Job ID = 10251895 sra ファイルのダウンロード中... Completed: 120091K bytes transferred in 17 seconds (55380K 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 6772794 spots for /home/okishinya/chipatlas/results/ce10/SRX3411421/SRR6311152.sra Written 6772794 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: 00:01:14 6772794 reads; of these: 6772794 (100.00%) were unpaired; of these: 35768 (0.53%) aligned 0 times 5660499 (83.58%) aligned exactly 1 time 1076527 (15.89%) aligned >1 times 99.47% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 476156 / 6737026 = 0.0707 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, 06 Dec 2017 07:36:32: # Command line: callpeak -t SRX3411421.bam -f BAM -g ce -n SRX3411421.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3411421.05 # format = BAM # ChIP-seq file = ['SRX3411421.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 06 Dec 2017 07:36:32: #1 read tag files... INFO @ Wed, 06 Dec 2017 07:36:32: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 07:36:32: # Command line: callpeak -t SRX3411421.bam -f BAM -g ce -n SRX3411421.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3411421.10 # format = BAM # ChIP-seq file = ['SRX3411421.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 06 Dec 2017 07:36:32: #1 read tag files... INFO @ Wed, 06 Dec 2017 07:36:32: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 07:36:32: # Command line: callpeak -t SRX3411421.bam -f BAM -g ce -n SRX3411421.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3411421.20 # format = BAM # ChIP-seq file = ['SRX3411421.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 06 Dec 2017 07:36:32: #1 read tag files... INFO @ Wed, 06 Dec 2017 07:36:32: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 07:36:38: 1000000 INFO @ Wed, 06 Dec 2017 07:36:38: 1000000 INFO @ Wed, 06 Dec 2017 07:36:38: 1000000 INFO @ Wed, 06 Dec 2017 07:36:43: 2000000 INFO @ Wed, 06 Dec 2017 07:36:43: 2000000 INFO @ Wed, 06 Dec 2017 07:36:44: 2000000 INFO @ Wed, 06 Dec 2017 07:36:49: 3000000 INFO @ Wed, 06 Dec 2017 07:36:49: 3000000 INFO @ Wed, 06 Dec 2017 07:36:50: 3000000 INFO @ Wed, 06 Dec 2017 07:36:55: 4000000 INFO @ Wed, 06 Dec 2017 07:36:55: 4000000 INFO @ Wed, 06 Dec 2017 07:36:56: 4000000 INFO @ Wed, 06 Dec 2017 07:37:00: 5000000 INFO @ Wed, 06 Dec 2017 07:37:01: 5000000 INFO @ Wed, 06 Dec 2017 07:37:02: 5000000 INFO @ Wed, 06 Dec 2017 07:37:06: 6000000 INFO @ Wed, 06 Dec 2017 07:37:07: 6000000 INFO @ Wed, 06 Dec 2017 07:37:08: #1 tag size is determined as 32 bps INFO @ Wed, 06 Dec 2017 07:37:08: #1 tag size = 32 INFO @ Wed, 06 Dec 2017 07:37:08: #1 total tags in treatment: 6260870 INFO @ Wed, 06 Dec 2017 07:37:08: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 07:37:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 07:37:08: #1 tags after filtering in treatment: 6260870 INFO @ Wed, 06 Dec 2017 07:37:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 07:37:08: #1 finished! INFO @ Wed, 06 Dec 2017 07:37:08: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 07:37:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 07:37:08: 6000000 INFO @ Wed, 06 Dec 2017 07:37:08: #1 tag size is determined as 32 bps INFO @ Wed, 06 Dec 2017 07:37:08: #1 tag size = 32 INFO @ Wed, 06 Dec 2017 07:37:08: #1 total tags in treatment: 6260870 INFO @ Wed, 06 Dec 2017 07:37:08: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 07:37:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 07:37:08: #2 number of paired peaks: 387 WARNING @ Wed, 06 Dec 2017 07:37:08: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Wed, 06 Dec 2017 07:37:08: start model_add_line... INFO @ Wed, 06 Dec 2017 07:37:08: #1 tags after filtering in treatment: 6260870 INFO @ Wed, 06 Dec 2017 07:37:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 07:37:08: #1 finished! INFO @ Wed, 06 Dec 2017 07:37:08: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 07:37:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 07:37:08: start X-correlation... INFO @ Wed, 06 Dec 2017 07:37:09: end of X-cor INFO @ Wed, 06 Dec 2017 07:37:09: #2 finished! INFO @ Wed, 06 Dec 2017 07:37:09: #2 predicted fragment length is 30 bps INFO @ Wed, 06 Dec 2017 07:37:09: #2 alternative fragment length(s) may be 3,30,573,596 bps INFO @ Wed, 06 Dec 2017 07:37:09: #2.2 Generate R script for model : SRX3411421.05_model.r WARNING @ Wed, 06 Dec 2017 07:37:09: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 