Job ID = 10480755 sra ファイルのダウンロード中... Completed: 489427K bytes transferred in 14 seconds (280808K 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 19946230 spots for /home/okishinya/chipatlas/results/dm3/SRX3380814/SRR6278177.sra Written 19946230 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: 00:00:00 Multiseed full-index search: 00:07:38 19946230 reads; of these: 19946230 (100.00%) were unpaired; of these: 1011274 (5.07%) aligned 0 times 14107698 (70.73%) aligned exactly 1 time 4827258 (24.20%) aligned >1 times 94.93% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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] 2731708 / 18934956 = 0.1443 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 @ Fri, 16 Mar 2018 08:01:14: # Command line: callpeak -t SRX3380814.bam -f BAM -g dm -n SRX3380814.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380814.05 # format = BAM # ChIP-seq file = ['SRX3380814.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 @ Fri, 16 Mar 2018 08:01:14: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:01:14: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:01:14: # Command line: callpeak -t SRX3380814.bam -f BAM -g dm -n SRX3380814.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380814.20 # format = BAM # ChIP-seq file = ['SRX3380814.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 @ Fri, 16 Mar 2018 08:01:14: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:01:14: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:01:14: # Command line: callpeak -t SRX3380814.bam -f BAM -g dm -n SRX3380814.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380814.10 # format = BAM # ChIP-seq file = ['SRX3380814.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 @ Fri, 16 Mar 2018 08:01:14: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:01:14: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:01:20: 1000000 INFO @ Fri, 16 Mar 2018 08:01:20: 1000000 INFO @ Fri, 16 Mar 2018 08:01:20: 1000000 INFO @ Fri, 16 Mar 2018 08:01:26: 2000000 INFO @ Fri, 16 Mar 2018 08:01:26: 2000000 INFO @ Fri, 16 Mar 2018 08:01:26: 2000000 INFO @ Fri, 16 Mar 2018 08:01:32: 3000000 INFO @ Fri, 16 Mar 2018 08:01:32: 3000000 INFO @ Fri, 16 Mar 2018 08:01:33: 3000000 INFO @ Fri, 16 Mar 2018 08:01:38: 4000000 INFO @ Fri, 16 Mar 2018 08:01:39: 4000000 INFO @ Fri, 16 Mar 2018 08:01:39: 4000000 INFO @ Fri, 16 Mar 2018 08:01:44: 5000000 INFO @ Fri, 16 Mar 2018 08:01:45: 5000000 INFO @ Fri, 16 Mar 2018 08:01:46: 5000000 INFO @ Fri, 16 Mar 2018 08:01:50: 6000000 INFO @ Fri, 16 Mar 2018 08:01:52: 6000000 INFO @ Fri, 16 Mar 2018 08:01:52: 6000000 INFO @ Fri, 16 Mar 2018 08:01:56: 7000000 INFO @ Fri, 16 Mar 2018 08:01:58: 7000000 INFO @ Fri, 16 Mar 2018 08:01:59: 7000000 INFO @ Fri, 16 Mar 2018 08:02:02: 8000000 INFO @ Fri, 16 Mar 2018 08:02:05: 8000000 INFO @ Fri, 16 Mar 2018 08:02:06: 8000000 INFO @ Fri, 16 Mar 2018 08:02:08: 9000000 INFO @ Fri, 16 Mar 2018 08:02:11: 9000000 INFO @ Fri, 16 Mar 2018 08:02:12: 9000000 INFO @ Fri, 16 Mar 2018 08:02:14: 10000000 INFO @ Fri, 16 Mar 2018 08:02:17: 10000000 INFO @ Fri, 16 Mar 2018 08:02:19: 10000000 INFO @ Fri, 16 Mar 2018 08:02:20: 11000000 INFO @ Fri, 16 Mar 2018 08:02:24: 11000000 INFO @ Fri, 16 Mar 2018 08:02:25: 11000000 INFO @ Fri, 16 Mar 2018 08:02:26: 12000000 INFO @ Fri, 16 Mar 2018 08:02:30: 12000000 INFO @ Fri, 16 Mar 2018 08:02:32: 13000000 INFO @ Fri, 16 Mar 2018 08:02:32: 12000000 INFO @ Fri, 16 Mar 2018 08:02:37: 13000000 INFO @ Fri, 16 Mar 2018 08:02:38: 14000000 INFO @ Fri, 16 Mar 2018 08:02:39: 13000000 INFO @ Fri, 16 Mar 2018 08:02:43: 14000000 INFO @ Fri, 16 Mar 2018 08:02:44: 15000000 INFO @ Fri, 16 Mar 2018 08:02:45: 14000000 INFO @ Fri, 16 Mar 2018 08:02:50: 16000000 INFO @ Fri, 16 Mar 2018 08:02:50: 15000000 INFO @ Fri, 16 Mar 2018 08:02:51: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 08:02:51: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 08:02:51: #1 total tags in treatment: 16203248 INFO @ Fri, 16 Mar 2018 08:02:51: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:02:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:02:51: #1 tags after filtering in treatment: 16203248 INFO @ Fri, 16 Mar 2018 08:02:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:02:51: #1 finished! INFO @ Fri, 16 Mar 2018 08:02:51: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:02:52: 15000000 INFO @ Fri, 16 Mar 2018 08:02:53: #2 number of paired peaks: 183 WARNING @ Fri, 16 Mar 2018 08:02:53: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 16 Mar 2018 08:02:53: start model_add_line... INFO @ Fri, 16 Mar 2018 08:02:53: start X-correlation... INFO @ Fri, 16 Mar 2018 08:02:53: end of X-cor INFO @ Fri, 16 Mar 2018 08:02:53: #2 finished! INFO @ Fri, 16 Mar 2018 08:02:53: #2 predicted fragment length is 47 bps INFO @ Fri, 16 Mar 2018 08:02:53: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 