Job ID = 10194943 sra ファイルのダウンロード中... Completed: 746068K bytes transferred in 11 seconds (528214K 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 19952832 spots for /home/okishinya/chipatlas/results/rn6/SRX2568196/SRR5264108.sra Written 19952832 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:49:28 19952832 reads; of these: 19952832 (100.00%) were unpaired; of these: 2735717 (13.71%) aligned 0 times 12780690 (64.05%) aligned exactly 1 time 4436425 (22.23%) aligned >1 times 86.29% overall alignment rate Time searching: 00:49:33 Overall time: 00:49:33 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] 3238615 / 17217115 = 0.1881 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 00:56:09: # Command line: callpeak -t SRX2568196.bam -f BAM -g 2.15e9 -n SRX2568196.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2568196.05 # format = BAM # ChIP-seq file = ['SRX2568196.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 00:56:09: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:56:09: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:56:09: # Command line: callpeak -t SRX2568196.bam -f BAM -g 2.15e9 -n SRX2568196.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2568196.10 # format = BAM # ChIP-seq file = ['SRX2568196.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 00:56:09: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:56:09: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:56:09: # Command line: callpeak -t SRX2568196.bam -f BAM -g 2.15e9 -n SRX2568196.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2568196.20 # format = BAM # ChIP-seq file = ['SRX2568196.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 00:56:09: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:56:09: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:56:18: 1000000 INFO @ Sat, 11 Nov 2017 00:56:20: 1000000 INFO @ Sat, 11 Nov 2017 00:56:20: 1000000 INFO @ Sat, 11 Nov 2017 00:56:27: 2000000 INFO @ Sat, 11 Nov 2017 00:56:33: 2000000 INFO @ Sat, 11 Nov 2017 00:56:33: 2000000 INFO @ Sat, 11 Nov 2017 00:56:37: 3000000 INFO @ Sat, 11 Nov 2017 00:56:46: 4000000 INFO @ Sat, 11 Nov 2017 00:56:49: 3000000 INFO @ Sat, 11 Nov 2017 00:56:49: 3000000 INFO @ Sat, 11 Nov 2017 00:56:55: 5000000 INFO @ Sat, 11 Nov 2017 00:57:02: 4000000 INFO @ Sat, 11 Nov 2017 00:57:02: 4000000 INFO @ Sat, 11 Nov 2017 00:57:04: 6000000 INFO @ Sat, 11 Nov 2017 00:57:13: 7000000 INFO @ Sat, 11 Nov 2017 00:57:15: 5000000 INFO @ Sat, 11 Nov 2017 00:57:16: 5000000 INFO @ Sat, 11 Nov 2017 00:57:22: 8000000 INFO @ Sat, 11 Nov 2017 00:57:25: 6000000 INFO @ Sat, 11 Nov 2017 00:57:30: 6000000 INFO @ Sat, 11 Nov 2017 00:57:32: 9000000 INFO @ Sat, 11 Nov 2017 00:57:37: 7000000 INFO @ Sat, 11 Nov 2017 00:57:41: 10000000 INFO @ Sat, 11 Nov 2017 00:57:43: 7000000 INFO @ Sat, 11 Nov 2017 00:57:50: 8000000 INFO @ Sat, 11 Nov 2017 00:57:50: 11000000 INFO @ Sat, 11 Nov 2017 00:57:56: 8000000 INFO @ Sat, 11 Nov 2017 00:57:59: 12000000 INFO @ Sat, 11 Nov 2017 00:58:03: 9000000 INFO @ Sat, 11 Nov 2017 00:58:06: 9000000 INFO @ Sat, 11 Nov 2017 00:58:09: 13000000 INFO @ Sat, 11 Nov 2017 00:58:16: 10000000 INFO @ Sat, 11 Nov 2017 00:58:16: 10000000 INFO @ Sat, 11 Nov 2017 00:58:18: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 00:58:18: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 00:58:18: #1 total tags in treatment: 13978500 INFO @ Sat, 11 Nov 2017 00:58:18: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:58:18: #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 00:58:19: #1 tags after filtering in treatment: 13978321 INFO @ Sat, 11 Nov 2017 00:58:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:58:19: #1 finished! INFO @ Sat, 11 Nov 2017 00:58:19: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:58:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:58:21: #2 number of paired peaks: 5386 INFO @ Sat, 11 Nov 2017 00:58:21: start model_add_line... INFO @ Sat, 11 Nov 2017 00:58:21: start X-correlation... INFO @ Sat, 11 Nov 2017 00:58:21: end of X-cor INFO @ Sat, 11 Nov 2017 00:58:21: #2 finished! INFO @ Sat, 11 Nov 2017 00:58:21: #2 predicted fragment length is 75 bps INFO @ Sat, 11 Nov 2017 00:58:21: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 11 Nov 2017 00:58:21: #2.2 Generate R script for model : SRX2568196.10_model.r WARNING @ Sat, 11 Nov 2017 00:58:21: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:58:21: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 11 Nov 2017 00:58:21: #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 00:58:21: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:58:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:58:26: 