Job ID = 9157221 sra ファイルのダウンロード中... Completed: 570850K bytes transferred in 6 seconds (691279K bits/sec), in 1 file, 2 directories. 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 12544790 spots for /home/okishinya/chipatlas/results/ce10/SRX2350727/SRR5024036.sra Written 12544790 spots total 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: 00:00:01 Multiseed full-index search: 00:03:52 12544790 reads; of these: 12544790 (100.00%) were unpaired; of these: 349096 (2.78%) aligned 0 times 9671951 (77.10%) aligned exactly 1 time 2523743 (20.12%) aligned >1 times 97.22% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 1554211 / 12195694 = 0.1274 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 @ Tue, 27 Jun 2017 11:12:56: # Command line: callpeak -t SRX2350727.bam -f BAM -g ce -n SRX2350727.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350727.05 # format = BAM # ChIP-seq file = ['SRX2350727.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 @ Tue, 27 Jun 2017 11:12:56: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:12:56: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:12:56: # Command line: callpeak -t SRX2350727.bam -f BAM -g ce -n SRX2350727.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350727.20 # format = BAM # ChIP-seq file = ['SRX2350727.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 @ Tue, 27 Jun 2017 11:12:56: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:12:56: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:12:56: # Command line: callpeak -t SRX2350727.bam -f BAM -g ce -n SRX2350727.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350727.10 # format = BAM # ChIP-seq file = ['SRX2350727.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 @ Tue, 27 Jun 2017 11:12:56: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:12:56: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:13:02: 1000000 INFO @ Tue, 27 Jun 2017 11:13:03: 1000000 INFO @ Tue, 27 Jun 2017 11:13:03: 1000000 INFO @ Tue, 27 Jun 2017 11:13:08: 2000000 INFO @ Tue, 27 Jun 2017 11:13:09: 2000000 INFO @ Tue, 27 Jun 2017 11:13:09: 2000000 INFO @ Tue, 27 Jun 2017 11:13:15: 3000000 INFO @ Tue, 27 Jun 2017 11:13:17: 3000000 INFO @ Tue, 27 Jun 2017 11:13:17: 3000000 INFO @ Tue, 27 Jun 2017 11:13:23: 4000000 INFO @ Tue, 27 Jun 2017 11:13:25: 4000000 INFO @ Tue, 27 Jun 2017 11:13:25: 4000000 INFO @ Tue, 27 Jun 2017 11:13:30: 5000000 INFO @ Tue, 27 Jun 2017 11:13:33: 5000000 INFO @ Tue, 27 Jun 2017 11:13:33: 5000000 INFO @ Tue, 27 Jun 2017 11:13:37: 6000000 INFO @ Tue, 27 Jun 2017 11:13:41: 6000000 INFO @ Tue, 27 Jun 2017 11:13:41: 6000000 INFO @ Tue, 27 Jun 2017 11:13:45: 7000000 INFO @ Tue, 27 Jun 2017 11:13:49: 7000000 INFO @ Tue, 27 Jun 2017 11:13:49: 7000000 INFO @ Tue, 27 Jun 2017 11:13:52: 8000000 INFO @ Tue, 27 Jun 2017 11:13:57: 8000000 INFO @ Tue, 27 Jun 2017 11:13:57: 8000000 INFO @ Tue, 27 Jun 2017 11:14:00: 9000000 INFO @ Tue, 27 Jun 2017 11:14:05: 9000000 INFO @ Tue, 27 Jun 2017 11:14:05: 9000000 INFO @ Tue, 27 Jun 2017 11:14:07: 10000000 INFO @ Tue, 27 Jun 2017 11:14:12: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:14:12: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:14:12: #1 total tags in treatment: 10641483 INFO @ Tue, 27 Jun 2017 11:14:12: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:14:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:14:12: #1 tags after filtering in treatment: 10641483 INFO @ Tue, 27 Jun 2017 11:14:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:14:12: #1 finished! INFO @ Tue, 27 Jun 2017 11:14:12: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:14:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:14:13: #2 number of paired peaks: 398 WARNING @ Tue, 27 Jun 2017 11:14:13: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Tue, 27 Jun 2017 11:14:13: start model_add_line... INFO @ Tue, 27 Jun 2017 11:14:13: 10000000 INFO @ Tue, 27 Jun 2017 11:14:13: 10000000 INFO @ Tue, 27 Jun 2017 11:14:13: start X-correlation... INFO @ Tue, 27 Jun 2017 11:14:13: end of X-cor INFO @ Tue, 27 Jun 2017 11:14:13: #2 finished! INFO @ Tue, 27 Jun 2017 11:14:13: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 11:14:13: #2 alternative fragment length(s) may be 2,48,596 bps INFO @ Tue, 27 Jun 2017 11:14:13: #2.2 Generate R script for model : SRX2350727.05_model.r WARNING @ Tue, 27 Jun 2017 11:14:13: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:14:13: #2 You may need to consider one of the other alternative d(s): 2,48,596 WARNING @ Tue, 27 Jun 2017 