Job ID = 10609064 sra ファイルのダウンロード中... Completed: 955839K bytes transferred in 14 seconds (542098K 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 30323524 spots for /home/okishinya/chipatlas/results/ce10/SRX2249332/SRR4427771.sra Written 30323524 spots for /home/okishinya/chipatlas/results/ce10/SRX2249332/SRR4427771.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: 00:13:47 30323524 reads; of these: 30323524 (100.00%) were unpaired; of these: 4754674 (15.68%) aligned 0 times 21347994 (70.40%) aligned exactly 1 time 4220856 (13.92%) aligned >1 times 84.32% overall alignment rate Time searching: 00:13:47 Overall time: 00:13:47 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 12 files... [bam_rmdupse_core] 4080306 / 25568850 = 0.1596 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, 04 May 2018 07:27:04: # Command line: callpeak -t SRX2249332.bam -f BAM -g ce -n SRX2249332.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2249332.05 # format = BAM # ChIP-seq file = ['SRX2249332.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 @ Fri, 04 May 2018 07:27:04: #1 read tag files... INFO @ Fri, 04 May 2018 07:27:04: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:27:04: # Command line: callpeak -t SRX2249332.bam -f BAM -g ce -n SRX2249332.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2249332.20 # format = BAM # ChIP-seq file = ['SRX2249332.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 @ Fri, 04 May 2018 07:27:04: #1 read tag files... INFO @ Fri, 04 May 2018 07:27:04: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:27:04: # Command line: callpeak -t SRX2249332.bam -f BAM -g ce -n SRX2249332.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2249332.10 # format = BAM # ChIP-seq file = ['SRX2249332.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 @ Fri, 04 May 2018 07:27:04: #1 read tag files... INFO @ Fri, 04 May 2018 07:27:04: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:27:12: 1000000 INFO @ Fri, 04 May 2018 07:27:13: 1000000 INFO @ Fri, 04 May 2018 07:27:13: 1000000 INFO @ Fri, 04 May 2018 07:27:20: 2000000 INFO @ Fri, 04 May 2018 07:27:22: 2000000 INFO @ Fri, 04 May 2018 07:27:22: 2000000 INFO @ Fri, 04 May 2018 07:27:29: 3000000 INFO @ Fri, 04 May 2018 07:27:31: 3000000 INFO @ Fri, 04 May 2018 07:27:31: 3000000 INFO @ Fri, 04 May 2018 07:27:37: 4000000 INFO @ Fri, 04 May 2018 07:27:40: 4000000 INFO @ Fri, 04 May 2018 07:27:40: 4000000 INFO @ Fri, 04 May 2018 07:27:46: 5000000 INFO @ Fri, 04 May 2018 07:27:50: 5000000 INFO @ Fri, 04 May 2018 07:27:50: 5000000 INFO @ Fri, 04 May 2018 07:27:54: 6000000 INFO @ Fri, 04 May 2018 07:28:01: 6000000 INFO @ Fri, 04 May 2018 07:28:01: 6000000 INFO @ Fri, 04 May 2018 07:28:02: 7000000 INFO @ Fri, 04 May 2018 07:28:11: 8000000 INFO @ Fri, 04 May 2018 07:28:11: 7000000 INFO @ Fri, 04 May 2018 07:28:11: 7000000 INFO @ Fri, 04 May 2018 07:28:19: 9000000 INFO @ Fri, 04 May 2018 07:28:22: 8000000 INFO @ Fri, 04 May 2018 07:28:22: 8000000 INFO @ Fri, 04 May 2018 07:28:27: 10000000 INFO @ Fri, 04 May 2018 07:28:32: 9000000 INFO @ Fri, 04 May 2018 07:28:32: 9000000 INFO @ Fri, 04 May 2018 07:28:36: 11000000 INFO @ Fri, 04 May 2018 07:28:42: 10000000 INFO @ Fri, 04 May 2018 07:28:42: 10000000 INFO @ Fri, 04 May 2018 07:28:44: 12000000 INFO @ Fri, 04 May 2018 07:28:51: 11000000 INFO @ Fri, 04 May 2018 07:28:51: 11000000 INFO @ Fri, 04 May 2018 07:28:52: 13000000 INFO @ Fri, 04 May 2018 07:29:00: 12000000 INFO @ Fri, 04 May 2018 07:29:00: 12000000 INFO @ Fri, 04 May 2018 07:29:01: 14000000 INFO @ Fri, 04 May 2018 