06 Dec 2017 07:37:09: #2 You may need to consider one of the other alternative d(s): 3,30,573,596 WARNING @ Wed, 06 Dec 2017 07:37:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 06 Dec 2017 07:37:09: #3 Call peaks... INFO @ Wed, 06 Dec 2017 07:37:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 07:37:09: #2 number of paired peaks: 387 WARNING @ Wed, 06 Dec 2017 07:37:09: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Wed, 06 Dec 2017 07:37:09: start model_add_line... INFO @ Wed, 06 Dec 2017 07:37:09: start X-correlation... INFO @ Wed, 06 Dec 2017 07:37:09: end of X-cor INFO @ Wed, 06 Dec 2017 07:37:09: #2 finished! INFO @ Wed, 06 Dec 2017 07:37:09: #2 predicted fragment length is 30 bps INFO @ Wed, 06 Dec 2017 07:37:09: #2 alternative fragment length(s) may be 3,30,573,596 bps INFO @ Wed, 06 Dec 2017 07:37:09: #2.2 Generate R script for model : SRX3411421.20_model.r WARNING @ Wed, 06 Dec 2017 07:37:09: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 06 Dec 2017 07:37:09: #2 You may need to consider one of the other alternative d(s): 3,30,573,596 WARNING @ Wed, 06 Dec 2017 07:37:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 06 Dec 2017 07:37:09: #3 Call peaks... INFO @ Wed, 06 Dec 2017 07:37:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 07:37:10: #1 tag size is determined as 32 bps INFO @ Wed, 06 Dec 2017 07:37:10: #1 tag size = 32 INFO @ Wed, 06 Dec 2017 07:37:10: #1 total tags in treatment: 6260870 INFO @ Wed, 06 Dec 2017 07:37:10: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 07:37:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 07:37:10: #1 tags after filtering in treatment: 6260870 INFO @ Wed, 06 Dec 2017 07:37:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 07:37:10: #1 finished! INFO @ Wed, 06 Dec 2017 07:37:10: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 07:37:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 07:37:10: #2 number of paired peaks: 387 WARNING @ Wed, 06 Dec 2017 07:37:10: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Wed, 06 Dec 2017 07:37:10: start model_add_line... INFO @ Wed, 06 Dec 2017 07:37:10: start X-correlation... INFO @ Wed, 06 Dec 2017 07:37:10: end of X-cor INFO @ Wed, 06 Dec 2017 07:37:10: #2 finished! INFO @ Wed, 06 Dec 2017 07:37:10: #2 predicted fragment length is 30 bps INFO @ Wed, 06 Dec 2017 07:37:10: #2 alternative fragment length(s) may be 3,30,573,596 bps INFO @ Wed, 06 Dec 2017 07:37:10: #2.2 Generate R script for model : SRX3411421.10_model.r WARNING @ Wed, 06 Dec 2017 07:37:10: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 06 Dec 2017 07:37:10: #2 You may need to consider one of the other alternative d(s): 3,30,573,596 WARNING @ Wed, 06 Dec 2017 07:37:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 06 Dec 2017 07:37:10: #3 Call peaks... INFO @ Wed, 06 Dec 2017 07:37:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 07:37:23: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 07:37:23: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 07:37:24: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 07:37:30: #4 Write output xls file... SRX3411421.20_peaks.xls INFO @ Wed, 06 Dec 2017 07:37:30: #4 Write peak in narrowPeak format file... SRX3411421.20_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 07:37:30: #4 Write summits bed file... SRX3411421.20_summits.bed INFO @ Wed, 06 Dec 2017 07:37:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (49 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 06 Dec 2017 07:37:31: #4 Write output xls file... SRX3411421.10_peaks.xls INFO @ Wed, 06 Dec 2017 07:37:31: #4 Write peak in narrowPeak format file... SRX3411421.10_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 07:37:31: #4 Write summits bed file... SRX3411421.10_summits.bed INFO @ Wed, 06 Dec 2017 07:37:31: Done! INFO @ Wed, 06 Dec 2017 07:37:31: #4 Write output xls file... SRX3411421.05_peaks.xls INFO @ Wed, 06 Dec 2017 07:37:31: #4 Write peak in narrowPeak format file... SRX3411421.05_peaks.narrowPeak pass1 - making usageList (6 chroms): 1 millis INFO @ Wed, 06 Dec 2017 07:37:31: #4 Write summits bed file... SRX3411421.05_summits.bed pass2 - checking and writing primary data (208 records, 4 fields): 2 millis INFO @ Wed, 06 Dec 2017 07:37:31: Done! CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (468 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。