11:14:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:14:13: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:14:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:14:18: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:14:18: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:14:18: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:14:18: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:14:18: #1 total tags in treatment: 10641483 INFO @ Tue, 27 Jun 2017 11:14:18: #1 total tags in treatment: 10641483 INFO @ Tue, 27 Jun 2017 11:14:18: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:14:18: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:14:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:14:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:14:19: #1 tags after filtering in treatment: 10641483 INFO @ Tue, 27 Jun 2017 11:14:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:14:19: #1 finished! INFO @ Tue, 27 Jun 2017 11:14:19: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:14:19: #1 tags after filtering in treatment: 10641483 INFO @ Tue, 27 Jun 2017 11:14:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:14:19: #1 finished! INFO @ Tue, 27 Jun 2017 11:14:19: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:14:19: #2 number of paired peaks: 398 WARNING @ Tue, 27 Jun 2017 11:14:19: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Tue, 27 Jun 2017 11:14:19: start model_add_line... INFO @ Tue, 27 Jun 2017 11:14:19: #2 number of paired peaks: 398 WARNING @ Tue, 27 Jun 2017 11:14:19: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Tue, 27 Jun 2017 11:14:19: start model_add_line... INFO @ Tue, 27 Jun 2017 11:14:19: start X-correlation... INFO @ Tue, 27 Jun 2017 11:14:19: end of X-cor INFO @ Tue, 27 Jun 2017 11:14:19: #2 finished! INFO @ Tue, 27 Jun 2017 11:14:19: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 11:14:19: #2 alternative fragment length(s) may be 2,48,596 bps INFO @ Tue, 27 Jun 2017 11:14:19: #2.2 Generate R script for model : SRX2350727.10_model.r INFO @ Tue, 27 Jun 2017 11:14:19: start X-correlation... WARNING @ Tue, 27 Jun 2017 11:14:19: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:14:19: #2 You may need to consider one of the other alternative d(s): 2,48,596 WARNING @ Tue, 27 Jun 2017 11:14:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:14:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:14:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:14:19: end of X-cor INFO @ Tue, 27 Jun 2017 11:14:19: #2 finished! INFO @ Tue, 27 Jun 2017 11:14:19: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 11:14:19: #2 alternative fragment length(s) may be 2,48,596 bps INFO @ Tue, 27 Jun 2017 11:14:19: #2.2 Generate R script for model : SRX2350727.20_model.r WARNING @ Tue, 27 Jun 2017 11:14:19: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:14:19: #2 You may need to consider one of the other alternative d(s): 2,48,596 WARNING @ Tue, 27 Jun 2017 11:14:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:14:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:14:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:14:35: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:14:41: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:14:42: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:14:47: #4 Write output xls file... SRX2350727.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:14:47: #4 Write peak in narrowPeak format file... SRX2350727.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:14:47: #4 Write summits bed file... SRX2350727.05_summits.bed INFO @ Tue, 27 Jun 2017 11:14:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (784 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:14:54: #4 Write output xls file... SRX2350727.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:14:54: #4 Write peak in narrowPeak format file... SRX2350727.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:14:54: #4 Write summits bed file... SRX2350727.10_summits.bed INFO @ Tue, 27 Jun 2017 11:14:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (453 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:14:56: #4 Write output xls file... SRX2350727.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:14:56: #4 Write peak in narrowPeak format file... SRX2350727.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:14:56: #4 Write summits bed file... SRX2350727.20_summits.bed INFO @ Tue, 27 Jun 2017 11:14:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (201 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。