Job ID = 11171230 sra ファイルのダウンロード中... Completed: 358219K bytes transferred in 15 seconds (195370K 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 18681022 spots for /home/okishinya/chipatlas/results/dm3/SRX2618549/SRR5319103.sra Written 18681022 spots for /home/okishinya/chipatlas/results/dm3/SRX2618549/SRR5319103.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: 00:09:18 18681022 reads; of these: 18681022 (100.00%) were unpaired; of these: 590061 (3.16%) aligned 0 times 11729504 (62.79%) aligned exactly 1 time 6361457 (34.05%) aligned >1 times 96.84% overall alignment rate Time searching: 00:09:18 Overall time: 00:09:18 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] 2409452 / 18090961 = 0.1332 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 13:21:37: # Command line: callpeak -t SRX2618549.bam -f BAM -g dm -n SRX2618549.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618549.10 # format = BAM # ChIP-seq file = ['SRX2618549.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 13:21:37: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:21:37: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:21:37: # Command line: callpeak -t SRX2618549.bam -f BAM -g dm -n SRX2618549.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618549.20 # format = BAM # ChIP-seq file = ['SRX2618549.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 13:21:37: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:21:37: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:21:37: # Command line: callpeak -t SRX2618549.bam -f BAM -g dm -n SRX2618549.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618549.05 # format = BAM # ChIP-seq file = ['SRX2618549.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 13:21:37: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:21:37: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:21:44: 1000000 INFO @ Sat, 08 Sep 2018 13:21:44: 1000000 INFO @ Sat, 08 Sep 2018 13:21:44: 1000000 INFO @ Sat, 08 Sep 2018 13:21:51: 2000000 INFO @ Sat, 08 Sep 2018 13:21:51: 2000000 INFO @ Sat, 08 Sep 2018 13:21:51: 2000000 INFO @ Sat, 08 Sep 2018 13:21:57: 3000000 INFO @ Sat, 08 Sep 2018 13:21:58: 3000000 INFO @ Sat, 08 Sep 2018 13:21:58: 3000000 INFO @ Sat, 08 Sep 2018 13:22:04: 4000000 INFO @ Sat, 08 Sep 2018 13:22:04: 4000000 INFO @ Sat, 08 Sep 2018 13:22:05: 4000000 INFO @ Sat, 08 Sep 2018 13:22:11: 5000000 INFO @ Sat, 08 Sep 2018 13:22:11: 5000000 INFO @ Sat, 08 Sep 2018 13:22:12: 5000000 INFO @ Sat, 08 Sep 2018 13:22:19: 6000000 INFO @ Sat, 08 Sep 2018 13:22:19: 6000000 INFO @ Sat, 08 Sep 2018 13:22:20: 6000000 INFO @ Sat, 08 Sep 2018 13:22:26: 7000000 INFO @ Sat, 08 Sep 2018 13:22:26: 7000000 INFO @ Sat, 08 Sep 2018 13:22:27: 7000000 INFO @ Sat, 08 Sep 2018 13:22:33: 8000000 INFO @ Sat, 08 Sep 2018 13:22:33: 8000000 INFO @ Sat, 08 Sep 2018 13:22:35: 8000000 INFO @ Sat, 08 Sep 2018 13:22:40: 9000000 INFO @ Sat, 08 Sep 2018 13:22:40: 9000000 INFO @ Sat, 08 Sep 2018 13:22:42: 9000000 INFO @ Sat, 08 Sep 2018 13:22:47: 10000000 INFO @ Sat, 08 Sep 2018 13:22:47: 10000000 INFO @ Sat, 08 Sep 2018 13:22:50: 10000000 INFO @ Sat, 08 Sep 2018 13:22:54: 11000000 INFO @ Sat, 08 Sep 2018 13:22:54: 11000000 INFO @ Sat, 08 Sep 2018 13:22:57: 11000000 INFO @ Sat, 08 Sep 2018 13:23:01: 12000000 INFO @ Sat, 08 Sep 2018 13:23:01: 12000000 INFO @ Sat, 08 Sep 2018 13:23:05: 12000000 INFO @ Sat, 08 Sep 2018 13:23:09: 13000000 INFO @ Sat, 08 Sep 2018 13:23:09: 13000000 INFO @ Sat, 08 Sep 2018 13:23:12: 13000000 INFO @ Sat, 08 Sep 2018 13:23:16: 14000000 INFO @ Sat, 08 Sep 2018 13:23:16: 14000000 INFO @ Sat, 08 Sep 2018 13:23:20: 14000000 INFO @ Sat, 08 Sep 2018 13:23:23: 15000000 INFO @ Sat, 08 Sep 2018 13:23:23: 15000000 INFO @ Sat, 08 Sep 2018 13:23:27: 15000000 INFO @ Sat, 08 Sep 2018 13:23:28: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:23:28: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:23:28: #1 total tags in treatment: 15681509 INFO @ Sat, 08 Sep 2018 13:23:28: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:23:28: #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 13:23:28: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:23:28: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:23:28: #1 total tags in treatment: 15681509 INFO @ Sat, 08 Sep 2018 13:23:28: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:23:28: #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 13:23:28: #1 tags after filtering in treatment: 15681509 INFO @ Sat, 08 Sep 2018 13:23:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:23:28: #1 finished! INFO @ Sat, 08 Sep 2018 13:23:28: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:23:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:23:28: #1 tags after filtering in treatment: 15681509 INFO @ Sat, 08 Sep 2018 