Job ID = 10320356 sra ファイルのダウンロード中... Completed: 2606745K bytes transferred in 213 seconds (100083K 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... Written 24192324 spots for /home/okishinya/chipatlas/results/dm3/SRX3293408/SRR6183235.sra Written 24192324 spots total 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:23:37 24192324 reads; of these: 24192324 (100.00%) were unpaired; of these: 16857020 (69.68%) aligned 0 times 5031404 (20.80%) aligned exactly 1 time 2303900 (9.52%) aligned >1 times 30.32% overall alignment rate Time searching: 01:23:38 Overall time: 01:23:38 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] 1263825 / 7335304 = 0.1723 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 @ Thu, 11 Jan 2018 03:43:11: # Command line: callpeak -t SRX3293408.bam -f BAM -g dm -n SRX3293408.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3293408.10 # format = BAM # ChIP-seq file = ['SRX3293408.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 @ Thu, 11 Jan 2018 03:43:11: #1 read tag files... INFO @ Thu, 11 Jan 2018 03:43:11: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 03:43:11: # Command line: callpeak -t SRX3293408.bam -f BAM -g dm -n SRX3293408.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3293408.20 # format = BAM # ChIP-seq file = ['SRX3293408.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 @ Thu, 11 Jan 2018 03:43:11: #1 read tag files... INFO @ Thu, 11 Jan 2018 03:43:11: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 03:43:11: # Command line: callpeak -t SRX3293408.bam -f BAM -g dm -n SRX3293408.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3293408.05 # format = BAM # ChIP-seq file = ['SRX3293408.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 @ Thu, 11 Jan 2018 03:43:11: #1 read tag files... INFO @ Thu, 11 Jan 2018 03:43:11: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 03:43:26: 1000000 INFO @ Thu, 11 Jan 2018 03:43:30: 1000000 INFO @ Thu, 11 Jan 2018 03:43:30: 1000000 INFO @ Thu, 11 Jan 2018 03:43:41: 2000000 INFO @ Thu, 11 Jan 2018 03:43:49: 2000000 INFO @ Thu, 11 Jan 2018 03:43:49: 2000000 INFO @ Thu, 11 Jan 2018 03:43:56: 3000000 INFO @ Thu, 11 Jan 2018 03:44:08: 3000000 INFO @ Thu, 11 Jan 2018 03:44:08: 3000000 INFO @ Thu, 11 Jan 2018 03:44:10: 4000000 INFO @ Thu, 11 Jan 2018 03:44:25: 5000000 INFO @ Thu, 11 Jan 2018 03:44:27: 4000000 INFO @ Thu, 11 Jan 2018 03:44:27: 4000000 INFO @ Thu, 11 Jan 2018 03:44:40: 6000000 INFO @ Thu, 11 Jan 2018 03:44:41: #1 tag size is determined as 250 bps INFO @ Thu, 11 Jan 2018 03:44:41: #1 tag size = 250 INFO @ Thu, 11 Jan 2018 03:44:41: #1 total tags in treatment: 6071479 INFO @ Thu, 11 Jan 2018 03:44:41: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 03:44:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 03:44:42: #1 tags after filtering in treatment: 6071479 INFO @ Thu, 11 Jan 2018 03:44:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 03:44:42: #1 finished! INFO @ Thu, 11 Jan 2018 03:44:42: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 03:44:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 03:44:42: #2 number of paired peaks: 392 WARNING @ Thu, 11 Jan 2018 03:44:42: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Thu, 11 Jan 2018 03:44:42: start model_add_line... INFO @ Thu, 11 Jan 2018 03:44:42: start X-correlation... INFO @ Thu, 11 Jan 2018 03:44:42: end of X-cor INFO @ Thu, 11 Jan 2018 03:44:42: #2 finished! INFO @ Thu, 11 Jan 2018 03:44:42: #2 predicted fragment length is 212 bps INFO @ Thu, 11 Jan 2018 03:44:42: #2 alternative fragment length(s) may be 212 bps INFO @ Thu, 11 Jan 2018 03:44:42: #2.2 Generate R script for model : SRX3293408.10_model.r WARNING @ Thu, 11 Jan 2018 03:44:42: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 03:44:42: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Thu, 11 Jan 2018 03:44:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 03:44:42: #3 Call peaks... INFO @ Thu, 11 Jan 2018 03:44:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 03:44:46: 5000000 INFO @ Thu, 11 Jan 2018 03:44:46: 5000000 INFO @ Thu, 11 Jan 2018 03:44:56: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 03:45:04: #4 Write output xls file... SRX3293408.10_peaks.xls INFO @ Thu, 11 Jan 2018 03:45:04: #4 Write peak in narrowPeak format file... SRX3293408.