Job ID = 11388799 sra ファイルのダウンロード中... Completed: 211566K bytes transferred in 10 seconds (168889K bits/sec), in 1 file. Completed: 219742K bytes transferred in 8 seconds (204908K 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 9464439 spots for /home/okishinya/chipatlas/results/rn6/SRX3657369/SRR6681055.sra Written 9464439 spots for /home/okishinya/chipatlas/results/rn6/SRX3657369/SRR6681055.sra Read 9716576 spots for /home/okishinya/chipatlas/results/rn6/SRX3657369/SRR6681056.sra Written 9716576 spots for /home/okishinya/chipatlas/results/rn6/SRX3657369/SRR6681056.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 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:34:12 19181015 reads; of these: 19181015 (100.00%) were unpaired; of these: 1446759 (7.54%) aligned 0 times 13023332 (67.90%) aligned exactly 1 time 4710924 (24.56%) aligned >1 times 92.46% overall alignment rate Time searching: 00:34:18 Overall time: 00:34:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4166652 / 17734256 = 0.2349 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, 12 Dec 2018 23:28:59: # Command line: callpeak -t SRX3657369.bam -f BAM -g 2.15e9 -n SRX3657369.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3657369.20 # format = BAM # ChIP-seq file = ['SRX3657369.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 12 Dec 2018 23:28:59: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:28:59: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:28:59: # Command line: callpeak -t SRX3657369.bam -f BAM -g 2.15e9 -n SRX3657369.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3657369.05 # format = BAM # ChIP-seq file = ['SRX3657369.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 12 Dec 2018 23:28:59: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:28:59: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:28:59: # Command line: callpeak -t SRX3657369.bam -f BAM -g 2.15e9 -n SRX3657369.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3657369.10 # format = BAM # ChIP-seq file = ['SRX3657369.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 12 Dec 2018 23:28:59: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:28:59: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:29:09: 1000000 INFO @ Wed, 12 Dec 2018 23:29:09: 1000000 INFO @ Wed, 12 Dec 2018 23:29:12: 1000000 INFO @ Wed, 12 Dec 2018 23:29:20: 2000000 INFO @ Wed, 12 Dec 2018 23:29:20: 2000000 INFO @ Wed, 12 Dec 2018 23:29:25: 2000000 INFO @ Wed, 12 Dec 2018 23:29:32: 3000000 INFO @ Wed, 12 Dec 2018 23:29:32: 3000000 INFO @ Wed, 12 Dec 2018 23:29:40: 3000000 INFO @ Wed, 12 Dec 2018 23:29:43: 4000000 INFO @ Wed, 12 Dec 2018 23:29:43: 4000000 INFO @ Wed, 12 Dec 2018 23:29:51: 4000000 INFO @ Wed, 12 Dec 2018 23:29:56: 5000000 INFO @ Wed, 12 Dec 2018 23:29:56: 5000000 INFO @ Wed, 12 Dec 2018 23:30:05: 5000000 INFO @ Wed, 12 Dec 2018 23:30:09: 6000000 INFO @ Wed, 12 Dec 2018 23:30:09: 6000000 INFO @ Wed, 12 Dec 2018 23:30:20: 6000000 INFO @ Wed, 12 Dec 2018 23:30:22: 7000000 INFO @ Wed, 12 Dec 2018 23:30:23: 7000000 INFO @ Wed, 12 Dec 2018 23:30:36: 8000000 INFO @ Wed, 12 Dec 2018 23:30:37: 8000000 INFO @ Wed, 12 Dec 2018 23:30:37: 7000000 INFO @ Wed, 12 Dec 2018 23:30:51: 9000000 INFO @ Wed, 12 Dec 2018 23:30:51: 9000000 INFO @ Wed, 12 Dec 2018 23:30:54: 8000000 INFO @ Wed, 12 Dec 2018 23:31:05: 10000000 INFO @ Wed, 12 Dec 2018 23:31:05: 10000000 INFO @ Wed, 12 Dec 2018 23:31:12: 9000000 INFO @ Wed, 12 Dec 2018 23:31:20: 11000000 INFO @ Wed, 12 Dec 2018 23:31:20: 11000000 INFO @ Wed, 12 Dec 2018 23:31:29: 10000000 INFO @ Wed, 12 Dec 2018 23:31:34: 12000000 INFO @ Wed, 12 Dec 2018 23:31:34: 12000000 INFO @ Wed, 12 Dec 2018 23:31:46: 11000000 INFO @ Wed, 12 Dec 2018 23:31:47: 13000000 INFO @ Wed, 12 Dec 2018 23:31:48: 13000000 INFO @ Wed, 12 Dec 2018 23:31:55: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:31:55: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:31:55: #1 total tags in treatment: 13567604 INFO @ Wed, 12 Dec 2018 23:31:55: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:31:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:31:56: #1 tags after filtering in treatment: 13567446 INFO @ Wed, 12 Dec 2018 23:31:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:31:56: #1 finished! INFO @ Wed, 12 Dec 2018 23:31:56: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:31:56: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:31:56: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:31:56: #1 total tags in treatment: 13567604 INFO @ Wed, 12 Dec 2018 23:31:56: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:31:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:31:57: #1 tags after filtering in treatment: 13567446 INFO @ Wed, 12 Dec 2018 23:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:31:57: #1 