Job ID = 11598007 sra ファイルのダウンロード中... Completed: 688181K bytes transferred in 10 seconds (530793K 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 28779797 spots for /home/okishinya/chipatlas/results/dm3/SRX4664662/SRR7813089.sra Written 28779797 spots for /home/okishinya/chipatlas/results/dm3/SRX4664662/SRR7813089.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: 00:14:52 28779797 reads; of these: 28779797 (100.00%) were unpaired; of these: 728191 (2.53%) aligned 0 times 18584686 (64.58%) aligned exactly 1 time 9466920 (32.89%) aligned >1 times 97.47% overall alignment rate Time searching: 00:14:52 Overall time: 00:14:52 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_sort_core] merging from 12 files... [bam_rmdupse_core] 3915057 / 28051606 = 0.1396 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 18:56:51: # Command line: callpeak -t SRX4664662.bam -f BAM -g dm -n SRX4664662.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664662.05 # format = BAM # ChIP-seq file = ['SRX4664662.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 18:56:51: #1 read tag files... INFO @ Wed, 30 Jan 2019 18:56:51: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 18:56:51: # Command line: callpeak -t SRX4664662.bam -f BAM -g dm -n SRX4664662.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664662.20 # format = BAM # ChIP-seq file = ['SRX4664662.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 18:56:51: #1 read tag files... INFO @ Wed, 30 Jan 2019 18:56:51: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 18:56:51: # Command line: callpeak -t SRX4664662.bam -f BAM -g dm -n SRX4664662.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664662.10 # format = BAM # ChIP-seq file = ['SRX4664662.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 18:56:51: #1 read tag files... INFO @ Wed, 30 Jan 2019 18:56:51: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 18:56:59: 1000000 INFO @ Wed, 30 Jan 2019 18:56:59: 1000000 INFO @ Wed, 30 Jan 2019 18:56:59: 1000000 INFO @ Wed, 30 Jan 2019 18:57:07: 2000000 INFO @ Wed, 30 Jan 2019 18:57:07: 2000000 INFO @ Wed, 30 Jan 2019 18:57:07: 2000000 INFO @ Wed, 30 Jan 2019 18:57:15: 3000000 INFO @ Wed, 30 Jan 2019 18:57:16: 3000000 INFO @ Wed, 30 Jan 2019 18:57:16: 3000000 INFO @ Wed, 30 Jan 2019 18:57:24: 4000000 INFO @ Wed, 30 Jan 2019 18:57:24: 4000000 INFO @ Wed, 30 Jan 2019 18:57:25: 4000000 INFO @ Wed, 30 Jan 2019 18:57:32: 5000000 INFO @ Wed, 30 Jan 2019 18:57:32: 5000000 INFO @ Wed, 30 Jan 2019 18:57:34: 5000000 INFO @ Wed, 30 Jan 2019 18:57:41: 6000000 INFO @ Wed, 30 Jan 2019 18:57:41: 6000000 INFO @ Wed, 30 Jan 2019 18:57:44: 6000000 INFO @ Wed, 30 Jan 2019 18:57:50: 7000000 INFO @ Wed, 30 Jan 2019 18:57:50: 7000000 INFO @ Wed, 30 Jan 2019 18:57:54: 7000000 INFO @ Wed, 30 Jan 2019 18:57:59: 8000000 INFO @ Wed, 30 Jan 2019 18:57:59: 8000000 INFO @ Wed, 30 Jan 2019 18:58:04: 8000000 INFO @ Wed, 30 Jan 2019 18:58:08: 9000000 INFO @ Wed, 30 Jan 2019 18:58:08: 9000000 INFO @ Wed, 30 Jan 2019 18:58:13: 9000000 INFO @ Wed, 30 Jan 2019 18:58:16: 10000000 INFO @ Wed, 30 Jan 2019 18:58:17: 10000000 INFO @ Wed, 30 Jan 2019 18:58:23: 10000000 INFO @ Wed, 30 Jan 2019 18:58:25: 11000000 INFO @ Wed, 30 Jan 2019 18:58:25: 11000000 INFO @ Wed, 30 Jan 2019 18:58:32: 11000000 INFO @ Wed, 30 Jan 2019 18:58:33: 12000000 INFO @ Wed, 30 Jan 2019 18:58:33: 12000000 INFO @ Wed, 30 Jan 2019 18:58:41: 12000000 INFO @ Wed, 30 Jan 2019 18:58:42: 13000000 INFO @ Wed, 30 Jan 2019 18:58:42: 13000000 INFO @ Wed, 30 Jan 2019 18:58:50: 14000000 INFO @ Wed, 30 Jan 2019 18:58:50: 13000000 INFO @ Wed, 30 Jan 2019 18:58:51: 14000000 INFO @ Wed, 30 Jan 2019 18:58:58: 15000000 INFO @ Wed, 30 Jan 2019 18:58:59: 14000000 INFO @ Wed, 30 Jan 2019 18:58:59: 