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 03:45:04: #4 Write summits bed file... SRX3293408.10_summits.bed INFO @ Thu, 11 Jan 2018 03:45:04: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (784 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 03:45:05: 6000000 INFO @ Thu, 11 Jan 2018 03:45:05: 6000000 INFO @ Thu, 11 Jan 2018 03:45:06: #1 tag size is determined as 250 bps INFO @ Thu, 11 Jan 2018 03:45:06: #1 tag size is determined as 250 bps INFO @ Thu, 11 Jan 2018 03:45:06: #1 tag size = 250 INFO @ Thu, 11 Jan 2018 03:45:06: #1 tag size = 250 INFO @ Thu, 11 Jan 2018 03:45:06: #1 total tags in treatment: 6071479 INFO @ Thu, 11 Jan 2018 03:45:06: #1 total tags in treatment: 6071479 INFO @ Thu, 11 Jan 2018 03:45:06: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 03:45:06: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 03:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 03:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 03:45:06: #1 tags after filtering in treatment: 6071479 INFO @ Thu, 11 Jan 2018 03:45:06: #1 tags after filtering in treatment: 6071479 INFO @ Thu, 11 Jan 2018 03:45:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 03:45:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 03:45:06: #1 finished! INFO @ Thu, 11 Jan 2018 03:45:06: #1 finished! INFO @ Thu, 11 Jan 2018 03:45:06: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 03:45:06: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 03:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 03:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 03:45:07: #2 number of paired peaks: 392 WARNING @ Thu, 11 Jan 2018 03:45:07: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Thu, 11 Jan 2018 03:45:07: start model_add_line... INFO @ Thu, 11 Jan 2018 03:45:07: #2 number of paired peaks: 392 WARNING @ Thu, 11 Jan 2018 03:45:07: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Thu, 11 Jan 2018 03:45:07: start model_add_line... INFO @ Thu, 11 Jan 2018 03:45:07: start X-correlation... INFO @ Thu, 11 Jan 2018 03:45:07: end of X-cor INFO @ Thu, 11 Jan 2018 03:45:07: #2 finished! INFO @ Thu, 11 Jan 2018 03:45:07: start X-correlation... INFO @ Thu, 11 Jan 2018 03:45:07: #2 predicted fragment length is 212 bps INFO @ Thu, 11 Jan 2018 03:45:07: #2 alternative fragment length(s) may be 212 bps INFO @ Thu, 11 Jan 2018 03:45:07: #2.2 Generate R script for model : SRX3293408.20_model.r INFO @ Thu, 11 Jan 2018 03:45:07: end of X-cor INFO @ Thu, 11 Jan 2018 03:45:07: #2 finished! INFO @ Thu, 11 Jan 2018 03:45:07: #2 predicted fragment length is 212 bps INFO @ Thu, 11 Jan 2018 03:45:07: #2 alternative fragment length(s) may be 212 bps INFO @ Thu, 11 Jan 2018 03:45:07: #2.2 Generate R script for model : SRX3293408.05_model.r WARNING @ Thu, 11 Jan 2018 03:45:07: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 03:45:07: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Thu, 11 Jan 2018 03:45:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 03:45:07: #3 Call peaks... INFO @ Thu, 11 Jan 2018 03:45:07: #3 Pre-compute pvalue-qvalue table... WARNING @ Thu, 11 Jan 2018 03:45:07: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 03:45:07: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Thu, 11 Jan 2018 03:45:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 03:45:07: #3 Call peaks... INFO @ Thu, 11 Jan 2018 03:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 03:45:22: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 03:45:22: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 03:45:29: #4 Write output xls file... SRX3293408.20_peaks.xls INFO @ Thu, 11 Jan 2018 03:45:29: #4 Write peak in narrowPeak format file... SRX3293408.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 03:45:29: #4 Write summits bed file... SRX3293408.20_summits.bed INFO @ Thu, 11 Jan 2018 03:45:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 03:45:30: #4 Write output xls file... SRX3293408.05_peaks.xls INFO @ Thu, 11 Jan 2018 03:45:30: #4 Write peak in narrowPeak format file... SRX3293408.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 03:45:30: #4 Write summits bed file... SRX3293408.05_summits.bed INFO @ Thu, 11 Jan 2018 03:45:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1338 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。