Job ID = 11171303 sra ファイルのダウンロード中... Completed: 531634K bytes transferred in 15 seconds (284430K 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 11884963 spots for /home/okishinya/chipatlas/results/dm3/SRX3511940/SRR6418925.sra Written 11884963 spots for /home/okishinya/chipatlas/results/dm3/SRX3511940/SRR6418925.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: 00:00:00 Multiseed full-index search: 00:05:52 11884963 reads; of these: 11884963 (100.00%) were unpaired; of these: 2276086 (19.15%) aligned 0 times 7795451 (65.59%) aligned exactly 1 time 1813426 (15.26%) aligned >1 times 80.85% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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] 745647 / 9608877 = 0.0776 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 @ Sat, 08 Sep 2018 13:44:24: # Command line: callpeak -t SRX3511940.bam -f BAM -g dm -n SRX3511940.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3511940.10 # format = BAM # ChIP-seq file = ['SRX3511940.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 @ Sat, 08 Sep 2018 13:44:24: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:44:24: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:44:24: # Command line: callpeak -t SRX3511940.bam -f BAM -g dm -n SRX3511940.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3511940.20 # format = BAM # ChIP-seq file = ['SRX3511940.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 @ Sat, 08 Sep 2018 13:44:24: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:44:24: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:44:24: # Command line: callpeak -t SRX3511940.bam -f BAM -g dm -n SRX3511940.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3511940.05 # format = BAM # ChIP-seq file = ['SRX3511940.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 @ Sat, 08 Sep 2018 13:44:24: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:44:24: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:44:33: 1000000 INFO @ Sat, 08 Sep 2018 13:44:33: 1000000 INFO @ Sat, 08 Sep 2018 13:44:33: 1000000 INFO @ Sat, 08 Sep 2018 13:44:41: 2000000 INFO @ Sat, 08 Sep 2018 13:44:41: 2000000 INFO @ Sat, 08 Sep 2018 13:44:41: 2000000 INFO @ Sat, 08 Sep 2018 13:44:50: 3000000 INFO @ Sat, 08 Sep 2018 13:44:50: 3000000 INFO @ Sat, 08 Sep 2018 13:44:50: 3000000 INFO @ Sat, 08 Sep 2018 13:44:58: 4000000 INFO @ Sat, 08 Sep 2018 13:44:59: 4000000 INFO @ Sat, 08 Sep 2018 13:44:59: 4000000 INFO @ Sat, 08 Sep 2018 13:45:07: 5000000 INFO @ Sat, 08 Sep 2018 13:45:08: 5000000 INFO @ Sat, 08 Sep 2018 13:45:09: 5000000 INFO @ Sat, 08 Sep 2018 13:45:16: 6000000 INFO @ Sat, 08 Sep 2018 13:45:17: 6000000 INFO @ Sat, 08 Sep 2018 13:45:18: 6000000 INFO @ Sat, 08 Sep 2018 13:45:26: 7000000 INFO @ Sat, 08 Sep 2018 13:45:26: 7000000 INFO @ Sat, 08 Sep 2018 13:45:28: 7000000 INFO @ Sat, 08 Sep 2018 13:45:35: 8000000 INFO @ Sat, 08 Sep 2018 13:45:36: 8000000 INFO @ Sat, 08 Sep 2018 13:45:37: 8000000 INFO @ Sat, 08 Sep 2018 13:45:43: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:45:43: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:45:43: #1 total tags in treatment: 8863230 INFO @ Sat, 08 Sep 2018 13:45:43: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:45:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:45:43: #1 tags after filtering in treatment: 8863230 INFO @ Sat, 08 Sep 2018 13:45:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:45:43: #1 finished! INFO @ Sat, 08 Sep 2018 13:45:43: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:45:44: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:45:44: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:45:44: #1 total tags in treatment: 8863230 INFO @ Sat, 08 Sep 2018 13:45:44: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:45:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:45:44: #1 tags after filtering in treatment: 8863230 INFO @ Sat, 08 Sep 2018 13:45:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:45:44: #1 finished! INFO @ Sat, 08 Sep 2018 13:45:44: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:45:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:45:44: #2 number of paired peaks: 2482 INFO @ Sat, 08 Sep 2018 13:45:44: start model_add_line... INFO @ Sat, 08 Sep 2018 13:45:44: start X-correlation... INFO @ Sat, 08 Sep 2018 13:45:44: end of X-cor INFO @ Sat, 08 Sep 