11000000 INFO @ Sat, 11 Nov 2017 00:58:29: 11000000 INFO @ Sat, 11 Nov 2017 00:58:36: 12000000 INFO @ Sat, 11 Nov 2017 00:58:43: 12000000 INFO @ Sat, 11 Nov 2017 00:58:45: 13000000 INFO @ Sat, 11 Nov 2017 00:58:56: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 00:58:56: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 00:58:56: #1 total tags in treatment: 13978500 INFO @ Sat, 11 Nov 2017 00:58:56: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:58:56: #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 00:58:56: #1 tags after filtering in treatment: 13978321 INFO @ Sat, 11 Nov 2017 00:58:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:58:56: #1 finished! INFO @ Sat, 11 Nov 2017 00:58:56: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:58:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:58:57: 13000000 INFO @ Sat, 11 Nov 2017 00:58:58: #2 number of paired peaks: 5386 INFO @ Sat, 11 Nov 2017 00:58:58: start model_add_line... INFO @ Sat, 11 Nov 2017 00:58:58: start X-correlation... INFO @ Sat, 11 Nov 2017 00:58:58: end of X-cor INFO @ Sat, 11 Nov 2017 00:58:58: #2 finished! INFO @ Sat, 11 Nov 2017 00:58:58: #2 predicted fragment length is 75 bps INFO @ Sat, 11 Nov 2017 00:58:58: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 11 Nov 2017 00:58:58: #2.2 Generate R script for model : SRX2568196.05_model.r WARNING @ Sat, 11 Nov 2017 00:58:58: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:58:58: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 11 Nov 2017 00:58:58: #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 00:58:58: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:58:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:59:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:59:09: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 00:59:09: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 00:59:09: #1 total tags in treatment: 13978500 INFO @ Sat, 11 Nov 2017 00:59:09: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:59:09: #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 00:59:10: #1 tags after filtering in treatment: 13978321 INFO @ Sat, 11 Nov 2017 00:59:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:59:10: #1 finished! INFO @ Sat, 11 Nov 2017 00:59:10: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:59:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:59:12: #2 number of paired peaks: 5386 INFO @ Sat, 11 Nov 2017 00:59:12: start model_add_line... INFO @ Sat, 11 Nov 2017 00:59:12: start X-correlation... INFO @ Sat, 11 Nov 2017 00:59:12: end of X-cor INFO @ Sat, 11 Nov 2017 00:59:12: #2 finished! INFO @ Sat, 11 Nov 2017 00:59:12: #2 predicted fragment length is 75 bps INFO @ Sat, 11 Nov 2017 00:59:12: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 11 Nov 2017 00:59:12: #2.2 Generate R script for model : SRX2568196.20_model.r WARNING @ Sat, 11 Nov 2017 00:59:12: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:59:12: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 11 Nov 2017 00:59:12: #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 00:59:12: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:59:24: #4 Write output xls file... SRX2568196.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:59:24: #4 Write peak in narrowPeak format file... SRX2568196.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:59:24: #4 Write summits bed file... SRX2568196.10_summits.bed INFO @ Sat, 11 Nov 2017 00:59:24: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (582 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:59:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:59:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:00:02: #4 Write output xls file... SRX2568196.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:00:02: #4 Write peak in narrowPeak format file... SRX2568196.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:00:02: #4 Write summits bed file... SRX2568196.05_summits.bed INFO @ Sat, 11 Nov 2017 01:00:02: Done! pass1 - making usageList (48 chroms): 2 millis pass2 - checking and writing primary data (985 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:00:15: #4 Write output xls file... SRX2568196.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:00:15: #4 Write peak in narrowPeak format file... SRX2568196.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:00:15: #4 Write summits bed file... SRX2568196.20_summits.bed INFO @ Sat, 11 Nov 2017 01:00:15: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (333 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。