Job ID = 10608885 sra ファイルのダウンロード中... Completed: 535292K bytes transferred in 23 seconds (184145K 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... Written 16593272 spots for /home/okishinya/chipatlas/results/rn6/SRX3145024/SRR5989255.sra Written 16593272 spots total 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:10 16593272 reads; of these: 16593272 (100.00%) were unpaired; of these: 328480 (1.98%) aligned 0 times 11348500 (68.39%) aligned exactly 1 time 4916292 (29.63%) aligned >1 times 98.02% overall alignment rate Time searching: 00:12:11 Overall time: 00:12:12 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] 575813 / 16264792 = 0.0354 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 @ Thu, 03 May 2018 22:40:09: # Command line: callpeak -t SRX3145024.bam -f BAM -g 2.15e9 -n SRX3145024.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3145024.10 # format = BAM # ChIP-seq file = ['SRX3145024.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 @ Thu, 03 May 2018 22:40:09: #1 read tag files... INFO @ Thu, 03 May 2018 22:40:09: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:40:09: # Command line: callpeak -t SRX3145024.bam -f BAM -g 2.15e9 -n SRX3145024.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3145024.20 # format = BAM # ChIP-seq file = ['SRX3145024.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 @ Thu, 03 May 2018 22:40:09: #1 read tag files... INFO @ Thu, 03 May 2018 22:40:09: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:40:09: # Command line: callpeak -t SRX3145024.bam -f BAM -g 2.15e9 -n SRX3145024.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3145024.05 # format = BAM # ChIP-seq file = ['SRX3145024.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 @ Thu, 03 May 2018 22:40:09: #1 read tag files... INFO @ Thu, 03 May 2018 22:40:09: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:40:17: 1000000 INFO @ Thu, 03 May 2018 22:40:17: 1000000 INFO @ Thu, 03 May 2018 22:40:17: 1000000 INFO @ Thu, 03 May 2018 22:40:24: 2000000 INFO @ Thu, 03 May 2018 22:40:24: 2000000 INFO @ Thu, 03 May 2018 22:40:24: 2000000 INFO @ Thu, 03 May 2018 22:40:31: 3000000 INFO @ Thu, 03 May 2018 22:40:32: 3000000 INFO @ Thu, 03 May 2018 22:40:32: 3000000 INFO @ Thu, 03 May 2018 22:40:38: 4000000 INFO @ Thu, 03 May 2018 22:40:39: 4000000 INFO @ Thu, 03 May 2018 22:40:39: 4000000 INFO @ Thu, 03 May 2018 22:40:45: 5000000 INFO @ Thu, 03 May 2018 22:40:46: 5000000 INFO @ Thu, 03 May 2018 22:40:46: 5000000 INFO @ Thu, 03 May 2018 22:40:52: 6000000 INFO @ Thu, 03 May 2018 22:40:54: 6000000 INFO @ Thu, 03 May 2018 22:40:54: 6000000 INFO @ Thu, 03 May 2018 22:40:59: 7000000 INFO @ Thu, 03 May 2018 22:41:01: 7000000 INFO @ Thu, 03 May 2018 22:41:01: 7000000 INFO @ Thu, 03 May 2018 22:41:06: 8000000 INFO @ Thu, 03 May 2018 22:41:09: 8000000 INFO @ Thu, 03 May 2018 22:41:09: 8000000 INFO @ Thu, 03 May 2018 22:41:13: 9000000 INFO @ Thu, 03 May 2018 22:41:16: 9000000 INFO @ Thu, 03 May 2018 22:41:16: 9000000 INFO @ Thu, 03 May 2018 22:41:20: 10000000 INFO @ Thu, 03 May 2018 22:41:24: 10000000 INFO @ Thu, 03 May 2018 22:41:24: 10000000 INFO @ Thu, 03 May 2018 22:41:27: 11000000 INFO @ Thu, 03 May 2018 22:41:31: 11000000 INFO @ Thu, 03 May 2018 22:41:31: 11000000 INFO @ Thu, 03 May 2018 22:41:35: 12000000 INFO @ Thu, 03 May 2018 22:41:39: 12000000 INFO @ Thu, 03 May 2018 22:41:39: 12000000 INFO @ Thu, 03 May 2018 22:41:42: 13000000 INFO @ Thu, 03 May 2018 22:41:46: 13000000 INFO @ Thu, 03 May 2018 22:41:46: 13000000 INFO @ Thu, 03 May 2018 22:41:49: 14000000 INFO @ Thu, 03 May 2018 22:41:54: 14000000 INFO @ Thu, 03 May 2018 22:41:54: 14000000 INFO @ Thu, 03 May 2018 22:41:56: 15000000 INFO @ Thu, 03 May 2018 22:42:01: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:42:01: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:42:01: #1 total tags in treatment: 15688979 INFO @ Thu, 03 May 2018 22:42:01: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:42:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:42:01: 15000000 INFO @ Thu, 03 May 2018 22:42:02: 15000000 INFO @ Thu, 03 May 2018 22:42:02: #1 tags after filtering in treatment: 15688812 INFO @ Thu, 03 May 2018 22:42:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:42:02: #1 finished! INFO @ Thu, 03 May 2018 22:42:02: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:42:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:42:04: #2 number of paired peaks: 6223 INFO @ Thu, 03 May 2018 22:42:04: start model_add_line... INFO @ Thu, 03 May 2018 22:42:04: start X-correlation... INFO @ Thu, 03 May 2018 22:42:04: end of X-cor INFO @ Thu, 03 May 2018 22:42:04: #2 finished! INFO @ Thu, 03 May 2018 22:42:04: #2 predicted fragment length is 51 bps INFO @ Thu, 03 May 2018 22:42:04: #2 alternative fragment length(s) may be 