15000000 INFO @ Wed, 30 Jan 2019 18:59:06: 16000000 INFO @ Wed, 30 Jan 2019 18:59:07: 16000000 INFO @ Wed, 30 Jan 2019 18:59:08: 15000000 INFO @ Wed, 30 Jan 2019 18:59:14: 17000000 INFO @ Wed, 30 Jan 2019 18:59:15: 17000000 INFO @ Wed, 30 Jan 2019 18:59:16: 16000000 INFO @ Wed, 30 Jan 2019 18:59:22: 18000000 INFO @ Wed, 30 Jan 2019 18:59:22: 18000000 INFO @ Wed, 30 Jan 2019 18:59:23: 17000000 INFO @ Wed, 30 Jan 2019 18:59:29: 19000000 INFO @ Wed, 30 Jan 2019 18:59:30: 19000000 INFO @ Wed, 30 Jan 2019 18:59:32: 18000000 INFO @ Wed, 30 Jan 2019 18:59:37: 20000000 INFO @ Wed, 30 Jan 2019 18:59:40: 20000000 INFO @ Wed, 30 Jan 2019 18:59:40: 19000000 INFO @ Wed, 30 Jan 2019 18:59:45: 21000000 INFO @ Wed, 30 Jan 2019 18:59:49: 20000000 INFO @ Wed, 30 Jan 2019 18:59:49: 21000000 INFO @ Wed, 30 Jan 2019 18:59:54: 22000000 INFO @ Wed, 30 Jan 2019 18:59:58: 21000000 INFO @ Wed, 30 Jan 2019 19:00:00: 22000000 INFO @ Wed, 30 Jan 2019 19:00:04: 23000000 INFO @ Wed, 30 Jan 2019 19:00:06: 22000000 INFO @ Wed, 30 Jan 2019 19:00:08: 23000000 INFO @ Wed, 30 Jan 2019 19:00:13: 24000000 INFO @ Wed, 30 Jan 2019 19:00:14: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 19:00:14: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 19:00:14: #1 total tags in treatment: 24136549 INFO @ Wed, 30 Jan 2019 19:00:14: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 19:00:14: #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 19:00:14: 23000000 INFO @ Wed, 30 Jan 2019 19:00:14: #1 tags after filtering in treatment: 24136549 INFO @ Wed, 30 Jan 2019 19:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 19:00:14: #1 finished! INFO @ Wed, 30 Jan 2019 19:00:14: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 19:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 19:00:16: #2 number of paired peaks: 485 WARNING @ Wed, 30 Jan 2019 19:00:16: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Wed, 30 Jan 2019 19:00:16: start model_add_line... INFO @ Wed, 30 Jan 2019 19:00:16: start X-correlation... INFO @ Wed, 30 Jan 2019 19:00:16: end of X-cor INFO @ Wed, 30 Jan 2019 19:00:16: #2 finished! INFO @ Wed, 30 Jan 2019 19:00:16: #2 predicted fragment length is 27 bps INFO @ Wed, 30 Jan 2019 19:00:16: #2 alternative fragment length(s) may be 3,27 bps INFO @ Wed, 30 Jan 2019 19:00:16: #2.2 Generate R script for model : SRX4664662.05_model.r WARNING @ Wed, 30 Jan 2019 19:00:16: #2 Since the d (27) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 19:00:16: #2 You may need to consider one of the other alternative d(s): 3,27 WARNING @ Wed, 30 Jan 2019 19:00:16: #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 19:00:16: #3 Call peaks... INFO @ Wed, 30 Jan 2019 19:00:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 19:00:16: 24000000 INFO @ Wed, 30 Jan 2019 19:00:18: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 19:00:18: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 19:00:18: #1 total tags in treatment: 24136549 INFO @ Wed, 30 Jan 2019 19:00:18: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 19:00:18: #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 19:00:18: #1 tags after filtering in treatment: 24136549 INFO @ Wed, 30 Jan 2019 19:00:18: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 19:00:18: #1 finished! INFO @ Wed, 30 Jan 2019 19:00:18: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 19:00:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 19:00:20: #2 number of paired peaks: 485 WARNING @ Wed, 30 Jan 2019 19:00:20: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Wed, 30 Jan 2019 19:00:20: start model_add_line... INFO @ Wed, 30 Jan 2019 19:00:20: start X-correlation... INFO @ Wed, 30 Jan 2019 19:00:20: end of X-cor INFO @ Wed, 30 Jan 2019 