Job ID = 11598011 sra ファイルのダウンロード中... Completed: 729367K bytes transferred in 9 seconds (633627K 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 32358551 spots for /home/okishinya/chipatlas/results/dm3/SRX4664666/SRR7813093.sra Written 32358551 spots for /home/okishinya/chipatlas/results/dm3/SRX4664666/SRR7813093.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: 00:00:01 Multiseed full-index search: 00:13:28 32358551 reads; of these: 32358551 (100.00%) were unpaired; of these: 1089569 (3.37%) aligned 0 times 21138523 (65.33%) aligned exactly 1 time 10130459 (31.31%) aligned >1 times 96.63% overall alignment rate Time searching: 00:13:29 Overall time: 00:13:29 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 16 files... [bam_rmdupse_core] 5977888 / 31268982 = 0.1912 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 17:16:52: # Command line: callpeak -t SRX4664666.bam -f BAM -g dm -n SRX4664666.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664666.20 # format = BAM # ChIP-seq file = ['SRX4664666.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 17:16:52: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:16:52: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:16:52: # Command line: callpeak -t SRX4664666.bam -f BAM -g dm -n SRX4664666.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664666.10 # format = BAM # ChIP-seq file = ['SRX4664666.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 17:16:52: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:16:52: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:16:52: # Command line: callpeak -t SRX4664666.bam -f BAM -g dm -n SRX4664666.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664666.05 # format = BAM # ChIP-seq file = ['SRX4664666.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 17:16:52: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:16:52: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:16:59: 1000000 INFO @ Wed, 30 Jan 2019 17:16:59: 1000000 INFO @ Wed, 30 Jan 2019 17:16:59: 1000000 INFO @ Wed, 30 Jan 2019 17:17:05: 2000000 INFO @ Wed, 30 Jan 2019 17:17:06: 2000000 INFO @ Wed, 30 Jan 2019 17:17:06: 2000000 INFO @ Wed, 30 Jan 2019 17:17:12: 3000000 INFO @ Wed, 30 Jan 2019 17:17:13: 3000000 INFO @ Wed, 30 Jan 2019 17:17:13: 3000000 INFO @ Wed, 30 Jan 2019 17:17:18: 4000000 INFO @ Wed, 30 Jan 2019 17:17:20: 4000000 INFO @ Wed, 30 Jan 2019 17:17:20: 4000000 INFO @ Wed, 30 Jan 2019 17:17:25: 5000000 INFO @ Wed, 30 Jan 2019 17:17:27: 5000000 INFO @ Wed, 30 Jan 2019 17:17:27: 5000000 INFO @ Wed, 30 Jan 2019 17:17:31: 6000000 INFO @ Wed, 30 Jan 2019 17:17:34: 6000000 INFO @ Wed, 30 Jan 2019 17:17:34: 6000000 INFO @ Wed, 30 Jan 2019 17:17:37: 7000000 INFO @ Wed, 30 Jan 2019 17:17:41: 7000000 INFO @ Wed, 30 Jan 2019 17:17:41: 7000000 INFO @ Wed, 30 Jan 2019 17:17:44: 8000000 INFO @ Wed, 30 Jan 2019 17:17:48: 8000000 INFO @ Wed, 30 Jan 2019 17:17:48: 8000000 INFO @ Wed, 30 Jan 2019 17:17:50: 9000000 INFO @ Wed, 30 Jan 2019 17:17:55: 9000000 INFO @ Wed, 30 Jan 2019 17:17:55: 9000000 INFO @ Wed, 30 Jan 2019 17:17:57: 10000000 INFO @ Wed, 30 Jan 2019 17:18:02: 10000000 INFO @ Wed, 30 Jan 2019 17:18:02: 10000000 INFO @ Wed, 30 Jan 2019 17:18:03: 11000000 INFO @ Wed, 30 Jan 2019 17:18:09: 11000000 INFO @ Wed, 30 Jan 2019 17:18:09: 11000000 INFO @ Wed, 30 Jan 2019 17:18:10: 12000000 INFO @ Wed, 30 Jan 2019 17:18:16: 13000000 INFO @ Wed, 30 Jan 2019 17:18:16: 12000000 INFO @ Wed, 30 Jan 2019 17:18:16: 12000000 INFO @ Wed, 30 Jan 2019 17:18:23: 14000000 INFO @ Wed, 30 Jan 2019 17:18:23: 13000000 INFO @ Wed, 30 Jan 2019 17:18:23: 13000000 INFO @ Wed, 30 Jan 2019 17:18:29: 15000000 INFO @ Wed, 30 Jan 2019 17:18:31: 14000000 INFO @ Wed, 30 Jan 2019 17:18:31: 14000000 INFO @ Wed, 30 Jan 2019 17:18:36: 16000000 INFO @ Wed, 30 Jan 2019 17:18:38: 15000000 