51,122,142,232,392 bps INFO @ Thu, 03 May 2018 22:42:04: #2.2 Generate R script for model : SRX3145024.10_model.r WARNING @ Thu, 03 May 2018 22:42:04: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:42:04: #2 You may need to consider one of the other alternative d(s): 51,122,142,232,392 WARNING @ Thu, 03 May 2018 22:42:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:42:04: #3 Call peaks... INFO @ Thu, 03 May 2018 22:42:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:42:07: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:42:07: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:42:07: #1 total tags in treatment: 15688979 INFO @ Thu, 03 May 2018 22:42:07: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:42:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:42:07: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:42:07: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:42:07: #1 total tags in treatment: 15688979 INFO @ Thu, 03 May 2018 22:42:07: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:42:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:42:07: #1 tags after filtering in treatment: 15688812 INFO @ Thu, 03 May 2018 22:42:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:42:07: #1 finished! INFO @ Thu, 03 May 2018 22:42:07: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:42:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:42:07: #1 tags after filtering in treatment: 15688812 INFO @ Thu, 03 May 2018 22:42:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:42:07: #1 finished! INFO @ Thu, 03 May 2018 22:42:07: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:42:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:42:09: #2 number of paired peaks: 6223 INFO @ Thu, 03 May 2018 22:42:09: start model_add_line... INFO @ Thu, 03 May 2018 22:42:09: start X-correlation... INFO @ Thu, 03 May 2018 22:42:09: end of X-cor INFO @ Thu, 03 May 2018 22:42:09: #2 finished! INFO @ Thu, 03 May 2018 22:42:09: #2 predicted fragment length is 51 bps INFO @ Thu, 03 May 2018 22:42:09: #2 alternative fragment length(s) may be 51,122,142,232,392 bps INFO @ Thu, 03 May 2018 22:42:09: #2.2 Generate R script for model : SRX3145024.20_model.r WARNING @ Thu, 03 May 2018 22:42:09: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:42:09: #2 You may need to consider one of the other alternative d(s): 51,122,142,232,392 WARNING @ Thu, 03 May 2018 22:42:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:42:09: #3 Call peaks... INFO @ Thu, 03 May 2018 22:42:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:42:10: #2 number of paired peaks: 6223 INFO @ Thu, 03 May 2018 22:42:10: start model_add_line... INFO @ Thu, 03 May 2018 22:42:10: start X-correlation... INFO @ Thu, 03 May 2018 22:42:10: end of X-cor INFO @ Thu, 03 May 2018 22:42:10: #2 finished! INFO @ Thu, 03 May 2018 22:42:10: #2 predicted fragment length is 51 bps INFO @ Thu, 03 May 2018 22:42:10: #2 alternative fragment length(s) may be 51,122,142,232,392 bps INFO @ Thu, 03 May 2018 22:42:10: #2.2 Generate R script for model : SRX3145024.05_model.r WARNING @ Thu, 03 May 2018 22:42:10: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:42:10: #2 You may need to consider one of the other alternative d(s): 51,122,142,232,392 WARNING @ Thu, 03 May 2018 22:42:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:42:10: #3 Call peaks... INFO @ Thu, 03 May 2018 22:42:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:42:41: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:42:45: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:42:52: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:43:00: #4 Write output xls file... SRX3145024.10_peaks.xls INFO @ Thu, 03 May 2018 22:43:00: #4 Write peak in narrowPeak format file... SRX3145024.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:43:00: #4 Write summits bed file... SRX3145024.10_summits.bed INFO @ Thu, 03 May 2018 22:43:00: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (850 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:43:07: #4 Write output xls file... SRX3145024.20_peaks.xls INFO @ Thu, 03 May 2018 22:43:07: #4 Write peak in narrowPeak format file... SRX3145024.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:43:07: #4 Write summits bed file... SRX3145024.20_summits.bed INFO @ Thu, 03 May 2018 22:43:07: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:43:14: #4 Write output xls file... SRX3145024.05_peaks.xls INFO @ Thu, 03 May 2018 22:43:14: #4 Write peak in narrowPeak format file... SRX3145024.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:43:14: #4 Write summits bed file... SRX3145024.05_summits.bed INFO @ Thu, 03 May 2018 22:43:14: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (1315 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。