Job ID = 10194824 sra ファイルのダウンロード中... Completed: 881210K bytes transferred in 15 seconds (467233K 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 45599094 spots for /home/okishinya/chipatlas/results/rn6/SRX1977114/SRR3952246.sra Written 45599094 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: 00:00:01 Multiseed full-index search: 01:00:22 45599094 reads; of these: 45599094 (100.00%) were unpaired; of these: 23479118 (51.49%) aligned 0 times 13820637 (30.31%) aligned exactly 1 time 8299339 (18.20%) aligned >1 times 48.51% overall alignment rate Time searching: 01:00:24 Overall time: 01:00:24 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 12 files... [bam_rmdupse_core] 2697230 / 22119976 = 0.1219 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 @ Sat, 11 Nov 2017 02:08:39: # Command line: callpeak -t SRX1977114.bam -f BAM -g 2.15e9 -n SRX1977114.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977114.05 # format = BAM # ChIP-seq file = ['SRX1977114.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 @ Sat, 11 Nov 2017 02:08:39: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:08:39: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:08:39: # Command line: callpeak -t SRX1977114.bam -f BAM -g 2.15e9 -n SRX1977114.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977114.10 # format = BAM # ChIP-seq file = ['SRX1977114.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 @ Sat, 11 Nov 2017 02:08:39: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:08:39: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:08:39: # Command line: callpeak -t SRX1977114.bam -f BAM -g 2.15e9 -n SRX1977114.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977114.20 # format = BAM # ChIP-seq file = ['SRX1977114.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 @ Sat, 11 Nov 2017 02:08:39: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:08:39: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:08:46: 1000000 INFO @ Sat, 11 Nov 2017 02:08:46: 1000000 INFO @ Sat, 11 Nov 2017 02:08:47: 1000000 INFO @ Sat, 11 Nov 2017 02:08:52: 2000000 INFO @ Sat, 11 Nov 2017 02:08:54: 2000000 INFO @ Sat, 11 Nov 2017 02:08:54: 2000000 INFO @ Sat, 11 Nov 2017 02:08:59: 3000000 INFO @ Sat, 11 Nov 2017 02:09:01: 3000000 INFO @ Sat, 11 Nov 2017 02:09:01: 3000000 INFO @ Sat, 11 Nov 2017 02:09:06: 4000000 INFO @ Sat, 11 Nov 2017 02:09:09: 4000000 INFO @ Sat, 11 Nov 2017 02:09:09: 4000000 INFO @ Sat, 11 Nov 2017 02:09:12: 5000000 INFO @ Sat, 11 Nov 2017 02:09:16: 5000000 INFO @ Sat, 11 Nov 2017 02:09:16: 5000000 INFO @ Sat, 11 Nov 2017 02:09:19: 6000000 INFO @ Sat, 11 Nov 2017 02:09:23: 6000000 INFO @ Sat, 11 Nov 2017 02:09:23: 6000000 INFO @ Sat, 11 Nov 2017 02:09:25: 7000000 INFO @ Sat, 11 Nov 2017 02:09:31: 7000000 INFO @ Sat, 11 Nov 2017 02:09:31: 7000000 INFO @ Sat, 11 Nov 2017 02:09:32: 8000000 INFO @ Sat, 11 Nov 2017 02:09:38: 8000000 INFO @ Sat, 11 Nov 2017 02:09:38: 8000000 INFO @ Sat, 11 Nov 2017 02:09:39: 9000000 INFO @ Sat, 11 Nov 2017 02:09:45: 9000000 INFO @ Sat, 11 Nov 2017 02:09:45: 9000000 INFO @ Sat, 11 Nov 2017 02:09:46: 10000000 INFO @ Sat, 11 Nov 2017 02:09:52: 11000000 INFO @ Sat, 11 Nov 2017 02:09:52: 10000000 INFO @ Sat, 11 Nov 2017 02:09:52: 10000000 INFO @ Sat, 11 Nov 2017 02:09:59: 12000000 INFO @ Sat, 11 Nov 2017 02:10:00: 11000000 INFO @ Sat, 11 Nov 2017 02:10:00: 11000000 INFO @ Sat, 11 Nov 2017 02:10:05: 13000000 INFO @ Sat, 11 Nov 2017 02:10:07: 12000000 INFO @ Sat, 11 Nov 2017 02:10:07: 12000000 INFO @ Sat, 11 Nov 2017 02:10:12: 14000000 INFO @ Sat, 11 Nov 2017 02:10:15: 13000000 INFO @ Sat, 11 Nov 2017 02:10:15: 13000000 INFO @ Sat, 11 Nov 2017 02:10:18: 15000000 INFO @ Sat, 11 Nov 2017 02:10:23: 14000000 INFO @ Sat, 11 Nov 2017 02:10:23: 14000000 INFO @ Sat, 11 Nov 2017 02:10:25: 16000000 INFO @ Sat, 11 Nov 2017 02:10:30: 15000000 INFO @ Sat, 11 Nov 2017 02:10:30: 15000000 INFO @ Sat, 11 Nov 2017 02:10:32: 17000000 INFO @ Sat, 11 Nov 2017 02:10:38: 16000000 INFO @ Sat, 11 Nov 2017 02:10:38: 16000000 INFO @ Sat, 11 Nov 2017 02:10:38: 18000000 INFO @ Sat, 11 Nov 2017 02:10:45: 17000000 INFO @ Sat, 11 Nov 2017 02:10:45: 17000000 INFO @ Sat, 11 Nov 2017 02:10:45: 19000000 INFO @ Sat, 11 Nov 2017 02:10:49: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:10:49: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:10:49: #1 total tags in treatment: 19422746 INFO @ Sat, 11 Nov 2017 02:10:49: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:10:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:10:49: #1 tags after filtering in treatment: 19422632 INFO @ Sat, 11 Nov 2017 02:10:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:10:49: #1 finished! INFO @ Sat, 11 Nov 2017 02:10:49: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:10:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:10:52: #2 number of paired peaks: 14585 INFO @ Sat, 11 Nov 2017 02:10:52: start model_add_line... INFO @ Sat, 11 Nov 2017 02:10:52: start X-correlation... INFO @ Sat, 11 Nov 2017 02:10:52: end of X-cor INFO @ Sat, 11 Nov 2017 02:10:52: #2 