Job ID = 10320333 sra ファイルのダウンロード中... Completed: 623956K bytes transferred in 41 seconds (123036K 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 30802466 spots for /home/okishinya/chipatlas/results/dm3/SRX3146122/SRR5990414.sra Written 30802466 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:04:26 30802466 reads; of these: 30802466 (100.00%) were unpaired; of these: 22143664 (71.89%) aligned 0 times 4565908 (14.82%) aligned exactly 1 time 4092894 (13.29%) aligned >1 times 28.11% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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_rmdupse_core] 2525861 / 8658802 = 0.2917 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 02:13:25: # Command line: callpeak -t SRX3146122.bam -f BAM -g dm -n SRX3146122.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3146122.10 # format = BAM # ChIP-seq file = ['SRX3146122.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 02:13:25: # Command line: callpeak -t SRX3146122.bam -f BAM -g dm -n SRX3146122.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3146122.20 # format = BAM # ChIP-seq file = ['SRX3146122.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 02:13:25: # Command line: callpeak -t SRX3146122.bam -f BAM -g dm -n SRX3146122.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3146122.05 # format = BAM # ChIP-seq file = ['SRX3146122.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 02:13:25: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:13:25: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:13:25: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:13:25: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:13:25: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:13:25: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:13:32: 1000000 INFO @ Thu, 11 Jan 2018 02:13:32: 1000000 INFO @ Thu, 11 Jan 2018 02:13:32: 1000000 INFO @ Thu, 11 Jan 2018 02:13:39: 2000000 INFO @ Thu, 11 Jan 2018 02:13:39: 2000000 INFO @ Thu, 11 Jan 2018 02:13:40: 2000000 INFO @ Thu, 11 Jan 2018 02:13:47: 3000000 INFO @ Thu, 11 Jan 2018 02:13:47: 3000000 INFO @ Thu, 11 Jan 2018 02:13:48: 3000000 INFO @ Thu, 11 Jan 2018 02:13:55: 4000000 INFO @ Thu, 11 Jan 2018 02:13:55: 4000000 INFO @ Thu, 11 Jan 2018 02:13:57: 4000000 INFO @ Thu, 11 Jan 2018 02:14:03: 5000000 INFO @ Thu, 11 Jan 2018 02:14:03: 5000000 INFO @ Thu, 11 Jan 2018 02:14:05: 5000000 INFO @ Thu, 11 Jan 2018 02:14:11: 6000000 INFO @ Thu, 11 Jan 2018 02:14:11: 6000000 INFO @ Thu, 11 Jan 2018 02:14:12: #1 tag size is determined as 40 bps INFO @ Thu, 11 Jan 2018 02:14:12: #1 tag size = 40 INFO @ Thu, 11 Jan 2018 02:14:12: #1 total tags in treatment: 6132941 INFO @ Thu, 11 Jan 2018 02:14:12: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:14:12: #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 02:14:12: #1 tag size is determined as 40 bps INFO @ Thu, 11 Jan 2018 02:14:12: #1 tag size = 40 INFO @ Thu, 11 Jan 2018 02:14:12: #1 total tags in treatment: 6132941 INFO @ Thu, 11 Jan 2018 02:14:12: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:14:12: #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 02:14:12: #1 tags after filtering in treatment: 6132941 INFO @ Thu, 11 Jan 2018 02:14:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:14:12: #1 finished! INFO @ Thu, 11 Jan 2018 02:14:12: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:14:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:14:13: #1 tags after filtering in treatment: 6132941 INFO @ Thu, 11 Jan 2018 02:14:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:14:13: #1 finished! INFO @ Thu, 11 Jan 2018 02:14:13: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:14:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:14:13: #2 number of paired peaks: 881 WARNING @ Thu, 11 Jan 2018 02:14:13: Fewer paired peaks (881) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 881 pairs to build model! INFO @ Thu, 11 Jan 2018 02:14:13: start model_add_line... INFO @ Thu, 11 Jan 2018 02:14:13: start X-correlation... INFO @ Thu, 11 Jan 2018 02:14:13: #2 number of paired peaks: 881 WARNING @ Thu, 11 Jan 2018 02:14:13: Fewer paired peaks (881) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 881 pairs to build model! INFO @ Thu, 11 Jan 2018 02:14:13: start model_add_line... INFO @ Thu, 11 Jan 2018 02:14:13: end of X-cor INFO @ Thu, 11 Jan 2018 02:14:13: #2 finished! INFO @ Thu, 11 Jan 2018 02:14:13: #2 predicted fragment length is 38 bps INFO @ Thu, 11 Jan 2018 02:14:13: #2 alternative fragment length(s) may be 38 bps INFO @ Thu, 11 Jan 2018 02:14:13: #2.2 Generate R script for model : SRX3146122.20_model.r INFO @ Thu, 11 Jan 2018 02:14:13: start X-correlation... INFO @ Thu, 11 Jan 2018 02:14:13: end of X-cor INFO @ Thu, 11 Jan 2018 02:14:13: #2 finished! INFO @ Thu, 11 Jan 2018 02:14:13: #2 predicted fragment length is 38 bps INFO @ Thu, 11 Jan 2018 02:14:13: #2 alternative fragment length(s) may be 38 bps INFO @ Thu, 11 Jan 2018 02:14:13: #2.2 Generate R script for model : SRX3146122.05_model.r WARNING @ Thu, 11 Jan 2018 02:14:13: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:14:13: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Thu, 11 Jan 2018 02:14:13: #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 02:14:13: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:14:13: #3 Pre-compute pvalue-qvalue table... WARNING @ Thu, 11 Jan 2018 02:14:13: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:14:13: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Thu, 11 Jan 2018 02:14:13: #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 02:14:13: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:14:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:14:14: 6000000 INFO @ Thu, 11 Jan 2018 02:14:15: #1 tag size is determined as 40 bps INFO @ Thu, 11 Jan 2018 02:14:15: #1 tag size = 40 INFO @ Thu, 11 Jan 2018 02:14:15: #1 total tags in treatment: 6132941 INFO @ Thu, 11 Jan 2018 02:14:15: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:14:15: #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 02:14:15: #1 tags after filtering in treatment: 6132941 INFO @ Thu, 11 Jan 2018 02:14:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:14:15: #1 finished! INFO @ Thu, 11 Jan 2018 02:14:15: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:14:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:14:15: #2 number of paired peaks: 881 WARNING @ Thu, 11 Jan 2018 02:14:15: Fewer paired peaks (881) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 881 pairs to build model! INFO @ Thu, 11 Jan 2018 02:14:15: start model_add_line... INFO @ Thu, 11 Jan 2018 02:14:15: start X-correlation... INFO @ Thu, 11 Jan 2018 02:14:15: end of X-cor INFO @ Thu, 11 Jan 2018 02:14:15: #2 finished! INFO @ Thu, 11 Jan 2018 02:14:15: #2 predicted fragment length is 38 bps INFO @ Thu, 11 Jan 2018 02:14:15: #2 alternative fragment length(s) may be 38 bps INFO @ Thu, 11 Jan 2018 02:14:15: #2.2 Generate R script for model : SRX3146122.10_model.r WARNING @ Thu, 11 Jan 2018 02:14:15: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:14:15: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Thu, 11 Jan 2018 02:14:15: #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 02:14:15: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:14:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:14:27: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:14:28: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:14:29: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:14:35: #4 Write output xls file... SRX3146122.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:14:35: #4 Write peak in narrowPeak format file... SRX3146122.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:14:35: #4 Write summits bed file... SRX3146122.05_summits.bed INFO @ Thu, 11 Jan 2018 02:14:35: Done! INFO @ Thu, 11 Jan 2018 02:14:35: #4 Write output xls file... SRX3146122.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:14:35: #4 Write peak in narrowPeak format file... SRX3146122.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:14:35: #4 Write summits bed file... SRX3146122.20_summits.bed INFO @ Thu, 11 Jan 2018 02:14:35: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1299 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2290 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:14:37: #4 Write output xls file... SRX3146122.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:14:37: #4 Write peak in narrowPeak format file... SRX3146122.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:14:37: #4 Write summits bed file... SRX3146122.10_summits.bed INFO @ Thu, 11 Jan 2018 02:14:37: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1945 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。