model_add_line... INFO @ Wed, 30 Jan 2019 17:17:42: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:17:42: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:17:42: #1 total tags in treatment: 21013506 INFO @ Wed, 30 Jan 2019 17:17:42: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:17:42: #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 17:17:42: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:17:42: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:17:42: #1 total tags in treatment: 21013506 INFO @ Wed, 30 Jan 2019 17:17:42: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:17:42: #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 17:17:42: start X-correlation... INFO @ Wed, 30 Jan 2019 17:17:42: end of X-cor INFO @ Wed, 30 Jan 2019 17:17:42: #2 finished! INFO @ Wed, 30 Jan 2019 17:17:42: #2 predicted fragment length is 60 bps INFO @ Wed, 30 Jan 2019 17:17:42: #2 alternative fragment length(s) may be 4,60 bps INFO @ Wed, 30 Jan 2019 17:17:42: #2.2 Generate R script for model : SRX4664669.05_model.r WARNING @ Wed, 30 Jan 2019 17:17:42: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:17:42: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Wed, 30 Jan 2019 17:17:42: #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 17:17:42: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:17:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:17:42: #1 tags after filtering in treatment: 21013506 INFO @ Wed, 30 Jan 2019 17:17:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:17:42: #1 finished! INFO @ Wed, 30 Jan 2019 17:17:42: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:17:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:17:42: #1 tags after filtering in treatment: 21013506 INFO @ Wed, 30 Jan 2019 17:17:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:17:42: #1 finished! INFO @ Wed, 30 Jan 2019 17:17:42: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:17:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:17:44: #2 number of paired peaks: 855 WARNING @ Wed, 30 Jan 2019 17:17:44: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Wed, 30 Jan 2019 17:17:44: start model_add_line... INFO @ Wed, 30 Jan 2019 17:17:44: #2 number of paired peaks: 855 WARNING @ Wed, 30 Jan 2019 17:17:44: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Wed, 30 Jan 2019 17:17:44: start model_add_line... INFO @ Wed, 30 Jan 2019 17:17:44: start X-correlation... INFO @ Wed, 30 Jan 2019 17:17:44: end of X-cor INFO @ Wed, 30 Jan 2019 17:17:44: #2 finished! INFO @ Wed, 30 Jan 2019 17:17:44: #2 predicted fragment length is 60 bps INFO @ Wed, 30 Jan 2019 17:17:44: #2 alternative fragment length(s) may be 4,60 bps INFO @ Wed, 30 Jan 2019 17:17:44: #2.2 Generate R script for model : SRX4664669.20_model.r WARNING @ Wed, 30 Jan 2019 17:17:44: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:17:44: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Wed, 30 Jan 2019 17:17:44: #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 17:17:44: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:17:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:17:44: start X-correlation... INFO @ Wed, 30 Jan 2019 17:17:44: end of X-cor INFO @ Wed, 30 Jan 2019 17:17:44: #2 finished! INFO @ Wed, 30 Jan 2019 17:17:44: #2 predicted fragment length is 60 bps INFO @ Wed, 30 Jan 2019 17:17:44: #2 alternative fragment length(s) may be 4,60 bps INFO @ Wed, 30 Jan 2019 17:17:44: #2.2 Generate R script for model : SRX4664669.10_model.r WARNING @ Wed, 30 Jan 2019 17:17:44: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:17:44: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Wed, 30 Jan 2019 17:17:44: #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 17:17:44: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:17:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:18:26: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:18:27: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:18:28: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:18:49: #4 Write output xls file... SRX4664669.10_peaks.xls INFO @ Wed, 30 Jan 2019 17:18:49: #4 Write peak in narrowPeak format file... SRX4664669.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:18:49: #4 Write summits bed file... SRX4664669.10_summits.bed INFO @ Wed, 30 Jan 2019 17:18:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3613 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:18:51: #4 Write output xls file... SRX4664669.05_peaks.xls INFO @ Wed, 30 Jan 2019 17:18:51: #4 Write peak in narrowPeak format file... SRX4664669.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:18:51: #4 Write summits bed file... SRX4664669.05_summits.bed INFO @ Wed, 30 Jan 2019 17:18:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5399 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:18:53: #4 Write output xls file... SRX4664669.20_peaks.xls INFO @ Wed, 30 Jan 2019 17:18:53: #4 Write peak in narrowPeak format file... SRX4664669.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:18:53: #4 Write summits bed file... SRX4664669.20_summits.bed INFO @ Wed, 30 Jan 2019 17:18:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2233 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。