finished! INFO @ Wed, 12 Dec 2018 23:31:57: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:31:58: #2 number of paired peaks: 8962 INFO @ Wed, 12 Dec 2018 23:31:58: start model_add_line... INFO @ Wed, 12 Dec 2018 23:31:58: start X-correlation... INFO @ Wed, 12 Dec 2018 23:31:58: end of X-cor INFO @ Wed, 12 Dec 2018 23:31:58: #2 finished! INFO @ Wed, 12 Dec 2018 23:31:58: #2 predicted fragment length is 57 bps INFO @ Wed, 12 Dec 2018 23:31:58: #2 alternative fragment length(s) may be 57 bps INFO @ Wed, 12 Dec 2018 23:31:58: #2.2 Generate R script for model : SRX3657369.20_model.r WARNING @ Wed, 12 Dec 2018 23:31:58: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:31:58: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Wed, 12 Dec 2018 23:31:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:31:58: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:31:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:31:59: #2 number of paired peaks: 8962 INFO @ Wed, 12 Dec 2018 23:31:59: start model_add_line... INFO @ Wed, 12 Dec 2018 23:31:59: start X-correlation... INFO @ Wed, 12 Dec 2018 23:31:59: end of X-cor INFO @ Wed, 12 Dec 2018 23:31:59: #2 finished! INFO @ Wed, 12 Dec 2018 23:31:59: #2 predicted fragment length is 57 bps INFO @ Wed, 12 Dec 2018 23:31:59: #2 alternative fragment length(s) may be 57 bps INFO @ Wed, 12 Dec 2018 23:31:59: #2.2 Generate R script for model : SRX3657369.05_model.r WARNING @ Wed, 12 Dec 2018 23:31:59: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:31:59: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Wed, 12 Dec 2018 23:31:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:31:59: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:32:01: 12000000 INFO @ Wed, 12 Dec 2018 23:32:16: 13000000 INFO @ Wed, 12 Dec 2018 23:32:24: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:32:24: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:32:24: #1 total tags in treatment: 13567604 INFO @ Wed, 12 Dec 2018 23:32:24: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:32:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:32:24: #1 tags after filtering in treatment: 13567446 INFO @ Wed, 12 Dec 2018 23:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:32:24: #1 finished! INFO @ Wed, 12 Dec 2018 23:32:24: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:32:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:32:27: #2 number of paired peaks: 8962 INFO @ Wed, 12 Dec 2018 23:32:27: start model_add_line... INFO @ Wed, 12 Dec 2018 23:32:27: start X-correlation... INFO @ Wed, 12 Dec 2018 23:32:27: end of X-cor INFO @ Wed, 12 Dec 2018 23:32:27: #2 finished! INFO @ Wed, 12 Dec 2018 23:32:27: #2 predicted fragment length is 57 bps INFO @ Wed, 12 Dec 2018 23:32:27: #2 alternative fragment length(s) may be 57 bps INFO @ Wed, 12 Dec 2018 23:32:27: #2.2 Generate R script for model : SRX3657369.10_model.r WARNING @ Wed, 12 Dec 2018 23:32:27: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:32:27: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Wed, 12 Dec 2018 23:32:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:32:27: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:32:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:32:41: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:32:41: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:33:05: #4 Write output xls file... SRX3657369.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:33:05: #4 Write peak in narrowPeak format file... SRX3657369.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:33:05: #4 Write summits bed file... SRX3657369.05_summits.bed INFO @ Wed, 12 Dec 2018 23:33:05: Done! pass1 - making usageList (55 chroms): 6 millis pass2 - checking and writing primary data (1955 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:33:06: #4 Write output xls file... SRX3657369.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:33:06: #4 Write peak in narrowPeak format file... SRX3657369.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:33:06: #4 Write summits bed file... SRX3657369.20_summits.bed INFO @ Wed, 12 Dec 2018 23:33:06: Done! pass1 - making usageList (37 chroms): 6 millis pass2 - checking and writing primary data (419 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:33:10: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:33:36: #4 Write output xls file... SRX3657369.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:33:36: #4 Write peak in narrowPeak format file... SRX3657369.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:33:36: #4 Write summits bed file... SRX3657369.10_summits.bed INFO @ Wed, 12 Dec 2018 23:33:36: Done! pass1 - making usageList (45 chroms): 5 millis pass2 - checking and writing primary data (998 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。