Job ID = 11598004 sra ファイルのダウンロード中... Completed: 394859K bytes transferred in 6 seconds (471812K 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 17456669 spots for /home/okishinya/chipatlas/results/dm3/SRX4664659/SRR7813086.sra Written 17456669 spots for /home/okishinya/chipatlas/results/dm3/SRX4664659/SRR7813086.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: 00:07:25 17456669 reads; of these: 17456669 (100.00%) were unpaired; of these: 425059 (2.43%) aligned 0 times 11796345 (67.58%) aligned exactly 1 time 5235265 (29.99%) aligned >1 times 97.57% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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] 1813918 / 17031610 = 0.1065 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 @ Wed, 30 Jan 2019 16:57:12: # Command line: callpeak -t SRX4664659.bam -f BAM -g dm -n SRX4664659.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664659.05 # format = BAM # ChIP-seq file = ['SRX4664659.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 @ Wed, 30 Jan 2019 16:57:12: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:57:12: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:57:12: # Command line: callpeak -t SRX4664659.bam -f BAM -g dm -n SRX4664659.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664659.20 # format = BAM # ChIP-seq file = ['SRX4664659.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 @ Wed, 30 Jan 2019 16:57:12: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:57:12: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:57:12: # Command line: callpeak -t SRX4664659.bam -f BAM -g dm -n SRX4664659.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664659.10 # format = BAM # ChIP-seq file = ['SRX4664659.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 @ Wed, 30 Jan 2019 16:57:12: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:57:12: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:57:18: 1000000 INFO @ Wed, 30 Jan 2019 16:57:18: 1000000 INFO @ Wed, 30 Jan 2019 16:57:19: 1000000 INFO @ Wed, 30 Jan 2019 16:57:24: 2000000 INFO @ Wed, 30 Jan 2019 16:57:25: 2000000 INFO @ Wed, 30 Jan 2019 16:57:27: 2000000 INFO @ Wed, 30 Jan 2019 16:57:30: 3000000 INFO @ Wed, 30 Jan 2019 16:57:31: 3000000 INFO @ Wed, 30 Jan 2019 16:57:35: 3000000 INFO @ Wed, 30 Jan 2019 16:57:36: 4000000 INFO @ Wed, 30 Jan 2019 16:57:38: 4000000 INFO @ Wed, 30 Jan 2019 16:57:43: 4000000 INFO @ Wed, 30 Jan 2019 16:57:43: 5000000 INFO @ Wed, 30 Jan 2019 16:57:45: 5000000 INFO @ Wed, 30 Jan 2019 16:57:49: 6000000 INFO @ Wed, 30 Jan 2019 16:57:50: 5000000 INFO @ Wed, 30 Jan 2019 16:57:51: 6000000 INFO @ Wed, 30 Jan 2019 16:57:55: 7000000 INFO @ Wed, 30 Jan 2019 16:57:56: 6000000 INFO @ Wed, 30 Jan 2019 16:57:58: 7000000 INFO @ Wed, 30 Jan 2019 16:58:01: 8000000 INFO @ Wed, 30 Jan 2019 16:58:03: 7000000 INFO @ Wed, 30 Jan 2019 16:58:04: 8000000 INFO @ Wed, 30 Jan 2019 16:58:07: 9000000 INFO @ Wed, 30 Jan 2019 16:58:10: 8000000 INFO @ Wed, 30 Jan 2019 16:58:10: 9000000 INFO @ Wed, 30 Jan 2019 16:58:13: 10000000 INFO @ Wed, 30 Jan 2019 16:58:16: 10000000 INFO @ Wed, 30 Jan 2019 16:58:16: 9000000 INFO @ Wed, 30 Jan 2019 16:58:19: 11000000 INFO @ Wed, 30 Jan 2019 16:58:22: 11000000 INFO @ Wed, 30 Jan 2019 16:58:23: 10000000 INFO @ Wed, 30 Jan 2019 16:58:25: 12000000 INFO @ Wed, 30 Jan 2019 16:58:28: 12000000 INFO @ Wed, 30 Jan 2019 16:58:30: 11000000 INFO @ Wed, 30 Jan 2019 16:58:32: 13000000 INFO @ Wed, 30 Jan 2019 16:58:34: 13000000 INFO @ Wed, 30 Jan 2019 16:58:37: 12000000 INFO @ Wed, 30 Jan 2019 16:58:39: 14000000 INFO @ Wed, 30 Jan 2019 16:58:40: 14000000 INFO @ Wed, 30 Jan 2019 16:58:44: 13000000 INFO @ Wed, 30 Jan 2019 16:58:45: 15000000 INFO @ Wed, 30 Jan 2019 16:58:45: 15000000 INFO @ Wed, 30 Jan 2019 16:58:47: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:58:47: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:58:47: #1 total tags in treatment: 15217692 INFO @ Wed, 30 Jan 2019 16:58:47: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:58:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:58:47: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:58:47: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:58:47: #1 total tags in treatment: 15217692 INFO @ Wed, 30 Jan 2019 16:58:47: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:58:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:58:47: #1 tags after filtering in treatment: 15217692 INFO @ Wed, 30 Jan 2019 16:58:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:58:47: #1 finished! INFO @ Wed, 30 Jan 2019 16:58:47: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:58:47: #1 tags after filtering in treatment: 15217692 INFO @ Wed, 30 Jan 2019 16:58:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:58:47: #1 finished! INFO @ Wed, 30 Jan 2019 16:58:47: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:58:48: #2 number of paired peaks: 969 WARNING @ Wed, 30 Jan 