Job ID = 9730456 sra ファイルのダウンロード中... Completed: 720095K bytes transferred in 46 seconds (127074K bits/sec), in 1 file, 2 directories. 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 23322541 spots for /home/okishinya/chipatlas/results/dm3/SRX2829096/SRR5569906.sra Written 23322541 spots total 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: 00:07:46 23322541 reads; of these: 23322541 (100.00%) were unpaired; of these: 5646849 (24.21%) aligned 0 times 11452783 (49.11%) aligned exactly 1 time 6222909 (26.68%) aligned >1 times 75.79% overall alignment rate Time searching: 00:07:46 Overall time: 00:07:46 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] 8593331 / 17675692 = 0.4862 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 @ Sun, 03 Sep 2017 01:08:00: # Command line: callpeak -t SRX2829096.bam -f BAM -g dm -n SRX2829096.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2829096.05 # format = BAM # ChIP-seq file = ['SRX2829096.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 @ Sun, 03 Sep 2017 01:08:00: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:08:00: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:08:00: # Command line: callpeak -t SRX2829096.bam -f BAM -g dm -n SRX2829096.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2829096.10 # format = BAM # ChIP-seq file = ['SRX2829096.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 @ Sun, 03 Sep 2017 01:08:00: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:08:00: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:08:00: # Command line: callpeak -t SRX2829096.bam -f BAM -g dm -n SRX2829096.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2829096.20 # format = BAM # ChIP-seq file = ['SRX2829096.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 @ Sun, 03 Sep 2017 01:08:00: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:08:00: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:08:06: 1000000 INFO @ Sun, 03 Sep 2017 01:08:06: 1000000 INFO @ Sun, 03 Sep 2017 01:08:06: 1000000 INFO @ Sun, 03 Sep 2017 01:08:12: 2000000 INFO @ Sun, 03 Sep 2017 01:08:12: 2000000 INFO @ Sun, 03 Sep 2017 01:08:12: 2000000 INFO @ Sun, 03 Sep 2017 01:08:18: 3000000 INFO @ Sun, 03 Sep 2017 01:08:19: 3000000 INFO @ Sun, 03 Sep 2017 01:08:19: 3000000 INFO @ Sun, 03 Sep 2017 01:08:24: 4000000 INFO @ Sun, 03 Sep 2017 01:08:25: 4000000 INFO @ Sun, 03 Sep 2017 01:08:25: 4000000 INFO @ Sun, 03 Sep 2017 01:08:31: 5000000 INFO @ Sun, 03 Sep 2017 01:08:31: 5000000 INFO @ Sun, 03 Sep 2017 01:08:31: 5000000 INFO @ Sun, 03 Sep 2017 01:08:37: 6000000 INFO @ Sun, 03 Sep 2017 01:08:37: 6000000 INFO @ Sun, 03 Sep 2017 01:08:37: 6000000 INFO @ Sun, 03 Sep 2017 01:08:43: 7000000 INFO @ Sun, 03 Sep 2017 01:08:44: 7000000 INFO @ Sun, 03 Sep 2017 01:08:44: 7000000 INFO @ Sun, 03 Sep 2017 01:08:50: 8000000 INFO @ Sun, 03 Sep 2017 01:08:50: 8000000 INFO @ Sun, 03 Sep 2017 01:08:50: 8000000 INFO @ Sun, 03 Sep 2017 01:08:56: 9000000 INFO @ Sun, 03 Sep 2017 01:08:56: 9000000 INFO @ Sun, 03 Sep 2017 01:08:56: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:08:56: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:08:56: #1 total tags in treatment: 9082361 INFO @ Sun, 03 Sep 2017 01:08:56: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:08:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:08:57: #1 tags after filtering in treatment: 9082361 INFO @ Sun, 03 Sep 2017 01:08:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:08:57: #1 finished! INFO @ Sun, 03 Sep 2017 01:08:57: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:08:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:08:57: 9000000 INFO @ Sun, 03 Sep 2017 01:08:57: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:08:57: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:08:57: #1 total tags in treatment: 9082361 INFO @ Sun, 03 Sep 2017 01:08:57: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:08:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:08:57: #1 tags after filtering in treatment: 9082361 INFO @ Sun, 03 Sep 2017 01:08:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:08:57: #1 finished! INFO @ Sun, 03 Sep 2017 01:08:57: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:08:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:08:57: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:08:57: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:08:57: #1 total tags in treatment: 9082361 INFO @ Sun, 03 Sep 2017 