Job ID = 9157175 sra ファイルのダウンロード中... Completed: 476738K bytes transferred in 6 seconds (576090K 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 15226514 spots for /home/okishinya/chipatlas/results/ce10/SRX2228896/SRR4380352.sra Written 15226514 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: 00:00:00 Multiseed full-index search: 00:03:57 15226514 reads; of these: 15226514 (100.00%) were unpaired; of these: 98932 (0.65%) aligned 0 times 12677765 (83.26%) aligned exactly 1 time 2449817 (16.09%) aligned >1 times 99.35% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 1348225 / 15127582 = 0.0891 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 11:01:47: # Command line: callpeak -t SRX2228896.bam -f BAM -g ce -n SRX2228896.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228896.05 # format = BAM # ChIP-seq file = ['SRX2228896.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 11:01:47: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:01:47: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:01:47: # Command line: callpeak -t SRX2228896.bam -f BAM -g ce -n SRX2228896.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228896.20 # format = BAM # ChIP-seq file = ['SRX2228896.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 11:01:47: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:01:47: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:01:47: # Command line: callpeak -t SRX2228896.bam -f BAM -g ce -n SRX2228896.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228896.10 # format = BAM # ChIP-seq file = ['SRX2228896.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 11:01:47: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:01:47: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:01:53: 1000000 INFO @ Tue, 27 Jun 2017 11:01:53: 1000000 INFO @ Tue, 27 Jun 2017 11:01:54: 1000000 INFO @ Tue, 27 Jun 2017 11:02:00: 2000000 INFO @ Tue, 27 Jun 2017 11:02:00: 2000000 INFO @ Tue, 27 Jun 2017 11:02:00: 2000000 INFO @ Tue, 27 Jun 2017 11:02:06: 3000000 INFO @ Tue, 27 Jun 2017 11:02:06: 3000000 INFO @ Tue, 27 Jun 2017 11:02:07: 3000000 INFO @ Tue, 27 Jun 2017 11:02:12: 4000000 INFO @ Tue, 27 Jun 2017 11:02:13: 4000000 INFO @ Tue, 27 Jun 2017 11:02:13: 4000000 INFO @ Tue, 27 Jun 2017 11:02:19: 5000000 INFO @ Tue, 27 Jun 2017 11:02:19: 5000000 INFO @ Tue, 27 Jun 2017 11:02:20: 5000000 INFO @ Tue, 27 Jun 2017 11:02:25: 6000000 INFO @ Tue, 27 Jun 2017 11:02:26: 6000000 INFO @ Tue, 27 Jun 2017 11:02:26: 6000000 INFO @ Tue, 27 Jun 2017 11:02:32: 7000000 INFO @ Tue, 27 Jun 2017 11:02:33: 7000000 INFO @ Tue, 27 Jun 2017 11:02:33: 7000000 INFO @ Tue, 27 Jun 2017 11:02:39: 8000000 INFO @ Tue, 27 Jun 2017 11:02:39: 8000000 INFO @ Tue, 27 Jun 2017 11:02:40: 8000000 INFO @ Tue, 27 Jun 2017 11:02:45: 9000000 INFO @ Tue, 27 Jun 2017 11:02:46: 9000000 INFO @ Tue, 27 Jun 2017 11:02:46: 9000000 INFO @ Tue, 27 Jun 2017 11:02:52: 10000000 INFO @ Tue, 27 Jun 2017 11:02:53: 10000000 INFO @ Tue, 27 Jun 2017 11:02:53: 10000000 INFO @ Tue, 27 Jun 2017 11:02:58: 11000000 INFO @ Tue, 27 Jun 2017 11:03:00: 11000000 INFO @ Tue, 27 Jun 2017 11:03:00: 11000000 INFO @ Tue, 27 Jun 2017 11:03:05: 12000000 INFO @ Tue, 27 Jun 2017 11:03:07: 12000000 INFO @ Tue, 27 Jun 2017 11:03:07: 12000000 INFO @ Tue, 27 Jun 2017 11:03:12: 13000000 INFO @ Tue, 27 Jun 2017 11:03:13: 13000000 INFO @ Tue, 27 Jun 2017 11:03:13: 13000000 INFO @ Tue, 27 Jun 2017 11:03:17: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:03:17: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:03:17: #1 total tags in treatment: 13779357 INFO @ Tue, 27 Jun 2017 11:03:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:03:17: #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 11:03:17: #1 tags after filtering in treatment: 13779357 INFO @ Tue, 27 Jun 2017 11:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:03:17: #1 finished! INFO @ Tue, 27 Jun 2017 11:03:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:03:18: #2 number of paired peaks: 224 WARNING @ Tue, 27 Jun 2017 11:03:18: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Tue, 27 Jun 2017 11:03:18: start model_add_line... INFO @ Tue, 27 Jun 2017 11:03:18: start X-correlation... INFO @ Tue, 27 Jun 2017 11:03:18: end of X-cor INFO @ Tue, 27 Jun 2017 11:03:18: #2 finished! INFO @ Tue, 27 Jun 2017 11:03:18: #2 predicted fragment length is 47 bps INFO @ Tue, 27 Jun 2017 11:03:18: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 27 Jun 2017 11:03:18: #2.2 Generate R script for model : SRX2228896.10_model.r WARNING @ Tue, 27 Jun 2017 11:03:18: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:03:18: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 27 Jun 2017 11:03:18: #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 11:03:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:03:19: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:03:19: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:03:19: #1 total tags in treatment: 13779357 INFO @ Tue, 27 Jun 2017 11:03:19: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:03:19: #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 11:03:19: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:03:19: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:03:19: #1 total tags in treatment: 13779357 INFO @ Tue, 27 Jun 2017 11:03:19: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:03:19: #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 11:03:19: #1 tags after filtering in treatment: 13779357 INFO @ Tue, 27 Jun 2017 11:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:03:19: #1 finished! INFO @ Tue, 27 Jun 2017 11:03:19: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:03:19: #1 tags after filtering in treatment: 13779357 INFO @ Tue, 27 Jun 2017 11:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:03:19: #1 finished! INFO @ Tue, 27 Jun 2017 11:03:19: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:03:20: #2 number of paired peaks: 224 WARNING @ Tue, 27 Jun 2017 11:03:20: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Tue, 27 Jun 2017 11:03:20: start model_add_line... INFO @ Tue, 27 Jun 2017 11:03:20: start X-correlation... INFO @ Tue, 27 Jun 2017 11:03:20: end of X-cor INFO @ Tue, 27 Jun 2017 11:03:20: #2 finished! INFO @ Tue, 27 Jun 2017 11:03:20: #2 predicted fragment length is 47 bps INFO @ Tue, 27 Jun 2017 11:03:20: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 27 Jun 2017 11:03:20: #2.2 Generate R script for model : SRX2228896.20_model.r WARNING @ Tue, 27 Jun 2017 11:03:20: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:03:20: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 27 Jun 2017 11:03:20: #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 11:03:20: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:03:20: #2 number of paired peaks: 224 WARNING @ Tue, 27 Jun 2017 11:03:20: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Tue, 27 Jun 2017 11:03:20: start model_add_line... INFO @ Tue, 27 Jun 2017 11:03:20: start X-correlation... INFO @ Tue, 27 Jun 2017 11:03:20: end of X-cor INFO @ Tue, 27 Jun 2017 11:03:20: #2 finished! INFO @ Tue, 27 Jun 2017 11:03:20: #2 predicted fragment length is 47 bps INFO @ Tue, 27 Jun 2017 11:03:20: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 27 Jun 2017 11:03:20: #2.2 Generate R script for model : SRX2228896.05_model.r WARNING @ Tue, 27 Jun 2017 11:03:20: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:03:20: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 27 Jun 2017 11:03:20: #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 11:03:20: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:03:46: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:03:48: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:03:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:04:02: #4 Write output xls file... SRX2228896.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:04:02: #4 Write peak in narrowPeak format file... SRX2228896.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:04:02: #4 Write summits bed file... SRX2228896.10_summits.bed INFO @ Tue, 27 Jun 2017 11:04:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (343 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:04:03: #4 Write output xls file... SRX2228896.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:04:03: #4 Write peak in narrowPeak format file... SRX2228896.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:04:03: #4 Write summits bed file... SRX2228896.05_summits.bed INFO @ Tue, 27 Jun 2017 11:04:03: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (600 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:04:04: #4 Write output xls file... SRX2228896.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:04:04: #4 Write peak in narrowPeak format file... SRX2228896.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:04:04: #4 Write summits bed file... SRX2228896.20_summits.bed INFO @ Tue, 27 Jun 2017 11:04:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (127 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。