Job ID = 11597782 sra ファイルのダウンロード中... Completed: 371848K bytes transferred in 6 seconds (497822K 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 13811955 spots for /home/okishinya/chipatlas/results/dm3/ERX1432619/ERR1361148.sra Written 13811955 spots for /home/okishinya/chipatlas/results/dm3/ERX1432619/ERR1361148.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: 00:05:45 13811955 reads; of these: 13811955 (100.00%) were unpaired; of these: 2526989 (18.30%) aligned 0 times 7424578 (53.75%) aligned exactly 1 time 3860388 (27.95%) aligned >1 times 81.70% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 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] 3152332 / 11284966 = 0.2793 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 21:28:28: # Command line: callpeak -t ERX1432619.bam -f BAM -g dm -n ERX1432619.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1432619.20 # format = BAM # ChIP-seq file = ['ERX1432619.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 21:28:28: #1 read tag files... INFO @ Wed, 30 Jan 2019 21:28:28: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 21:28:28: # Command line: callpeak -t ERX1432619.bam -f BAM -g dm -n ERX1432619.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1432619.10 # format = BAM # ChIP-seq file = ['ERX1432619.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 21:28:28: #1 read tag files... INFO @ Wed, 30 Jan 2019 21:28:28: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 21:28:28: # Command line: callpeak -t ERX1432619.bam -f BAM -g dm -n ERX1432619.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1432619.05 # format = BAM # ChIP-seq file = ['ERX1432619.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 21:28:28: #1 read tag files... INFO @ Wed, 30 Jan 2019 21:28:28: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 21:28:34: 1000000 INFO @ Wed, 30 Jan 2019 21:28:34: 1000000 INFO @ Wed, 30 Jan 2019 21:28:35: 1000000 INFO @ Wed, 30 Jan 2019 21:28:41: 2000000 INFO @ Wed, 30 Jan 2019 21:28:41: 2000000 INFO @ Wed, 30 Jan 2019 21:28:41: 2000000 INFO @ Wed, 30 Jan 2019 21:28:47: 3000000 INFO @ Wed, 30 Jan 2019 21:28:47: 3000000 INFO @ Wed, 30 Jan 2019 21:28:48: 3000000 INFO @ Wed, 30 Jan 2019 21:28:54: 4000000 INFO @ Wed, 30 Jan 2019 21:28:54: 4000000 INFO @ Wed, 30 Jan 2019 21:28:54: 4000000 INFO @ Wed, 30 Jan 2019 21:29:00: 5000000 INFO @ Wed, 30 Jan 2019 21:29:00: 5000000 INFO @ Wed, 30 Jan 2019 21:29:01: 5000000 INFO @ Wed, 30 Jan 2019 21:29:07: 6000000 INFO @ Wed, 30 Jan 2019 21:29:07: 6000000 INFO @ Wed, 30 Jan 2019 21:29:07: 6000000 INFO @ Wed, 30 Jan 2019 21:29:13: 7000000 INFO @ Wed, 30 Jan 2019 21:29:13: 7000000 INFO @ Wed, 30 Jan 2019 21:29:14: 7000000 INFO @ Wed, 30 Jan 2019 21:29:20: 8000000 INFO @ Wed, 30 Jan 2019 21:29:20: 8000000 INFO @ Wed, 30 Jan 2019 21:29:21: 8000000 INFO @ Wed, 30 Jan 2019 21:29:21: #1 tag size is determined as 44 bps INFO @ Wed, 30 Jan 2019 21:29:21: #1 tag size = 44 INFO @ Wed, 30 Jan 2019 21:29:21: #1 total tags in treatment: 8132634 INFO @ Wed, 30 Jan 2019 21:29:21: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 21:29:21: #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 21:29:21: #1 tag size is determined as 44 bps INFO @ Wed, 30 Jan 2019 21:29:21: #1 tag size = 44 INFO @ Wed, 30 Jan 2019 21:29:21: #1 total tags in treatment: 8132634 INFO @ Wed, 30 Jan 2019 21:29:21: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 21:29:21: #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 21:29:21: #1 tags after filtering in treatment: 8132634 INFO @ Wed, 30 Jan 2019 21:29:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 21:29:21: #1 finished! INFO @ Wed, 30 Jan 2019 21:29:21: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 21:29:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 21:29:21: #1 tags after filtering in treatment: 8132634 INFO @ Wed, 30 Jan 2019 21:29:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 21:29:21: #1 finished! INFO @ Wed, 30 Jan 2019 21:29:21: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 21:29:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 21:29:21: #1 tag size is determined as 44 bps INFO @ Wed, 30 Jan 2019 21:29:21: #1 tag size = 44 INFO @ Wed, 30 Jan 2019 21:29:21: #1 total tags in treatment: 8132634 INFO @ Wed, 30 Jan 2019 21:29:21: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 21:29:21: #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 21:29:22: #2 number of paired peaks: 831 WARNING @ Wed, 30 Jan 2019 21:29:22: Fewer paired peaks (831) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 