2019 16:58:48: Fewer paired peaks (969) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 969 pairs to build model! INFO @ Wed, 30 Jan 2019 16:58:48: start model_add_line... INFO @ Wed, 30 Jan 2019 16:58:48: #2 number of paired peaks: 969 WARNING @ Wed, 30 Jan 2019 16:58:48: Fewer paired peaks (969) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 969 pairs to build model! INFO @ Wed, 30 Jan 2019 16:58:48: start model_add_line... INFO @ Wed, 30 Jan 2019 16:58:49: start X-correlation... INFO @ Wed, 30 Jan 2019 16:58:49: end of X-cor INFO @ Wed, 30 Jan 2019 16:58:49: #2 finished! INFO @ Wed, 30 Jan 2019 16:58:49: #2 predicted fragment length is 48 bps INFO @ Wed, 30 Jan 2019 16:58:49: #2 alternative fragment length(s) may be 4,48 bps INFO @ Wed, 30 Jan 2019 16:58:49: #2.2 Generate R script for model : SRX4664659.20_model.r WARNING @ Wed, 30 Jan 2019 16:58:49: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:58:49: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Wed, 30 Jan 2019 16:58:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:58:49: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:58:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:58:49: start X-correlation... INFO @ Wed, 30 Jan 2019 16:58:49: end of X-cor INFO @ Wed, 30 Jan 2019 16:58:49: #2 finished! INFO @ Wed, 30 Jan 2019 16:58:49: #2 predicted fragment length is 48 bps INFO @ Wed, 30 Jan 2019 16:58:49: #2 alternative fragment length(s) may be 4,48 bps INFO @ Wed, 30 Jan 2019 16:58:49: #2.2 Generate R script for model : SRX4664659.05_model.r WARNING @ Wed, 30 Jan 2019 16:58:49: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:58:49: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Wed, 30 Jan 2019 16:58:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:58:49: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:58:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:58:51: 14000000 INFO @ Wed, 30 Jan 2019 16:58:57: 15000000 INFO @ Wed, 30 Jan 2019 16:58:59: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:58:59: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:58:59: #1 total tags in treatment: 15217692 INFO @ Wed, 30 Jan 2019 16:58:59: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:58:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:58:59: #1 tags after filtering in treatment: 15217692 INFO @ Wed, 30 Jan 2019 16:58:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:58:59: #1 finished! INFO @ Wed, 30 Jan 2019 16:58:59: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:59:00: #2 number of paired peaks: 969 WARNING @ Wed, 30 Jan 2019 16:59:00: Fewer paired peaks (969) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 969 pairs to build model! INFO @ Wed, 30 Jan 2019 16:59:00: start model_add_line... INFO @ Wed, 30 Jan 2019 16:59:00: start X-correlation... INFO @ Wed, 30 Jan 2019 16:59:00: end of X-cor INFO @ Wed, 30 Jan 2019 16:59:00: #2 finished! INFO @ Wed, 30 Jan 2019 16:59:00: #2 predicted fragment length is 48 bps INFO @ Wed, 30 Jan 2019 16:59:00: #2 alternative fragment length(s) may be 4,48 bps INFO @ Wed, 30 Jan 2019 16:59:00: #2.2 Generate R script for model : SRX4664659.10_model.r WARNING @ Wed, 30 Jan 2019 16:59:00: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:59:00: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Wed, 30 Jan 2019 16:59:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:59:00: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:59:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:59:21: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:59:22: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:59:32: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:59:37: #4 Write output xls file... SRX4664659.20_peaks.xls INFO @ Wed, 30 Jan 2019 16:59:37: #4 Write peak in narrowPeak format file... SRX4664659.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:59:37: #4 Write summits bed file... SRX4664659.20_summits.bed INFO @ Wed, 30 Jan 2019 16:59:37: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1452 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:59:39: #4 Write output xls file... SRX4664659.05_peaks.xls INFO @ Wed, 30 Jan 2019 16:59:39: #4 Write peak in narrowPeak format file... SRX4664659.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:59:39: #4 Write summits bed file... SRX4664659.05_summits.bed INFO @ Wed, 30 Jan 2019 16:59:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3846 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:59:50: #4 Write output xls file... SRX4664659.10_peaks.xls INFO @ Wed, 30 Jan 2019 16:59:50: #4 Write peak in narrowPeak format file... SRX4664659.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:59:50: #4 Write summits bed file... SRX4664659.10_summits.bed INFO @ Wed, 30 Jan 2019 16:59:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2583 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。