Job ID = 10480680 sra ファイルのダウンロード中... Completed: 410579K bytes transferred in 12 seconds (274054K 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 12440424 spots for /home/okishinya/chipatlas/results/dm3/SRX3009521/SRR5832222.sra Written 12440424 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: 00:04:18 12440424 reads; of these: 12440424 (100.00%) were unpaired; of these: 6512956 (52.35%) aligned 0 times 3755566 (30.19%) aligned exactly 1 time 2171902 (17.46%) aligned >1 times 47.65% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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_rmdupse_core] 2031853 / 5927468 = 0.3428 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 07:38:06: # Command line: callpeak -t SRX3009521.bam -f BAM -g dm -n SRX3009521.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3009521.10 # format = BAM # ChIP-seq file = ['SRX3009521.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 07:38:06: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:38:06: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:38:06: # Command line: callpeak -t SRX3009521.bam -f BAM -g dm -n SRX3009521.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3009521.20 # format = BAM # ChIP-seq file = ['SRX3009521.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 07:38:06: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:38:06: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:38:06: # Command line: callpeak -t SRX3009521.bam -f BAM -g dm -n SRX3009521.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3009521.05 # format = BAM # ChIP-seq file = ['SRX3009521.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 07:38:06: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:38:06: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:38:12: 1000000 INFO @ Fri, 16 Mar 2018 07:38:12: 1000000 INFO @ Fri, 16 Mar 2018 07:38:12: 1000000 INFO @ Fri, 16 Mar 2018 07:38:18: 2000000 INFO @ Fri, 16 Mar 2018 07:38:18: 2000000 INFO @ Fri, 16 Mar 2018 07:38:19: 2000000 INFO @ Fri, 16 Mar 2018 07:38:24: 3000000 INFO @ Fri, 16 Mar 2018 07:38:25: 3000000 INFO @ Fri, 16 Mar 2018 07:38:25: 3000000 INFO @ Fri, 16 Mar 2018 07:38:30: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:38:30: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:38:30: #1 total tags in treatment: 3895615 INFO @ Fri, 16 Mar 2018 07:38:30: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:38:30: #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 07:38:30: #1 tags after filtering in treatment: 3895615 INFO @ Fri, 16 Mar 2018 07:38:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:38:30: #1 finished! INFO @ Fri, 16 Mar 2018 07:38:30: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:38:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:38:30: #2 number of paired peaks: 949 WARNING @ Fri, 16 Mar 2018 07:38:30: Fewer paired peaks (949) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 949 pairs to build model! INFO @ Fri, 16 Mar 2018 07:38:30: start model_add_line... INFO @ Fri, 16 Mar 2018 07:38:30: start X-correlation... INFO @ Fri, 16 Mar 2018 07:38:30: end of X-cor INFO @ Fri, 16 Mar 2018 07:38:30: #2 finished! INFO @ Fri, 16 Mar 2018 07:38:30: #2 predicted fragment length is 49 bps INFO @ Fri, 16 Mar 2018 07:38:30: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 16 Mar 2018 07:38:30: #2.2 Generate R script for model : SRX3009521.10_model.r WARNING @ Fri, 16 Mar 2018 07:38:30: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:38:30: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 16 Mar 2018 07:38:30: #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 07:38:30: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:38:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:38:31: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:38:31: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:38:31: #1 total tags in treatment: 3895615 INFO @ Fri, 16 Mar 2018 07:38:31: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:38:31: #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 07:38:31: #1 tags after filtering in treatment: 3895615 INFO @ Fri, 16 Mar 2018 07:38:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:38:31: #1 finished! INFO @ Fri, 16 Mar 2018 07:38:31: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:38:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:38:31: #2 number of paired peaks: 949 WARNING @ Fri, 16 Mar 2018 07:38:31: Fewer paired peaks (949) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 949 pairs to build model! INFO @ Fri, 16 Mar 2018 07:38:31: start model_add_line... INFO @ Fri, 16 Mar 2018 07:38:31: start X-correlation... INFO @ Fri, 16 Mar 2018 07:38:31: end of X-cor INFO @ Fri, 16 Mar 2018 07:38:31: #2 finished! INFO @ Fri, 16 Mar 2018 07:38:31: #2 predicted fragment length is 49 bps INFO @ Fri, 16 Mar 2018 07:38:31: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 16 Mar 2018 07:38:31: #2.2 Generate R script for model : SRX3009521.05_model.r WARNING @ Fri, 16 Mar 2018 07:38:31: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:38:31: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 16 Mar 2018 07:38:31: #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 07:38:31: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:38:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:38:31: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:38:31: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:38:31: #1 total tags in treatment: 3895615 INFO @ Fri, 16 Mar 2018 07:38:31: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:38:31: #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 07:38:32: #1 tags after filtering in treatment: 3895615 INFO @ Fri, 16 Mar 2018 07:38:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:38:32: #1 finished! INFO @ Fri, 16 Mar 2018 07:38:32: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:38:32: #2 number of paired peaks: 949 WARNING @ Fri, 16 Mar 2018 07:38:32: Fewer paired peaks (949) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 949 pairs to build model! INFO @ Fri, 16 Mar 2018 07:38:32: start model_add_line... INFO @ Fri, 16 Mar 2018 07:38:32: start X-correlation... INFO @ Fri, 16 Mar 2018 07:38:32: end of X-cor INFO @ Fri, 16 Mar 2018 07:38:32: #2 finished! INFO @ Fri, 16 Mar 2018 07:38:32: #2 predicted fragment length is 49 bps INFO @ Fri, 16 Mar 2018 07:38:32: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 16 Mar 2018 07:38:32: #2.2 Generate R script for model : SRX3009521.20_model.r WARNING @ Fri, 16 Mar 2018 07:38:32: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:38:32: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 16 Mar 2018 07:38:32: #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 07:38:32: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:38:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:38:40: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:38:40: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:38:42: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:38:45: #4 Write output xls file... SRX3009521.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:38:45: #4 Write peak in narrowPeak format file... SRX3009521.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:38:45: #4 Write summits bed file... SRX3009521.10_summits.bed INFO @ Fri, 16 Mar 2018 07:38:45: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1037 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:38:45: #4 Write output xls file... SRX3009521.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:38:45: #4 Write peak in narrowPeak format file... SRX3009521.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:38:45: #4 Write summits bed file... SRX3009521.05_summits.bed INFO @ Fri, 16 Mar 2018 07:38:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1286 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:38:47: #4 Write output xls file... SRX3009521.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:38:47: #4 Write peak in narrowPeak format file... SRX3009521.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:38:47: #4 Write summits bed file... SRX3009521.20_summits.bed INFO @ Fri, 16 Mar 2018 07:38:47: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (890 records, 4 fields): 51 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。