19:00:20: #2 finished! INFO @ Wed, 30 Jan 2019 19:00:20: #2 predicted fragment length is 27 bps INFO @ Wed, 30 Jan 2019 19:00:20: #2 alternative fragment length(s) may be 3,27 bps INFO @ Wed, 30 Jan 2019 19:00:20: #2.2 Generate R script for model : SRX4664662.10_model.r WARNING @ Wed, 30 Jan 2019 19:00:20: #2 Since the d (27) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 19:00:20: #2 You may need to consider one of the other alternative d(s): 3,27 WARNING @ Wed, 30 Jan 2019 19:00:20: #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 19:00:20: #3 Call peaks... INFO @ Wed, 30 Jan 2019 19:00:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 19:00:22: 24000000 INFO @ Wed, 30 Jan 2019 19:00:23: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 19:00:23: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 19:00:23: #1 total tags in treatment: 24136549 INFO @ Wed, 30 Jan 2019 19:00:23: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 19:00:23: #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 19:00:24: #1 tags after filtering in treatment: 24136549 INFO @ Wed, 30 Jan 2019 19:00:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 19:00:24: #1 finished! INFO @ Wed, 30 Jan 2019 19:00:24: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 19:00:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 19:00:25: #2 number of paired peaks: 485 WARNING @ Wed, 30 Jan 2019 19:00:25: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Wed, 30 Jan 2019 19:00:25: start model_add_line... INFO @ Wed, 30 Jan 2019 19:00:26: start X-correlation... INFO @ Wed, 30 Jan 2019 19:00:26: end of X-cor INFO @ Wed, 30 Jan 2019 19:00:26: #2 finished! INFO @ Wed, 30 Jan 2019 19:00:26: #2 predicted fragment length is 27 bps INFO @ Wed, 30 Jan 2019 19:00:26: #2 alternative fragment length(s) may be 3,27 bps INFO @ Wed, 30 Jan 2019 19:00:26: #2.2 Generate R script for model : SRX4664662.20_model.r WARNING @ Wed, 30 Jan 2019 19:00:26: #2 Since the d (27) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 19:00:26: #2 You may need to consider one of the other alternative d(s): 3,27 WARNING @ Wed, 30 Jan 2019 19:00:26: #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 19:00:26: #3 Call peaks... INFO @ Wed, 30 Jan 2019 19:00:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 19:01:04: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 19:01:09: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 19:01:12: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 19:01:32: #4 Write output xls file... SRX4664662.05_peaks.xls INFO @ Wed, 30 Jan 2019 19:01:32: #4 Write peak in narrowPeak format file... SRX4664662.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 19:01:32: #4 Write summits bed file... SRX4664662.05_summits.bed INFO @ Wed, 30 Jan 2019 19:01:32: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (3903 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 19:01:35: #4 Write output xls file... SRX4664662.20_peaks.xls INFO @ Wed, 30 Jan 2019 19:01:35: #4 Write peak in narrowPeak format file... SRX4664662.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 19:01:35: #4 Write summits bed file... SRX4664662.20_summits.bed INFO @ Wed, 30 Jan 2019 19:01:35: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (891 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 19:01:35: #4 Write output xls file... SRX4664662.10_peaks.xls INFO @ Wed, 30 Jan 2019 19:01:35: #4 Write peak in narrowPeak format file... SRX4664662.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 19:01:35: #4 Write summits bed file... SRX4664662.10_summits.bed INFO @ Wed, 30 Jan 2019 19:01:35: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (2448 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。