INFO @ Wed, 30 Jan 2019 17:18:38: 15000000 INFO @ Wed, 30 Jan 2019 17:18:42: 17000000 INFO @ Wed, 30 Jan 2019 17:18:45: 16000000 INFO @ Wed, 30 Jan 2019 17:18:45: 16000000 INFO @ Wed, 30 Jan 2019 17:18:49: 18000000 INFO @ Wed, 30 Jan 2019 17:18:52: 17000000 INFO @ Wed, 30 Jan 2019 17:18:52: 17000000 INFO @ Wed, 30 Jan 2019 17:18:55: 19000000 INFO @ Wed, 30 Jan 2019 17:18:59: 18000000 INFO @ Wed, 30 Jan 2019 17:18:59: 18000000 INFO @ Wed, 30 Jan 2019 17:19:01: 20000000 INFO @ Wed, 30 Jan 2019 17:19:06: 19000000 INFO @ Wed, 30 Jan 2019 17:19:06: 19000000 INFO @ Wed, 30 Jan 2019 17:19:08: 21000000 INFO @ Wed, 30 Jan 2019 17:19:13: 20000000 INFO @ Wed, 30 Jan 2019 17:19:13: 20000000 INFO @ Wed, 30 Jan 2019 17:19:14: 22000000 INFO @ Wed, 30 Jan 2019 17:19:21: 21000000 INFO @ Wed, 30 Jan 2019 17:19:21: 21000000 INFO @ Wed, 30 Jan 2019 17:19:21: 23000000 INFO @ Wed, 30 Jan 2019 17:19:27: 24000000 INFO @ Wed, 30 Jan 2019 17:19:28: 22000000 INFO @ Wed, 30 Jan 2019 17:19:28: 22000000 INFO @ Wed, 30 Jan 2019 17:19:34: 25000000 INFO @ Wed, 30 Jan 2019 17:19:35: 23000000 INFO @ Wed, 30 Jan 2019 17:19:35: 23000000 INFO @ Wed, 30 Jan 2019 17:19:36: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:19:36: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:19:36: #1 total tags in treatment: 25291094 INFO @ Wed, 30 Jan 2019 17:19:36: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:19:36: #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 17:19:36: #1 tags after filtering in treatment: 25291094 INFO @ Wed, 30 Jan 2019 17:19:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:19:36: #1 finished! INFO @ Wed, 30 Jan 2019 17:19:36: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:19:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:19:38: #2 number of paired peaks: 595 WARNING @ Wed, 30 Jan 2019 17:19:38: Fewer paired peaks (595) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 595 pairs to build model! INFO @ Wed, 30 Jan 2019 17:19:38: start model_add_line... INFO @ Wed, 30 Jan 2019 17:19:38: start X-correlation... INFO @ Wed, 30 Jan 2019 17:19:38: end of X-cor INFO @ Wed, 30 Jan 2019 17:19:38: #2 finished! INFO @ Wed, 30 Jan 2019 17:19:38: #2 predicted fragment length is 50 bps INFO @ Wed, 30 Jan 2019 17:19:38: #2 alternative fragment length(s) may be 3,50,577 bps INFO @ Wed, 30 Jan 2019 17:19:38: #2.2 Generate R script for model : SRX4664666.10_model.r WARNING @ Wed, 30 Jan 2019 17:19:38: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:19:38: #2 You may need to consider one of the other alternative d(s): 3,50,577 WARNING @ Wed, 30 Jan 2019 17:19:38: #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 17:19:38: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:19:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:19:42: 24000000 INFO @ Wed, 30 Jan 2019 17:19:42: 24000000 INFO @ Wed, 30 Jan 2019 17:19:49: 25000000 INFO @ Wed, 30 Jan 2019 17:19:49: 25000000 INFO @ Wed, 30 Jan 2019 17:19:51: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:19:51: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:19:51: #1 total tags in treatment: 25291094 INFO @ Wed, 30 Jan 2019 17:19:51: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:19:51: #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 17:19:51: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:19:51: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:19:51: #1 total tags in treatment: 25291094 INFO @ Wed, 30 Jan 2019 17:19:51: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:19:51: #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 17:19:52: #1 tags after filtering in treatment: 25291094 INFO @ Wed, 30 Jan 2019 17:19:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:19:52: #1 finished! INFO @ Wed, 30 Jan 2019 