Job ID = 10714414 sra ファイルのダウンロード中... Completed: 265045K bytes transferred in 25 seconds (86121K 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 11738901 spots for /home/okishinya/chipatlas/results/ce10/SRX4082374/SRR7164192.sra Written 11738901 spots for /home/okishinya/chipatlas/results/ce10/SRX4082374/SRR7164192.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: 00:03:07 11738901 reads; of these: 11738901 (100.00%) were unpaired; of these: 1111151 (9.47%) aligned 0 times 8074743 (68.79%) aligned exactly 1 time 2553007 (21.75%) aligned >1 times 90.53% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1706263 / 10627750 = 0.1605 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 @ Sun, 03 Jun 2018 12:35:34: # Command line: callpeak -t SRX4082374.bam -f BAM -g ce -n SRX4082374.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082374.05 # format = BAM # ChIP-seq file = ['SRX4082374.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 @ Sun, 03 Jun 2018 12:35:34: # Command line: callpeak -t SRX4082374.bam -f BAM -g ce -n SRX4082374.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082374.10 # format = BAM # ChIP-seq file = ['SRX4082374.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 @ Sun, 03 Jun 2018 12:35:34: # Command line: callpeak -t SRX4082374.bam -f BAM -g ce -n SRX4082374.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082374.20 # format = BAM # ChIP-seq file = ['SRX4082374.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 @ Sun, 03 Jun 2018 12:35:34: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:34: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:34: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:34: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:34: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:34: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:43: 1000000 INFO @ Sun, 03 Jun 2018 12:35:43: 1000000 INFO @ Sun, 03 Jun 2018 12:35:43: 1000000 INFO @ Sun, 03 Jun 2018 12:35:51: 2000000 INFO @ Sun, 03 Jun 2018 12:35:52: 2000000 INFO @ Sun, 03 Jun 2018 12:35:52: 2000000 INFO @ Sun, 03 Jun 2018 12:36:00: 3000000 INFO @ Sun, 03 Jun 2018 12:36:01: 3000000 INFO @ Sun, 03 Jun 2018 12:36:01: 3000000 INFO @ Sun, 03 Jun 2018 12:36:09: 4000000 INFO @ Sun, 03 Jun 2018 12:36:09: 4000000 INFO @ Sun, 03 Jun 2018 12:36:09: 4000000 INFO @ Sun, 03 Jun 2018 12:36:18: 5000000 INFO @ Sun, 03 Jun 2018 12:36:18: 5000000 INFO @ Sun, 03 Jun 2018 12:36:18: 5000000 INFO @ Sun, 03 Jun 2018 12:36:26: 6000000 INFO @ Sun, 03 Jun 2018 12:36:27: 6000000 INFO @ Sun, 03 Jun 2018 12:36:27: 6000000 INFO @ Sun, 03 Jun 2018 12:36:35: 7000000 INFO @ Sun, 03 Jun 2018 12:36:35: 7000000 INFO @ Sun, 03 Jun 2018 12:36:35: 7000000 INFO @ Sun, 03 Jun 2018 12:36:43: 8000000 INFO @ Sun, 03 Jun 2018 12:36:44: 8000000 INFO @ Sun, 03 Jun 2018 12:36:44: 8000000 INFO @ Sun, 03 Jun 2018 12:36:50: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:36:50: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:36:50: #1 total tags in treatment: 8921487 INFO @ Sun, 03 Jun 2018 12:36:50: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:36:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:36:51: #1 tags after filtering in treatment: 8921487 INFO @ Sun, 03 Jun 2018 12:36:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:36:51: #1 finished! INFO @ Sun, 03 Jun 2018 12:36:51: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:36:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:36:51: #2 number of paired peaks: 460 WARNING @ Sun, 03 Jun 2018 12:36:51: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 03 Jun 2018 12:36:51: start model_add_line... INFO @ Sun, 03 Jun 2018 12:36:51: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:36:51: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:36:51: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:36:51: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:36:51: #1 total tags in treatment: 8921487 INFO @ Sun, 03 Jun 2018 12:36:51: #1 total tags in treatment: 8921487 INFO @ Sun, 03 Jun 2018 12:36:51: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:36:51: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:36:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:36:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:36:51: start X-correlation... INFO @ Sun, 03 Jun 2018 12:36:52: #1 tags after filtering in treatment: 8921487 INFO @ Sun, 03 Jun 2018 12:36:52: #1 tags after filtering in treatment: 8921487 INFO @ Sun, 03 Jun 2018 12:36:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:36:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:36:52: #1 finished! INFO @ Sun, 03 Jun 2018 12:36:52: #1 finished! INFO @ Sun, 03 Jun 2018 12:36:52: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:36:52: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:36:52: end of X-cor INFO @ Sun, 03 Jun 2018 12:36:52: #2 finished! INFO @ Sun, 03 Jun 2018 12:36:52: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 12:36:52: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sun, 03 Jun 2018 12:36:52: #2.2 Generate R script for model : SRX4082374.20_model.r WARNING @ Sun, 03 Jun 2018 12:36:52: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:36:52: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sun, 03 Jun 2018 12:36:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:36:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:36:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:36:52: #2 number of paired peaks: 460 WARNING @ Sun, 03 Jun 2018 12:36:52: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 03 Jun 2018 12:36:52: start model_add_line... INFO @ Sun, 03 Jun 2018 12:36:52: #2 number of paired peaks: 460 WARNING @ Sun, 03 Jun 2018 12:36:52: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 03 Jun 2018 12:36:52: start model_add_line... INFO @ Sun, 03 Jun 2018 12:36:52: start X-correlation... INFO @ Sun, 03 Jun 2018 12:36:52: start X-correlation... INFO @ Sun, 03 Jun 2018 12:36:52: end of X-cor INFO @ Sun, 03 Jun 2018 12:36:52: end of X-cor INFO @ Sun, 03 Jun 2018 12:36:52: #2 finished! INFO @ Sun, 03 Jun 2018 12:36:52: #2 finished! INFO @ Sun, 03 Jun 2018 12:36:52: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 12:36:52: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 12:36:52: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sun, 03 Jun 2018 12:36:52: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sun, 03 Jun 2018 12:36:52: #2.2 Generate R script for model : SRX4082374.05_model.r INFO @ Sun, 03 Jun 2018 12:36:52: #2.2 Generate R script for model : SRX4082374.10_model.r WARNING @ Sun, 03 Jun 2018 12:36:52: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:36:52: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sun, 03 Jun 2018 12:36:52: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:36:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Sun, 03 Jun 2018 12:36:52: #2 You may need to consider one of the other alternative d(s): 3,48 INFO @ Sun, 03 Jun 2018 12:36:52: #3 Call peaks... WARNING @ Sun, 03 Jun 2018 12:36:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:36:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:36:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:36:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:37:12: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:12: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:12: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:22: #4 Write output xls file... SRX4082374.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:22: #4 Write peak in narrowPeak format file... SRX4082374.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:22: #4 Write summits bed file... SRX4082374.20_summits.bed INFO @ Sun, 03 Jun 2018 12:37:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (172 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:37:22: #4 Write output xls file... SRX4082374.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:22: #4 Write peak in narrowPeak format file... SRX4082374.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:22: #4 Write summits bed file... SRX4082374.10_summits.bed INFO @ Sun, 03 Jun 2018 12:37:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (424 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:37:23: #4 Write output xls file... SRX4082374.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:23: #4 Write peak in narrowPeak format file... SRX4082374.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:23: #4 Write summits bed file... SRX4082374.05_summits.bed INFO @ Sun, 03 Jun 2018 12:37:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (780 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。