finished! INFO @ Sat, 11 Nov 2017 02:10:52: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Nov 2017 02:10:52: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Nov 2017 02:10:52: #2.2 Generate R script for model : SRX1977114.20_model.r WARNING @ Sat, 11 Nov 2017 02:10:52: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 02:10:52: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Nov 2017 02:10:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 02:10:52: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:10:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:10:52: 18000000 INFO @ Sat, 11 Nov 2017 02:10:53: 18000000 INFO @ Sat, 11 Nov 2017 02:11:00: 19000000 INFO @ Sat, 11 Nov 2017 02:11:00: 19000000 INFO @ Sat, 11 Nov 2017 02:11:03: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:11:03: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:11:03: #1 total tags in treatment: 19422746 INFO @ Sat, 11 Nov 2017 02:11:03: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:11:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:11:03: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:11:03: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:11:03: #1 total tags in treatment: 19422746 INFO @ Sat, 11 Nov 2017 02:11:03: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:11:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:11:04: #1 tags after filtering in treatment: 19422632 INFO @ Sat, 11 Nov 2017 02:11:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:11:04: #1 finished! INFO @ Sat, 11 Nov 2017 02:11:04: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:11:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:11:04: #1 tags after filtering in treatment: 19422632 INFO @ Sat, 11 Nov 2017 02:11:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:11:04: #1 finished! INFO @ Sat, 11 Nov 2017 02:11:04: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:11:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:11:06: #2 number of paired peaks: 14585 INFO @ Sat, 11 Nov 2017 02:11:06: start model_add_line... INFO @ Sat, 11 Nov 2017 02:11:06: #2 number of paired peaks: 14585 INFO @ Sat, 11 Nov 2017 02:11:06: start model_add_line... INFO @ Sat, 11 Nov 2017 02:11:06: start X-correlation... INFO @ Sat, 11 Nov 2017 02:11:06: end of X-cor INFO @ Sat, 11 Nov 2017 02:11:06: #2 finished! INFO @ Sat, 11 Nov 2017 02:11:06: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Nov 2017 02:11:06: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Nov 2017 02:11:06: #2.2 Generate R script for model : SRX1977114.05_model.r WARNING @ Sat, 11 Nov 2017 02:11:06: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 02:11:06: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Nov 2017 02:11:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 02:11:06: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:11:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:11:06: start X-correlation... INFO @ Sat, 11 Nov 2017 02:11:06: end of X-cor INFO @ Sat, 11 Nov 2017 02:11:06: #2 finished! INFO @ Sat, 11 Nov 2017 02:11:06: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Nov 2017 02:11:06: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Nov 2017 02:11:06: #2.2 Generate R script for model : SRX1977114.10_model.r WARNING @ Sat, 11 Nov 2017 02:11:07: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 02:11:07: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Nov 2017 02:11:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 02:11:07: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:11:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:11:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:11:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:11:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:12:06: #4 Write output xls file... SRX1977114.20_peaks.xls INFO @ Sat, 11 Nov 2017 02:12:06: #4 Write peak in narrowPeak format file... SRX1977114.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:12:06: #4 Write summits bed file... SRX1977114.20_summits.bed INFO @ Sat, 11 Nov 2017 02:12:06: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (1025 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:12:20: #4 Write output xls file... SRX1977114.10_peaks.xls INFO @ Sat, 11 Nov 2017 02:12:20: #4 Write peak in narrowPeak format file... SRX1977114.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:12:20: #4 Write summits bed file... SRX1977114.10_summits.bed INFO @ Sat, 11 Nov 2017 02:12:20: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (4359 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:12:22: #4 Write output xls file... SRX1977114.05_peaks.xls INFO @ Sat, 11 Nov 2017 02:12:22: #4 Write peak in narrowPeak format file... SRX1977114.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:12:22: #4 Write summits bed file... SRX1977114.05_summits.bed INFO @ Sat, 11 Nov 2017 02:12:22: Done! pass1 - making usageList (141 chroms): 3 millis pass2 - checking and writing primary data (15463 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。