17:19:52: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:19:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:19:52: #1 tags after filtering in treatment: 25291094 INFO @ Wed, 30 Jan 2019 17:19:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:19:52: #1 finished! INFO @ Wed, 30 Jan 2019 17:19:52: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:19:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:19:54: #2 number of paired peaks: 595 WARNING @ Wed, 30 Jan 2019 17:19:54: Fewer paired peaks (595) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 595 pairs to build model! INFO @ Wed, 30 Jan 2019 17:19:54: start model_add_line... INFO @ Wed, 30 Jan 2019 17:19:54: #2 number of paired peaks: 595 WARNING @ Wed, 30 Jan 2019 17:19:54: Fewer paired peaks (595) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 595 pairs to build model! INFO @ Wed, 30 Jan 2019 17:19:54: start model_add_line... INFO @ Wed, 30 Jan 2019 17:19:54: start X-correlation... INFO @ Wed, 30 Jan 2019 17:19:54: end of X-cor INFO @ Wed, 30 Jan 2019 17:19:54: #2 finished! INFO @ Wed, 30 Jan 2019 17:19:54: #2 predicted fragment length is 50 bps INFO @ Wed, 30 Jan 2019 17:19:54: #2 alternative fragment length(s) may be 3,50,577 bps INFO @ Wed, 30 Jan 2019 17:19:54: #2.2 Generate R script for model : SRX4664666.20_model.r WARNING @ Wed, 30 Jan 2019 17:19:54: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:19:54: #2 You may need to consider one of the other alternative d(s): 3,50,577 WARNING @ Wed, 30 Jan 2019 17:19:54: #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 17:19:54: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:19:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:19:54: start X-correlation... INFO @ Wed, 30 Jan 2019 17:19:54: end of X-cor INFO @ Wed, 30 Jan 2019 17:19:54: #2 finished! INFO @ Wed, 30 Jan 2019 17:19:54: #2 predicted fragment length is 50 bps INFO @ Wed, 30 Jan 2019 17:19:54: #2 alternative fragment length(s) may be 3,50,577 bps INFO @ Wed, 30 Jan 2019 17:19:54: #2.2 Generate R script for model : SRX4664666.05_model.r WARNING @ Wed, 30 Jan 2019 17:19:54: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:19:54: #2 You may need to consider one of the other alternative d(s): 3,50,577 WARNING @ Wed, 30 Jan 2019 17:19:54: #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 17:19:54: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:19:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:20:30: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:20:43: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:20:43: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:20:58: #4 Write output xls file... SRX4664666.10_peaks.xls INFO @ Wed, 30 Jan 2019 17:20:58: #4 Write peak in narrowPeak format file... SRX4664666.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:20:58: #4 Write summits bed file... SRX4664666.10_summits.bed INFO @ Wed, 30 Jan 2019 17:20:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4027 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:21:11: #4 Write output xls file... SRX4664666.20_peaks.xls INFO @ Wed, 30 Jan 2019 17:21:11: #4 Write peak in narrowPeak format file... SRX4664666.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:21:11: #4 Write summits bed file... SRX4664666.20_summits.bed INFO @ Wed, 30 Jan 2019 17:21:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2368 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:21:12: #4 Write output xls file... SRX4664666.05_peaks.xls INFO @ Wed, 30 Jan 2019 17:21:12: #4 Write peak in narrowPeak format file... SRX4664666.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:21:12: #4 Write summits bed file... SRX4664666.05_summits.bed INFO @ Wed, 30 Jan 2019 17:21:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5999 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。