Job ID = 11597769 sra ファイルのダウンロード中... Completed: 320244K bytes transferred in 11 seconds (219483K bits/sec), in 1 file. Completed: 295044K bytes transferred in 14 seconds (172395K 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 11635521 spots for /home/okishinya/chipatlas/results/dm3/ERX1266823/ERR1193509.sra Written 11635521 spots for /home/okishinya/chipatlas/results/dm3/ERX1266823/ERR1193509.sra Read 12748598 spots for /home/okishinya/chipatlas/results/dm3/ERX1266823/ERR1193505.sra Written 12748598 spots for /home/okishinya/chipatlas/results/dm3/ERX1266823/ERR1193505.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 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: 00:10:06 24384119 reads; of these: 24384119 (100.00%) were unpaired; of these: 1869858 (7.67%) aligned 0 times 15036899 (61.67%) aligned exactly 1 time 7477362 (30.66%) aligned >1 times 92.33% overall alignment rate Time searching: 00:10:06 Overall time: 00:10:06 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] 4161128 / 22514261 = 0.1848 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 14:53:27: # Command line: callpeak -t ERX1266823.bam -f BAM -g dm -n ERX1266823.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1266823.10 # format = BAM # ChIP-seq file = ['ERX1266823.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 14:53:27: # Command line: callpeak -t ERX1266823.bam -f BAM -g dm -n ERX1266823.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1266823.05 # format = BAM # ChIP-seq file = ['ERX1266823.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 14:53:27: # Command line: callpeak -t ERX1266823.bam -f BAM -g dm -n ERX1266823.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1266823.20 # format = BAM # ChIP-seq file = ['ERX1266823.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 14:53:27: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:53:27: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:53:27: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:53:27: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:53:27: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:53:27: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:53:33: 1000000 INFO @ Wed, 30 Jan 2019 14:53:33: 1000000 INFO @ Wed, 30 Jan 2019 14:53:34: 1000000 INFO @ Wed, 30 Jan 2019 14:53:40: 2000000 INFO @ Wed, 30 Jan 2019 14:53:40: 2000000 INFO @ Wed, 30 Jan 2019 14:53:40: 2000000 INFO @ Wed, 30 Jan 2019 14:53:46: 3000000 INFO @ Wed, 30 Jan 2019 14:53:47: 3000000 INFO @ Wed, 30 Jan 2019 14:53:47: 3000000 INFO @ Wed, 30 Jan 2019 14:53:52: 4000000 INFO @ Wed, 30 Jan 2019 14:53:54: 4000000 INFO @ Wed, 30 Jan 2019 14:53:54: 4000000 INFO @ Wed, 30 Jan 2019 14:53:59: 5000000 INFO @ Wed, 30 Jan 2019 14:54:01: 5000000 INFO @ Wed, 30 Jan 2019 14:54:01: 5000000 INFO @ Wed, 30 Jan 2019 14:54:05: 6000000 INFO @ Wed, 30 Jan 2019 14:54:07: 6000000 INFO @ Wed, 30 Jan 2019 14:54:08: 6000000 INFO @ Wed, 30 Jan 2019 14:54:11: 7000000 INFO @ Wed, 30 Jan 2019 14:54:14: 7000000 INFO @ Wed, 30 Jan 2019 14:54:15: 7000000 INFO @ Wed, 30 Jan 2019 14:54:18: 8000000 INFO @ Wed, 30 Jan 2019 14:54:21: 8000000 INFO @ Wed, 30 Jan 2019 14:54:22: 8000000 INFO @ Wed, 30 Jan 2019 14:54:24: 9000000 INFO @ Wed, 30 Jan 2019 14:54:28: 9000000 INFO @ Wed, 30 Jan 2019 14:54:30: 9000000 INFO @ Wed, 30 Jan 2019 14:54:30: 10000000 INFO @ Wed, 30 Jan 2019 14:54:35: 10000000 INFO @ Wed, 30 Jan 2019 14:54:37: 11000000 INFO @ Wed, 30 Jan 2019 14:54:37: 10000000 INFO @ Wed, 30 Jan 2019 14:54:42: 11000000 INFO @ Wed, 30 Jan 2019 14:54:43: 12000000 INFO @ Wed, 30 Jan 2019 14:54:44: 11000000 INFO @ Wed, 30 Jan 2019 14:54:49: 13000000 INFO @ Wed, 30 Jan 2019 14:54:49: 12000000 INFO @ Wed, 30 Jan 2019 14:54:51: 12000000 INFO @ Wed, 30 Jan 2019 14:54:55: 14000000 INFO @ Wed, 30 Jan 2019 14:54:56: 13000000 INFO @ Wed, 30 Jan 2019 14:54:58: 13000000 INFO @ Wed, 30 Jan 2019 14:55:02: 15000000 INFO @ Wed, 30 Jan 2019 14:55:03: 14000000 INFO @ Wed, 30 Jan 2019 14:55:05: 14000000 INFO @ Wed, 30 Jan 2019 14:55:08: 16000000 INFO @ Wed, 30 Jan 2019 14:55:10: 15000000 INFO @ Wed, 30 Jan 2019 14:55:12: 15000000 INFO @ Wed, 30 Jan 2019 14:55:14: 17000000 INFO @ Wed, 30 Jan 2019 14:55:17: 16000000 INFO @ Wed, 30 Jan 2019 14:55:19: 16000000 INFO @ Wed, 30 Jan 2019 14:55:21: 18000000 INFO @ Wed, 30 Jan 2019 14:55:23: #1 tag size is determined as 44 bps INFO @ Wed, 30 Jan 2019 14:55:23: #1 tag size = 44 INFO @ Wed, 30 Jan 2019 14:55:23: #1 total tags in treatment: 18353133 INFO @ Wed, 30 Jan 2019 14:55:23: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:55:23: #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 14:55:24: #1 tags after filtering in treatment: 18353133 INFO @ Wed, 30 Jan 2019 14:55:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:55:24: #1 finished! INFO @ Wed, 30 Jan 2019 14:55:24: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:55:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:55:24: 17000000 INFO @ Wed, 30 Jan 2019 14:55:25: #2 number of paired peaks: 241 WARNING @ Wed, 30 Jan 2019 14:55:25: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Wed, 30 Jan 2019 14:55:25: start model_add_line... INFO @ Wed, 30 Jan 2019 14:55:25: start X-correlation... INFO @ Wed, 30 Jan 2019 14:55:25: end of X-cor INFO @ Wed, 30 Jan 2019 14:55:25: #2 finished! INFO @ Wed, 30 Jan 2019 14:55:25: #2 predicted fragment length is 44 bps INFO @ Wed, 30 Jan 2019 14:55:25: #2 alternative fragment length(s) may be 44 bps INFO @ Wed, 30 Jan 2019 14:55:25: #2.2 Generate R script for model : ERX1266823.10_model.r WARNING @ Wed, 30 Jan 2019 14:55:25: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:55:25: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Wed, 30 Jan 2019 14:55:25: #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 14:55:25: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:55:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:55:27: 17000000 INFO @ Wed, 30 Jan 2019 14:55:31: 18000000 INFO @ Wed, 30 Jan 2019 14:55:34: #1 tag size is determined as 44 bps INFO @ Wed, 30 Jan 2019 14:55:34: #1 tag size = 44 INFO @ Wed, 30 Jan 2019 14:55:34: #1 total tags in treatment: 18353133 INFO @ Wed, 30 Jan 2019 14:55:34: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:55:34: #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 14:55:34: 18000000 INFO @ Wed, 30 Jan 2019 14:55:34: #1 tags after filtering in treatment: 18353133 INFO @ Wed, 30 Jan 2019 14:55:34: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:55:34: #1 finished! INFO @ Wed, 30 Jan 2019 14:55:34: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:55:35: #2 number of paired peaks: 241 WARNING @ Wed, 30 Jan 2019 14:55:35: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Wed, 30 Jan 2019 14:55:35: start model_add_line... INFO @ Wed, 30 Jan 2019 14:55:35: start X-correlation... INFO @ Wed, 30 Jan 2019 14:55:35: end of X-cor INFO @ Wed, 30 Jan 2019 14:55:35: #2 finished! INFO @ Wed, 30 Jan 2019 14:55:35: #2 predicted fragment length is 44 bps INFO @ Wed, 30 Jan 2019 14:55:35: #2 alternative fragment length(s) may be 44 bps INFO @ Wed, 30 Jan 2019 14:55:35: #2.2 Generate R script for model : ERX1266823.20_model.r WARNING @ Wed, 30 Jan 2019 14:55:35: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:55:35: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Wed, 30 Jan 2019 14:55:35: #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 14:55:35: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:55:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:55:36: #1 tag size is determined as 44 bps INFO @ Wed, 30 Jan 2019 14:55:36: #1 tag size = 44 INFO @ Wed, 30 Jan 2019 14:55:36: #1 total tags in treatment: 18353133 INFO @ Wed, 30 Jan 2019 14:55:36: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:55:36: #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 14:55:36: #1 tags after filtering in treatment: 18353133 INFO @ Wed, 30 Jan 2019 14:55:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:55:36: #1 finished! INFO @ Wed, 30 Jan 2019 14:55:36: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:55:38: #2 number of paired peaks: 241 WARNING @ Wed, 30 Jan 2019 14:55:38: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Wed, 30 Jan 2019 14:55:38: start model_add_line... INFO @ Wed, 30 Jan 2019 14:55:38: start X-correlation... INFO @ Wed, 30 Jan 2019 14:55:38: end of X-cor INFO @ Wed, 30 Jan 2019 14:55:38: #2 finished! INFO @ Wed, 30 Jan 2019 14:55:38: #2 predicted fragment length is 44 bps INFO @ Wed, 30 Jan 2019 14:55:38: #2 alternative fragment length(s) may be 44 bps INFO @ Wed, 30 Jan 2019 14:55:38: #2.2 Generate R script for model : ERX1266823.05_model.r WARNING @ Wed, 30 Jan 2019 14:55:38: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:55:38: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Wed, 30 Jan 2019 14:55:38: #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 14:55:38: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:55:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:56:01: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:56:10: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:56:16: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:56:19: #4 Write output xls file... ERX1266823.10_peaks.xls INFO @ Wed, 30 Jan 2019 14:56:19: #4 Write peak in narrowPeak format file... ERX1266823.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:56:19: #4 Write summits bed file... ERX1266823.10_summits.bed INFO @ Wed, 30 Jan 2019 14:56:19: Done! pass1 - making usageList (12 chroms): 9 millis pass2 - checking and writing primary data (1619 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 14:56:31: #4 Write output xls file... ERX1266823.20_peaks.xls INFO @ Wed, 30 Jan 2019 14:56:31: #4 Write peak in narrowPeak format file... ERX1266823.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:56:31: #4 Write summits bed file... ERX1266823.20_summits.bed INFO @ Wed, 30 Jan 2019 14:56:31: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1237 records, 4 fields): 534 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 14:56:39: #4 Write output xls file... ERX1266823.05_peaks.xls INFO @ Wed, 30 Jan 2019 14:56:39: #4 Write peak in narrowPeak format file... ERX1266823.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:56:39: #4 Write summits bed file... ERX1266823.05_summits.bed INFO @ Wed, 30 Jan 2019 14:56:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1938 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。