13:23:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:23:28: #1 finished! INFO @ Sat, 08 Sep 2018 13:23:28: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:23:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:23:29: #2 number of paired peaks: 115 WARNING @ Sat, 08 Sep 2018 13:23:29: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 08 Sep 2018 13:23:29: start model_add_line... INFO @ Sat, 08 Sep 2018 13:23:29: start X-correlation... INFO @ Sat, 08 Sep 2018 13:23:29: end of X-cor INFO @ Sat, 08 Sep 2018 13:23:29: #2 finished! INFO @ Sat, 08 Sep 2018 13:23:29: #2 predicted fragment length is 44 bps INFO @ Sat, 08 Sep 2018 13:23:29: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sat, 08 Sep 2018 13:23:29: #2.2 Generate R script for model : SRX2618549.20_model.r WARNING @ Sat, 08 Sep 2018 13:23:29: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:23:29: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sat, 08 Sep 2018 13:23:29: #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 13:23:29: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:23:29: #2 number of paired peaks: 115 WARNING @ Sat, 08 Sep 2018 13:23:29: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 08 Sep 2018 13:23:29: start model_add_line... INFO @ Sat, 08 Sep 2018 13:23:29: start X-correlation... INFO @ Sat, 08 Sep 2018 13:23:29: end of X-cor INFO @ Sat, 08 Sep 2018 13:23:29: #2 finished! INFO @ Sat, 08 Sep 2018 13:23:29: #2 predicted fragment length is 44 bps INFO @ Sat, 08 Sep 2018 13:23:29: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sat, 08 Sep 2018 13:23:29: #2.2 Generate R script for model : SRX2618549.10_model.r WARNING @ Sat, 08 Sep 2018 13:23:29: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:23:29: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sat, 08 Sep 2018 13:23:29: #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 13:23:29: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:23:31: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:23:31: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:23:31: #1 total tags in treatment: 15681509 INFO @ Sat, 08 Sep 2018 13:23:31: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:23:31: #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 13:23:32: #1 tags after filtering in treatment: 15681509 INFO @ Sat, 08 Sep 2018 13:23:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:23:32: #1 finished! INFO @ Sat, 08 Sep 2018 13:23:32: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:23:33: #2 number of paired peaks: 115 WARNING @ Sat, 08 Sep 2018 13:23:33: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 08 Sep 2018 13:23:33: start model_add_line... INFO @ Sat, 08 Sep 2018 13:23:33: start X-correlation... INFO @ Sat, 08 Sep 2018 13:23:33: end of X-cor INFO @ Sat, 08 Sep 2018 13:23:33: #2 finished! INFO @ Sat, 08 Sep 2018 13:23:33: #2 predicted fragment length is 44 bps INFO @ Sat, 08 Sep 2018 13:23:33: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sat, 08 Sep 2018 13:23:33: #2.2 Generate R script for model : SRX2618549.05_model.r WARNING @ Sat, 08 Sep 2018 13:23:33: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:23:33: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sat, 08 Sep 2018 13:23:33: #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 13:23:33: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:24:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:24:02: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:24:04: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:24:17: #4 Write output xls file... SRX2618549.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:24:17: #4 Write peak in narrowPeak format file... SRX2618549.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:24:17: #4 Write summits bed file... SRX2618549.20_summits.bed INFO @ Sat, 08 Sep 2018 13:24:17: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (710 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:24:18: #4 Write output xls file... SRX2618549.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:24:18: #4 Write peak in narrowPeak format file... SRX2618549.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:24:18: #4 Write summits bed file... SRX2618549.10_summits.bed INFO @ Sat, 08 Sep 2018 13:24:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1477 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:24:22: #4 Write output xls file... SRX2618549.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:24:22: #4 Write peak in narrowPeak format file... SRX2618549.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:24:22: #4 Write summits bed file... SRX2618549.05_summits.bed INFO @ Sat, 08 Sep 2018 13:24:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2123 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。