01:08:57: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:08:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:08:57: #2 number of paired peaks: 544 WARNING @ Sun, 03 Sep 2017 01:08:57: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Sun, 03 Sep 2017 01:08:57: start model_add_line... INFO @ Sun, 03 Sep 2017 01:08:57: start X-correlation... INFO @ Sun, 03 Sep 2017 01:08:57: end of X-cor INFO @ Sun, 03 Sep 2017 01:08:57: #2 finished! INFO @ Sun, 03 Sep 2017 01:08:57: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Sep 2017 01:08:57: #2 alternative fragment length(s) may be 47 bps INFO @ Sun, 03 Sep 2017 01:08:57: #2.2 Generate R script for model : SRX2829096.05_model.r INFO @ Sun, 03 Sep 2017 01:08:57: #1 tags after filtering in treatment: 9082361 INFO @ Sun, 03 Sep 2017 01:08:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:08:57: #1 finished! INFO @ Sun, 03 Sep 2017 01:08:57: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:08:57: #2 looking for paired plus/minus strand peaks... WARNING @ Sun, 03 Sep 2017 01:08:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:08:57: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sun, 03 Sep 2017 01:08:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:08:57: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:08:58: #2 number of paired peaks: 544 WARNING @ Sun, 03 Sep 2017 01:08:58: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Sun, 03 Sep 2017 01:08:58: start model_add_line... INFO @ Sun, 03 Sep 2017 01:08:58: start X-correlation... INFO @ Sun, 03 Sep 2017 01:08:58: end of X-cor INFO @ Sun, 03 Sep 2017 01:08:58: #2 finished! INFO @ Sun, 03 Sep 2017 01:08:58: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Sep 2017 01:08:58: #2 alternative fragment length(s) may be 47 bps INFO @ Sun, 03 Sep 2017 01:08:58: #2.2 Generate R script for model : SRX2829096.20_model.r WARNING @ Sun, 03 Sep 2017 01:08:58: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:08:58: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sun, 03 Sep 2017 01:08:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:08:58: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:08:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:08:58: #2 number of paired peaks: 544 WARNING @ Sun, 03 Sep 2017 01:08:58: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Sun, 03 Sep 2017 01:08:58: start model_add_line... INFO @ Sun, 03 Sep 2017 01:08:58: start X-correlation... INFO @ Sun, 03 Sep 2017 01:08:58: end of X-cor INFO @ Sun, 03 Sep 2017 01:08:58: #2 finished! INFO @ Sun, 03 Sep 2017 01:08:58: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Sep 2017 01:08:58: #2 alternative fragment length(s) may be 47 bps INFO @ Sun, 03 Sep 2017 01:08:58: #2.2 Generate R script for model : SRX2829096.10_model.r WARNING @ Sun, 03 Sep 2017 01:08:58: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:08:58: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sun, 03 Sep 2017 01:08:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:08:58: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:08:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:09:17: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:09:18: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:09:19: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:09:28: #4 Write output xls file... SRX2829096.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:09:28: #4 Write peak in narrowPeak format file... SRX2829096.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:09:28: #4 Write summits bed file... SRX2829096.05_summits.bed INFO @ Sun, 03 Sep 2017 01:09:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2191 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:09:29: #4 Write output xls file... SRX2829096.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:09:29: #4 Write peak in narrowPeak format file... SRX2829096.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:09:29: #4 Write summits bed file... SRX2829096.10_summits.bed INFO @ Sun, 03 Sep 2017 01:09:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1618 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:09:29: #4 Write output xls file... SRX2829096.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:09:29: #4 Write peak in narrowPeak format file... SRX2829096.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:09:29: #4 Write summits bed file... SRX2829096.20_summits.bed INFO @ Sun, 03 Sep 2017 01:09:29: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1146 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。