07:29:09: 13000000 INFO @ Fri, 04 May 2018 07:29:09: 13000000 INFO @ Fri, 04 May 2018 07:29:09: 15000000 INFO @ Fri, 04 May 2018 07:29:17: 14000000 INFO @ Fri, 04 May 2018 07:29:18: 14000000 INFO @ Fri, 04 May 2018 07:29:18: 16000000 INFO @ Fri, 04 May 2018 07:29:26: 15000000 INFO @ Fri, 04 May 2018 07:29:26: 15000000 INFO @ Fri, 04 May 2018 07:29:27: 17000000 INFO @ Fri, 04 May 2018 07:29:34: 16000000 INFO @ Fri, 04 May 2018 07:29:36: 16000000 INFO @ Fri, 04 May 2018 07:29:36: 18000000 INFO @ Fri, 04 May 2018 07:29:42: 17000000 INFO @ Fri, 04 May 2018 07:29:45: 17000000 INFO @ Fri, 04 May 2018 07:29:46: 19000000 INFO @ Fri, 04 May 2018 07:29:51: 18000000 INFO @ Fri, 04 May 2018 07:29:54: 18000000 INFO @ Fri, 04 May 2018 07:29:54: 20000000 INFO @ Fri, 04 May 2018 07:30:00: 19000000 INFO @ Fri, 04 May 2018 07:30:03: 19000000 INFO @ Fri, 04 May 2018 07:30:04: 21000000 INFO @ Fri, 04 May 2018 07:30:08: #1 tag size is determined as 101 bps INFO @ Fri, 04 May 2018 07:30:08: #1 tag size = 101 INFO @ Fri, 04 May 2018 07:30:08: #1 total tags in treatment: 21488544 INFO @ Fri, 04 May 2018 07:30:08: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:30:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:30:08: 20000000 INFO @ Fri, 04 May 2018 07:30:09: #1 tags after filtering in treatment: 21488544 INFO @ Fri, 04 May 2018 07:30:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:30:09: #1 finished! INFO @ Fri, 04 May 2018 07:30:09: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:30:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:30:10: #2 number of paired peaks: 178 WARNING @ Fri, 04 May 2018 07:30:10: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Fri, 04 May 2018 07:30:10: start model_add_line... INFO @ Fri, 04 May 2018 07:30:10: start X-correlation... INFO @ Fri, 04 May 2018 07:30:10: end of X-cor INFO @ Fri, 04 May 2018 07:30:10: #2 finished! INFO @ Fri, 04 May 2018 07:30:10: #2 predicted fragment length is 96 bps INFO @ Fri, 04 May 2018 07:30:10: #2 alternative fragment length(s) may be 2,96 bps INFO @ Fri, 04 May 2018 07:30:10: #2.2 Generate R script for model : SRX2249332.05_model.r WARNING @ Fri, 04 May 2018 07:30:10: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:30:10: #2 You may need to consider one of the other alternative d(s): 2,96 WARNING @ Fri, 04 May 2018 07:30:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 May 2018 07:30:10: #3 Call peaks... INFO @ Fri, 04 May 2018 07:30:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:30:12: 20000000 INFO @ Fri, 04 May 2018 07:30:18: 21000000 INFO @ Fri, 04 May 2018 07:30:20: 21000000 INFO @ Fri, 04 May 2018 07:30:23: #1 tag size is determined as 101 bps INFO @ Fri, 04 May 2018 07:30:23: #1 tag size = 101 INFO @ Fri, 04 May 2018 07:30:23: #1 total tags in treatment: 21488544 INFO @ Fri, 04 May 2018 07:30:23: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:30:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:30:23: #1 tags after filtering in treatment: 21488544 INFO @ Fri, 04 May 2018 07:30:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:30:23: #1 finished! INFO @ Fri, 04 May 2018 07:30:23: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:30:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:30:24: #1 tag size is determined as 101 bps INFO @ Fri, 04 May 2018 07:30:24: #1 tag size = 101 INFO @ Fri, 04 May 2018 07:30:24: #1 total tags in treatment: 21488544 INFO @ Fri, 04 May 2018 07:30:24: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:30:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:30:24: #2 number of paired peaks: 178 WARNING @ Fri, 04 May 2018 07:30:24: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Fri, 04 May 2018 07:30:24: start model_add_line... INFO @ Fri, 04 May 2018 07:30:25: start X-correlation... INFO @ Fri, 04 May 2018 07:30:25: end of X-cor INFO @ Fri, 04 May 2018 07:30:25: #2 finished! INFO @ Fri, 04 May 2018 07:30:25: #2 predicted fragment length is 96 bps INFO @ Fri, 04 May 2018 07:30:25: #2 alternative fragment length(s) may be 2,96 bps INFO @ Fri, 04 May 2018 07:30:25: #2.2 Generate R script for model : SRX2249332.20_model.r INFO @ Fri, 04 May 2018 07:30:25: #1 tags after filtering in treatment: 21488544 INFO @ Fri, 04 May 2018 07:30:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:30:25: #1 finished! INFO @ Fri, 04 May 2018 07:30:25: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:30:25: #2 looking for paired plus/minus strand peaks... WARNING @ Fri, 04 May 2018 07:30:25: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:30:25: #2 You may need to consider one of the other alternative d(s): 2,96 WARNING @ Fri, 04 May 2018 07:30:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 May 2018 07:30:25: #3 Call peaks... INFO @ Fri, 04 May 2018 07:30:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:30:26: #2 number of paired peaks: 178 WARNING @ Fri, 04 May 2018 07:30:26: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Fri, 04 May 2018 07:30:26: start model_add_line... INFO @ Fri, 04 May 2018 07:30:26: start X-correlation... INFO @ Fri, 04 May 2018 07:30:26: end of X-cor INFO @ Fri, 04 May 2018 07:30:26: #2 finished! INFO @ Fri, 04 May 2018 07:30:26: #2 predicted fragment length is 96 bps INFO @ Fri, 04 May 2018 07:30:26: #2 alternative fragment length(s) may be 2,96 bps INFO @ Fri, 04 May 2018 07:30:26: #2.2 Generate R script for model : SRX2249332.10_model.r WARNING @ Fri, 04 May 2018 07:30:26: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:30:26: #2 You may need to consider one of the other alternative d(s): 2,96 WARNING @ Fri, 04 May 2018 07:30:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 May 2018 07:30:26: #3 Call peaks... INFO @ Fri, 04 May 2018 07:30:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:30:50: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:31:05: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:31:05: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:31:09: #4 Write output xls file... SRX2249332.05_peaks.xls INFO @ Fri, 04 May 2018 07:31:09: #4 Write peak in narrowPeak format file... SRX2249332.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:31:09: #4 Write summits bed file... SRX2249332.05_summits.bed INFO @ Fri, 04 May 2018 07:31:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (564 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:31:23: #4 Write output xls file... SRX2249332.20_peaks.xls INFO @ Fri, 04 May 2018 07:31:23: #4 Write peak in narrowPeak format file... SRX2249332.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:31:23: #4 Write summits bed file... SRX2249332.20_summits.bed INFO @ Fri, 04 May 2018 07:31:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:31:24: #4 Write output xls file... SRX2249332.10_peaks.xls INFO @ Fri, 04 May 2018 07:31:24: #4 Write peak in narrowPeak format file... SRX2249332.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:31:24: #4 Write summits bed file... SRX2249332.10_summits.bed INFO @ Fri, 04 May 2018 07:31:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (404 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。