831 pairs to build model! INFO @ Wed, 30 Jan 2019 21:29:22: start model_add_line... INFO @ Wed, 30 Jan 2019 21:29:22: #1 tags after filtering in treatment: 8132634 INFO @ Wed, 30 Jan 2019 21:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 21:29:22: #1 finished! INFO @ Wed, 30 Jan 2019 21:29:22: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 21:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 21:29:22: #2 number of paired peaks: 831 WARNING @ Wed, 30 Jan 2019 21:29:22: Fewer paired peaks (831) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 831 pairs to build model! INFO @ Wed, 30 Jan 2019 21:29:22: start model_add_line... INFO @ Wed, 30 Jan 2019 21:29:22: start X-correlation... INFO @ Wed, 30 Jan 2019 21:29:22: end of X-cor INFO @ Wed, 30 Jan 2019 21:29:22: #2 finished! INFO @ Wed, 30 Jan 2019 21:29:22: #2 predicted fragment length is 49 bps INFO @ Wed, 30 Jan 2019 21:29:22: #2 alternative fragment length(s) may be 49 bps INFO @ Wed, 30 Jan 2019 21:29:22: #2.2 Generate R script for model : ERX1432619.20_model.r WARNING @ Wed, 30 Jan 2019 21:29:22: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 21:29:22: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Wed, 30 Jan 2019 21:29:22: #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 21:29:22: #3 Call peaks... INFO @ Wed, 30 Jan 2019 21:29:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 21:29:22: start X-correlation... INFO @ Wed, 30 Jan 2019 21:29:22: end of X-cor INFO @ Wed, 30 Jan 2019 21:29:22: #2 finished! INFO @ Wed, 30 Jan 2019 21:29:22: #2 predicted fragment length is 49 bps INFO @ Wed, 30 Jan 2019 21:29:22: #2 alternative fragment length(s) may be 49 bps INFO @ Wed, 30 Jan 2019 21:29:22: #2.2 Generate R script for model : ERX1432619.05_model.r WARNING @ Wed, 30 Jan 2019 21:29:22: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 21:29:22: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Wed, 30 Jan 2019 21:29:22: #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 21:29:22: #3 Call peaks... INFO @ Wed, 30 Jan 2019 21:29:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 21:29:22: #2 number of paired peaks: 831 WARNING @ Wed, 30 Jan 2019 21:29:22: Fewer paired peaks (831) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 831 pairs to build model! INFO @ Wed, 30 Jan 2019 21:29:22: start model_add_line... INFO @ Wed, 30 Jan 2019 21:29:22: start X-correlation... INFO @ Wed, 30 Jan 2019 21:29:22: end of X-cor INFO @ Wed, 30 Jan 2019 21:29:22: #2 finished! INFO @ Wed, 30 Jan 2019 21:29:22: #2 predicted fragment length is 49 bps INFO @ Wed, 30 Jan 2019 21:29:22: #2 alternative fragment length(s) may be 49 bps INFO @ Wed, 30 Jan 2019 21:29:22: #2.2 Generate R script for model : ERX1432619.10_model.r WARNING @ Wed, 30 Jan 2019 21:29:22: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 21:29:22: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Wed, 30 Jan 2019 21:29:22: #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 21:29:22: #3 Call peaks... INFO @ Wed, 30 Jan 2019 21:29:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 21:29:39: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 21:29:40: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 21:29:40: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 21:29:50: #4 Write output xls file... ERX1432619.05_peaks.xls INFO @ Wed, 30 Jan 2019 21:29:50: #4 Write peak in narrowPeak format file... ERX1432619.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 21:29:50: #4 Write output xls file... ERX1432619.20_peaks.xls INFO @ Wed, 30 Jan 2019 21:29:50: #4 Write summits bed file... ERX1432619.05_summits.bed INFO @ Wed, 30 Jan 2019 21:29:50: #4 Write peak in narrowPeak format file... ERX1432619.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 21:29:50: #4 Write summits bed file... ERX1432619.20_summits.bed INFO @ Wed, 30 Jan 2019 21:29:50: Done! INFO @ Wed, 30 Jan 2019 21:29:50: Done! pass1 - making usageList (12 chroms): 3 millis pass2 - checking and writing primary data (1233 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (6135 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 21:29:51: #4 Write output xls file... ERX1432619.10_peaks.xls INFO @ Wed, 30 Jan 2019 21:29:51: #4 Write peak in narrowPeak format file... ERX1432619.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 21:29:51: #4 Write summits bed file... ERX1432619.10_summits.bed INFO @ Wed, 30 Jan 2019 21:29:51: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2067 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。