Job ID = 10845178 sra ファイルのダウンロード中... Completed: 104076K bytes transferred in 11 seconds (76718K 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 2360750 spots for /home/okishinya/chipatlas/results/dm3/SRX2642394/SRR5345734.sra Written 2360750 spots for /home/okishinya/chipatlas/results/dm3/SRX2642394/SRR5345734.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: 00:01:20 2360750 reads; of these: 2360750 (100.00%) were unpaired; of these: 168356 (7.13%) aligned 0 times 1630583 (69.07%) aligned exactly 1 time 561811 (23.80%) aligned >1 times 92.87% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 25049 / 2192394 = 0.0114 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, 04 Jul 2018 09:28:38: # Command line: callpeak -t SRX2642394.bam -f BAM -g dm -n SRX2642394.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2642394.05 # format = BAM # ChIP-seq file = ['SRX2642394.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, 04 Jul 2018 09:28:38: # Command line: callpeak -t SRX2642394.bam -f BAM -g dm -n SRX2642394.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2642394.20 # format = BAM # ChIP-seq file = ['SRX2642394.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, 04 Jul 2018 09:28:38: # Command line: callpeak -t SRX2642394.bam -f BAM -g dm -n SRX2642394.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2642394.10 # format = BAM # ChIP-seq file = ['SRX2642394.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, 04 Jul 2018 09:28:38: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:28:38: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:28:38: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:28:38: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:28:38: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:28:38: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:28:47: 1000000 INFO @ Wed, 04 Jul 2018 09:28:47: 1000000 INFO @ Wed, 04 Jul 2018 09:28:47: 1000000 INFO @ Wed, 04 Jul 2018 09:28:55: 2000000 INFO @ Wed, 04 Jul 2018 09:28:56: 2000000 INFO @ Wed, 04 Jul 2018 09:28:56: 2000000 INFO @ Wed, 04 Jul 2018 09:28:57: #1 tag size is determined as 97 bps INFO @ Wed, 04 Jul 2018 09:28:57: #1 tag size = 97 INFO @ Wed, 04 Jul 2018 09:28:57: #1 total tags in treatment: 2167345 INFO @ Wed, 04 Jul 2018 09:28:57: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:28:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:28:57: #1 tags after filtering in treatment: 2167345 INFO @ Wed, 04 Jul 2018 09:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:28:57: #1 finished! INFO @ Wed, 04 Jul 2018 09:28:57: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:28:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:28:57: #2 number of paired peaks: 196 WARNING @ Wed, 04 Jul 2018 09:28:57: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Wed, 04 Jul 2018 09:28:57: start model_add_line... INFO @ Wed, 04 Jul 2018 09:28:57: start X-correlation... INFO @ Wed, 04 Jul 2018 09:28:57: end of X-cor INFO @ Wed, 04 Jul 2018 09:28:57: #2 finished! INFO @ Wed, 04 Jul 2018 09:28:57: #2 predicted fragment length is 108 bps INFO @ Wed, 04 Jul 2018 09:28:57: #2 alternative fragment length(s) may be 108,488,570,579,586 bps INFO @ Wed, 04 Jul 2018 09:28:57: #2.2 Generate R script for model : SRX2642394.20_model.r WARNING @ Wed, 04 Jul 2018 09:28:57: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:28:57: #2 You may need to consider one of the other alternative d(s): 108,488,570,579,586 WARNING @ Wed, 04 Jul 2018 09:28:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:28:57: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:28:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:28:58: #1 tag size is determined as 97 bps INFO @ Wed, 04 Jul 2018 09:28:58: #1 tag size = 97 INFO @ Wed, 04 Jul 2018 09:28:58: #1 total tags in treatment: 2167345 INFO @ Wed, 04 Jul 2018 09:28:58: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:28:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:28:58: #1 tags after filtering in treatment: 2167345 INFO @ Wed, 04 Jul 2018 09:28:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:28:58: #1 finished! INFO @ Wed, 04 Jul 2018 09:28:58: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:28:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:28:58: #1 tag size is determined as 97 bps INFO @ Wed, 04 Jul 2018 09:28:58: #1 tag size = 97 INFO @ Wed, 04 Jul 2018 09:28:58: #1 total tags in treatment: 2167345 INFO @ Wed, 04 Jul 2018 09:28:58: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:28:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:28:58: #1 tags after filtering in treatment: 2167345 INFO @ Wed, 04 Jul 2018 09:28:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:28:58: #1 finished! INFO @ Wed, 04 Jul 2018 09:28:58: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:28:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:28:58: #2 number of paired peaks: 196 WARNING @ Wed, 04 Jul 2018 09:28:58: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Wed, 04 Jul 2018 09:28:58: start model_add_line... INFO @ Wed, 04 Jul 2018 09:28:58: start X-correlation... INFO @ Wed, 04 Jul 2018 09:28:58: end of X-cor INFO @ Wed, 04 Jul 2018 09:28:58: #2 finished! INFO @ Wed, 04 Jul 2018 09:28:58: #2 predicted fragment length is 108 bps INFO @ Wed, 04 Jul 2018 09:28:58: #2 alternative fragment length(s) may be 108,488,570,579,586 bps INFO @ Wed, 04 Jul 2018 09:28:58: #2.2 Generate R script for model : SRX2642394.10_model.r WARNING @ Wed, 04 Jul 2018 09:28:58: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:28:58: #2 You may need to consider one of the other alternative d(s): 108,488,570,579,586 WARNING @ Wed, 04 Jul 2018 09:28:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:28:58: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:28:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:28:58: #2 number of paired peaks: 196 WARNING @ Wed, 04 Jul 2018 09:28:58: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Wed, 04 Jul 2018 09:28:58: start model_add_line... INFO @ Wed, 04 Jul 2018 09:28:58: start X-correlation... INFO @ Wed, 04 Jul 2018 09:28:58: end of X-cor INFO @ Wed, 04 Jul 2018 09:28:58: #2 finished! INFO @ Wed, 04 Jul 2018 09:28:58: #2 predicted fragment length is 108 bps INFO @ Wed, 04 Jul 2018 09:28:58: #2 alternative fragment length(s) may be 108,488,570,579,586 bps INFO @ Wed, 04 Jul 2018 09:28:58: #2.2 Generate R script for model : SRX2642394.05_model.r WARNING @ Wed, 04 Jul 2018 09:28:58: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:28:58: #2 You may need to consider one of the other alternative d(s): 108,488,570,579,586 WARNING @ Wed, 04 Jul 2018 09:28:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:28:58: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:28:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:29:02: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:29:03: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:29:03: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:29:05: #4 Write output xls file... SRX2642394.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:29:05: #4 Write peak in narrowPeak format file... SRX2642394.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:29:05: #4 Write summits bed file... SRX2642394.20_summits.bed INFO @ Wed, 04 Jul 2018 09:29:05: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:29:06: #4 Write output xls file... SRX2642394.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:29:06: #4 Write peak in narrowPeak format file... SRX2642394.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:29:06: #4 Write summits bed file... SRX2642394.05_summits.bed INFO @ Wed, 04 Jul 2018 09:29:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (180 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:29:06: #4 Write output xls file... SRX2642394.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:29:06: #4 Write peak in narrowPeak format file... SRX2642394.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:29:06: #4 Write summits bed file... SRX2642394.10_summits.bed INFO @ Wed, 04 Jul 2018 09:29:06: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (96 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。