16 Mar 2018 08:02:53: #2.2 Generate R script for model : SRX3380814.10_model.r WARNING @ Fri, 16 Mar 2018 08:02:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 08:02:53: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 16 Mar 2018 08:02:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 08:02:53: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:02:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:02:56: 16000000 INFO @ Fri, 16 Mar 2018 08:02:58: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 08:02:58: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 08:02:58: #1 total tags in treatment: 16203248 INFO @ Fri, 16 Mar 2018 08:02:58: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:02:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:02:58: #1 tags after filtering in treatment: 16203248 INFO @ Fri, 16 Mar 2018 08:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:02:58: #1 finished! INFO @ Fri, 16 Mar 2018 08:02:58: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:02:59: 16000000 INFO @ Fri, 16 Mar 2018 08:02:59: #2 number of paired peaks: 183 WARNING @ Fri, 16 Mar 2018 08:02:59: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 16 Mar 2018 08:02:59: start model_add_line... INFO @ Fri, 16 Mar 2018 08:02:59: start X-correlation... INFO @ Fri, 16 Mar 2018 08:02:59: end of X-cor INFO @ Fri, 16 Mar 2018 08:02:59: #2 finished! INFO @ Fri, 16 Mar 2018 08:02:59: #2 predicted fragment length is 47 bps INFO @ Fri, 16 Mar 2018 08:02:59: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 16 Mar 2018 08:02:59: #2.2 Generate R script for model : SRX3380814.05_model.r WARNING @ Fri, 16 Mar 2018 08:02:59: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 08:02:59: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 16 Mar 2018 08:02:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 08:02:59: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:02:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:03:00: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 08:03:00: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 08:03:00: #1 total tags in treatment: 16203248 INFO @ Fri, 16 Mar 2018 08:03:00: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:03:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:03:00: #1 tags after filtering in treatment: 16203248 INFO @ Fri, 16 Mar 2018 08:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:03:00: #1 finished! INFO @ Fri, 16 Mar 2018 08:03:00: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:03:01: #2 number of paired peaks: 183 WARNING @ Fri, 16 Mar 2018 08:03:01: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 16 Mar 2018 08:03:01: start model_add_line... INFO @ Fri, 16 Mar 2018 08:03:01: start X-correlation... INFO @ Fri, 16 Mar 2018 08:03:01: end of X-cor INFO @ Fri, 16 Mar 2018 08:03:01: #2 finished! INFO @ Fri, 16 Mar 2018 08:03:01: #2 predicted fragment length is 47 bps INFO @ Fri, 16 Mar 2018 08:03:01: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 16 Mar 2018 08:03:01: #2.2 Generate R script for model : SRX3380814.20_model.r WARNING @ Fri, 16 Mar 2018 08:03:01: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 08:03:01: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 16 Mar 2018 08:03:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 08:03:01: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:03:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:03:25: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:03:31: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:03:36: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:03:43: #4 Write output xls file... SRX3380814.10_peaks.xls INFO @ Fri, 16 Mar 2018 08:03:43: #4 Write peak in narrowPeak format file... SRX3380814.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:03:43: #4 Write summits bed file... SRX3380814.10_summits.bed INFO @ Fri, 16 Mar 2018 08:03:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1453 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:03:50: #4 Write output xls file... SRX3380814.05_peaks.xls INFO @ Fri, 16 Mar 2018 08:03:50: #4 Write peak in narrowPeak format file... SRX3380814.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:03:50: #4 Write summits bed file... SRX3380814.05_summits.bed INFO @ Fri, 16 Mar 2018 08:03:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2374 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:03:54: #4 Write output xls file... SRX3380814.20_peaks.xls INFO @ Fri, 16 Mar 2018 08:03:54: #4 Write peak in narrowPeak format file... SRX3380814.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:03:54: #4 Write summits bed file... SRX3380814.20_summits.bed INFO @ Fri, 16 Mar 2018 08:03:54: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (1032 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。