Job ID = 11388789 sra ファイルのダウンロード中... Completed: 227171K bytes transferred in 6 seconds (286838K 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 8689502 spots for /home/okishinya/chipatlas/results/rn6/SRX1453553/SRR2962629.sra Written 8689502 spots for /home/okishinya/chipatlas/results/rn6/SRX1453553/SRR2962629.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: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:21:33 8689502 reads; of these: 8689502 (100.00%) were unpaired; of these: 523868 (6.03%) aligned 0 times 5919329 (68.12%) aligned exactly 1 time 2246305 (25.85%) aligned >1 times 93.97% overall alignment rate Time searching: 00:21:39 Overall time: 00:21:39 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_rmdupse_core] 1388128 / 8165634 = 0.1700 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 22:50:18: # Command line: callpeak -t SRX1453553.bam -f BAM -g 2.15e9 -n SRX1453553.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1453553.05 # format = BAM # ChIP-seq file = ['SRX1453553.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 22:50:18: #1 read tag files... INFO @ Wed, 12 Dec 2018 22:50:18: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 22:50:18: # Command line: callpeak -t SRX1453553.bam -f BAM -g 2.15e9 -n SRX1453553.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1453553.10 # format = BAM # ChIP-seq file = ['SRX1453553.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 22:50:18: #1 read tag files... INFO @ Wed, 12 Dec 2018 22:50:18: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 22:50:18: # Command line: callpeak -t SRX1453553.bam -f BAM -g 2.15e9 -n SRX1453553.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1453553.20 # format = BAM # ChIP-seq file = ['SRX1453553.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 22:50:18: #1 read tag files... INFO @ Wed, 12 Dec 2018 22:50:18: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 22:50:29: 1000000 INFO @ Wed, 12 Dec 2018 22:50:35: 1000000 INFO @ Wed, 12 Dec 2018 22:50:40: 1000000 INFO @ Wed, 12 Dec 2018 22:50:42: 2000000 INFO @ Wed, 12 Dec 2018 22:50:53: 2000000 INFO @ Wed, 12 Dec 2018 22:50:57: 3000000 INFO @ Wed, 12 Dec 2018 22:50:59: 2000000 INFO @ Wed, 12 Dec 2018 22:51:10: 3000000 INFO @ Wed, 12 Dec 2018 22:51:11: 4000000 INFO @ Wed, 12 Dec 2018 22:51:22: 3000000 INFO @ Wed, 12 Dec 2018 22:51:25: 5000000 INFO @ Wed, 12 Dec 2018 22:51:29: 4000000 INFO @ Wed, 12 Dec 2018 22:51:41: 6000000 INFO @ Wed, 12 Dec 2018 22:51:42: 5000000 INFO @ Wed, 12 Dec 2018 22:51:44: 4000000 INFO @ Wed, 12 Dec 2018 22:51:53: 6000000 INFO @ Wed, 12 Dec 2018 22:51:55: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 22:51:55: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 22:51:55: #1 total tags in treatment: 6777506 INFO @ Wed, 12 Dec 2018 22:51:55: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 22:51:55: #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 22:51:56: #1 tags after filtering in treatment: 6777303 INFO @ Wed, 12 Dec 2018 22:51:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 22:51:56: #1 finished! INFO @ Wed, 12 Dec 2018 22:51:56: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 22:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 22:51:58: #2 number of paired peaks: 15566 INFO @ Wed, 12 Dec 2018 22:51:58: start model_add_line... INFO @ Wed, 12 Dec 2018 22:51:58: start X-correlation... INFO @ Wed, 12 Dec 2018 22:51:58: end of X-cor INFO @ Wed, 12 Dec 2018 22:51:58: #2 finished! INFO @ Wed, 12 Dec 2018 22:51:58: #2 predicted fragment length is 102 bps INFO @ Wed, 12 Dec 2018 22:51:58: #2 alternative fragment length(s) may be 58,102 bps INFO @ Wed, 12 Dec 2018 22:51:58: #2.2 Generate R script for model : SRX1453553.10_model.r WARNING @ Wed, 12 Dec 2018 22:51:58: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 22:51:58: #2 You may need to consider one of the other alternative d(s): 58,102 WARNING @ Wed, 12 Dec 2018 22:51:58: #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 22:51:58: #3 Call peaks... INFO @ Wed, 12 Dec 2018 22:51:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 22:52:02: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 22:52:02: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 22:52:02: #1 total tags in treatment: 6777506 INFO @ Wed, 12 Dec 2018 22:52:02: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 22:52:02: #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 22:52:03: #1 tags after filtering in treatment: 6777303 INFO @ Wed, 12 Dec 2018 22:52:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 22:52:03: #1 finished! INFO @ Wed, 12 Dec 2018 22:52:03: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 22:52:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 22:52:03: 5000000 INFO @ Wed, 12 Dec 2018 22:52:05: #2 number of paired peaks: 15566 INFO @ Wed, 12 Dec 2018 22:52:05: start model_add_line... INFO @ Wed, 12 Dec 2018 22:52:05: start X-correlation... INFO @ Wed, 12 Dec 2018 22:52:05: end of X-cor INFO @ Wed, 12 Dec 2018 22:52:05: #2 finished! INFO @ Wed, 12 Dec 2018 22:52:05: #2 predicted fragment length is 102 bps INFO @ Wed, 12 Dec 2018 22:52:05: #2 alternative fragment length(s) may be 58,102 bps INFO @ Wed, 12 Dec 2018 22:52:05: #2.2 Generate R script for model : SRX1453553.05_model.r WARNING @ Wed, 12 Dec 2018 22:52:05: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 22:52:05: #2 You may need to consider one of the other alternative d(s): 58,102 WARNING @ Wed, 12 Dec 2018 22:52:05: #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 22:52:05: #3 Call peaks... INFO @ Wed, 12 Dec 2018 22:52:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 22:52:21: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 22:52:24: 6000000 INFO @ Wed, 12 Dec 2018 22:52:28: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 22:52:34: #4 Write output xls file... SRX1453553.10_peaks.xls INFO @ Wed, 12 Dec 2018 22:52:34: #4 Write peak in narrowPeak format file... SRX1453553.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 22:52:34: #4 Write summits bed file... SRX1453553.10_summits.bed INFO @ Wed, 12 Dec 2018 22:52:34: Done! pass1 - making usageList (34 chroms): 5 millis pass2 - checking and writing primary data (358 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 22:52:38: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 22:52:38: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 22:52:38: #1 total tags in treatment: 6777506 INFO @ Wed, 12 Dec 2018 22:52:38: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 22:52:38: #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 22:52:38: #1 tags after filtering in treatment: 6777303 INFO @ Wed, 12 Dec 2018 22:52:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 22:52:38: #1 finished! INFO @ Wed, 12 Dec 2018 22:52:38: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 22:52:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 22:52:40: #4 Write output xls file... SRX1453553.05_peaks.xls INFO @ Wed, 12 Dec 2018 22:52:40: #4 Write peak in narrowPeak format file... SRX1453553.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 22:52:40: #4 Write summits bed file... SRX1453553.05_summits.bed INFO @ Wed, 12 Dec 2018 22:52:40: Done! pass1 - making usageList (43 chroms): 4 millis pass2 - checking and writing primary data (691 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 22:52:41: #2 number of paired peaks: 15566 INFO @ Wed, 12 Dec 2018 22:52:41: start model_add_line... INFO @ Wed, 12 Dec 2018 22:52:41: start X-correlation... INFO @ Wed, 12 Dec 2018 22:52:41: end of X-cor INFO @ Wed, 12 Dec 2018 22:52:41: #2 finished! INFO @ Wed, 12 Dec 2018 22:52:41: #2 predicted fragment length is 102 bps INFO @ Wed, 12 Dec 2018 22:52:41: #2 alternative fragment length(s) may be 58,102 bps INFO @ Wed, 12 Dec 2018 22:52:41: #2.2 Generate R script for model : SRX1453553.20_model.r WARNING @ Wed, 12 Dec 2018 22:52:41: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 22:52:41: #2 You may need to consider one of the other alternative d(s): 58,102 WARNING @ Wed, 12 Dec 2018 22:52:41: #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 22:52:41: #3 Call peaks... INFO @ Wed, 12 Dec 2018 22:52:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 22:53:03: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 22:53:17: #4 Write output xls file... SRX1453553.20_peaks.xls INFO @ Wed, 12 Dec 2018 22:53:17: #4 Write peak in narrowPeak format file... SRX1453553.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 22:53:17: #4 Write summits bed file... SRX1453553.20_summits.bed INFO @ Wed, 12 Dec 2018 22:53:17: Done! pass1 - making usageList (24 chroms): 4 millis pass2 - checking and writing primary data (175 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。