2018 13:45:44: #2 finished! INFO @ Sat, 08 Sep 2018 13:45:44: #2 predicted fragment length is 190 bps INFO @ Sat, 08 Sep 2018 13:45:44: #2 alternative fragment length(s) may be 190 bps INFO @ Sat, 08 Sep 2018 13:45:44: #2.2 Generate R script for model : SRX3511940.20_model.r WARNING @ Sat, 08 Sep 2018 13:45:44: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:45:44: #2 You may need to consider one of the other alternative d(s): 190 WARNING @ Sat, 08 Sep 2018 13:45:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:45:44: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:45:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:45:45: #2 number of paired peaks: 2482 INFO @ Sat, 08 Sep 2018 13:45:45: start model_add_line... INFO @ Sat, 08 Sep 2018 13:45:45: start X-correlation... INFO @ Sat, 08 Sep 2018 13:45:45: end of X-cor INFO @ Sat, 08 Sep 2018 13:45:45: #2 finished! INFO @ Sat, 08 Sep 2018 13:45:45: #2 predicted fragment length is 190 bps INFO @ Sat, 08 Sep 2018 13:45:45: #2 alternative fragment length(s) may be 190 bps INFO @ Sat, 08 Sep 2018 13:45:45: #2.2 Generate R script for model : SRX3511940.05_model.r WARNING @ Sat, 08 Sep 2018 13:45:45: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:45:45: #2 You may need to consider one of the other alternative d(s): 190 WARNING @ Sat, 08 Sep 2018 13:45:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:45:45: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:45:45: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:45:45: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:45:45: #1 total tags in treatment: 8863230 INFO @ Sat, 08 Sep 2018 13:45:45: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:45:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:45:45: #1 tags after filtering in treatment: 8863230 INFO @ Sat, 08 Sep 2018 13:45:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:45:45: #1 finished! INFO @ Sat, 08 Sep 2018 13:45:45: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:45:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:45:46: #2 number of paired peaks: 2482 INFO @ Sat, 08 Sep 2018 13:45:46: start model_add_line... INFO @ Sat, 08 Sep 2018 13:45:46: start X-correlation... INFO @ Sat, 08 Sep 2018 13:45:46: end of X-cor INFO @ Sat, 08 Sep 2018 13:45:46: #2 finished! INFO @ Sat, 08 Sep 2018 13:45:46: #2 predicted fragment length is 190 bps INFO @ Sat, 08 Sep 2018 13:45:46: #2 alternative fragment length(s) may be 190 bps INFO @ Sat, 08 Sep 2018 13:45:46: #2.2 Generate R script for model : SRX3511940.10_model.r WARNING @ Sat, 08 Sep 2018 13:45:46: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:45:46: #2 You may need to consider one of the other alternative d(s): 190 WARNING @ Sat, 08 Sep 2018 13:45:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:45:46: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:45:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:46:08: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:46:09: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:46:09: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:46:20: #4 Write output xls file... SRX3511940.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:46:20: #4 Write peak in narrowPeak format file... SRX3511940.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:46:21: #4 Write summits bed file... SRX3511940.05_summits.bed INFO @ Sat, 08 Sep 2018 13:46:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1525 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:46:21: #4 Write output xls file... SRX3511940.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:46:21: #4 Write peak in narrowPeak format file... SRX3511940.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:46:21: #4 Write summits bed file... SRX3511940.10_summits.bed INFO @ Sat, 08 Sep 2018 13:46:21: Done! INFO @ Sat, 08 Sep 2018 13:46:21: #4 Write output xls file... SRX3511940.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:46:21: #4 Write peak in narrowPeak format file... SRX3511940.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:46:21: #4 Write summits bed file... SRX3511940.20_summits.bed INFO @ Sat, 08 Sep 2018 13:46:21: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (10 chroms): 45 millis pass2 - checking and writing primary data (180 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。