Job ID = 10194721 sra ファイルのダウンロード中... Completed: 5565201K bytes transferred in 67 seconds (674867K 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 93107681 spots for /home/okishinya/chipatlas/results/rn6/SRX1037556/SRR2039160.sra Written 93107681 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: 00:00:02 Time loading forward index: 00:00:04 Time loading mirror index: 00:00:02 Multiseed full-index search: 04:59:38 93107681 reads; of these: 93107681 (100.00%) were unpaired; of these: 1945427 (2.09%) aligned 0 times 68491182 (73.56%) aligned exactly 1 time 22671072 (24.35%) aligned >1 times 97.91% overall alignment rate Time searching: 04:59:46 Overall time: 04:59:46 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 40 files... [bam_rmdupse_core] 83775806 / 91162254 = 0.9190 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 00:40:23: # Command line: callpeak -t SRX1037556.bam -f BAM -g 2.15e9 -n SRX1037556.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1037556.10 # format = BAM # ChIP-seq file = ['SRX1037556.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 00:40:23: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:40:23: # Command line: callpeak -t SRX1037556.bam -f BAM -g 2.15e9 -n SRX1037556.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1037556.05 # format = BAM # ChIP-seq file = ['SRX1037556.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 00:40:23: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:40:23: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:40:23: # Command line: callpeak -t SRX1037556.bam -f BAM -g 2.15e9 -n SRX1037556.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1037556.20 # format = BAM # ChIP-seq file = ['SRX1037556.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 00:40:23: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:40:23: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:40:23: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:40:34: 1000000 INFO @ Sat, 11 Nov 2017 00:40:34: 1000000 INFO @ Sat, 11 Nov 2017 00:40:34: 1000000 INFO @ Sat, 11 Nov 2017 00:40:45: 2000000 INFO @ Sat, 11 Nov 2017 00:40:45: 2000000 INFO @ Sat, 11 Nov 2017 00:40:45: 2000000 INFO @ Sat, 11 Nov 2017 00:40:55: 3000000 INFO @ Sat, 11 Nov 2017 00:40:55: 3000000 INFO @ Sat, 11 Nov 2017 00:40:56: 3000000 INFO @ Sat, 11 Nov 2017 00:41:05: 4000000 INFO @ Sat, 11 Nov 2017 00:41:06: 4000000 INFO @ Sat, 11 Nov 2017 00:41:06: 4000000 INFO @ Sat, 11 Nov 2017 00:41:15: 5000000 INFO @ Sat, 11 Nov 2017 00:41:16: 5000000 INFO @ Sat, 11 Nov 2017 00:41:16: 5000000 INFO @ Sat, 11 Nov 2017 00:41:25: 6000000 INFO @ Sat, 11 Nov 2017 00:41:26: 6000000 INFO @ Sat, 11 Nov 2017 00:41:27: 6000000 INFO @ Sat, 11 Nov 2017 00:41:36: 7000000 INFO @ Sat, 11 Nov 2017 00:41:36: 7000000 INFO @ Sat, 11 Nov 2017 00:41:37: 7000000 INFO @ Sat, 11 Nov 2017 00:41:40: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 00:41:40: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 00:41:40: #1 total tags in treatment: 7386448 INFO @ Sat, 11 Nov 2017 00:41:40: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:41:40: #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 00:41:40: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 00:41:40: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 00:41:40: #1 total tags in treatment: 7386448 INFO @ Sat, 11 Nov 2017 00:41:40: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:41:40: #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 00:41:40: #1 tags after filtering in treatment: 7386221 INFO @ Sat, 11 Nov 2017 00:41:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:41:40: #1 finished! INFO @ Sat, 11 Nov 2017 00:41:40: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:41:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:41:41: #1 tags after filtering in treatment: 7386221 INFO @ Sat, 11 Nov 2017 00:41:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:41:41: #1 finished! INFO @ Sat, 11 Nov 2017 00:41:41: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:41:41: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 00:41:41: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 00:41:41: #1 total tags in treatment: 7386448 INFO @ Sat, 11 Nov 2017 00:41:41: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:41:41: #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 00:41:42: #1 tags after filtering in treatment: 7386221 INFO @ Sat, 11 Nov 2017 00:41:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:41:42: #1 finished! INFO @ Sat, 11 Nov 2017 00:41:42: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:41:44: #2 number of paired peaks: 72697 INFO @ Sat, 11 Nov 2017 00:41:44: start model_add_line... INFO @ Sat, 11 Nov 2017 00:41:44: start X-correlation... INFO @ Sat, 11 Nov 2017 00:41:44: end of X-cor INFO @ Sat, 11 Nov 2017 00:41:44: #2 finished! INFO @ Sat, 11 Nov 2017 00:41:44: #2 predicted fragment length is 124 bps INFO @ Sat, 11 Nov 2017 00:41:44: #2 alternative fragment length(s) may be 124 bps INFO @ Sat, 11 Nov 2017 00:41:44: #2.2 Generate R script for model : SRX1037556.10_model.r WARNING @ Sat, 11 Nov 2017 00:41:44: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:41:44: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Sat, 11 Nov 2017 00:41:44: #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 00:41:44: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:41:45: #2 number of paired peaks: 72697 INFO @ Sat, 11 Nov 2017 00:41:45: start model_add_line... INFO @ Sat, 11 Nov 2017 00:41:45: start X-correlation... INFO @ Sat, 11 Nov 2017 00:41:45: end of X-cor INFO @ Sat, 11 Nov 2017 00:41:45: #2 finished! INFO @ Sat, 11 Nov 2017 00:41:45: #2 predicted fragment length is 124 bps INFO @ Sat, 11 Nov 2017 00:41:45: #2 alternative fragment length(s) may be 124 bps INFO @ Sat, 11 Nov 2017 00:41:45: #2.2 Generate R script for model : SRX1037556.20_model.r WARNING @ Sat, 11 Nov 2017 00:41:45: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:41:45: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Sat, 11 Nov 2017 00:41:45: #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 00:41:45: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:41:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:41:46: #2 number of paired peaks: 72697 INFO @ Sat, 11 Nov 2017 00:41:46: start model_add_line... INFO @ Sat, 11 Nov 2017 00:41:46: start X-correlation... INFO @ Sat, 11 Nov 2017 00:41:46: end of X-cor INFO @ Sat, 11 Nov 2017 00:41:46: #2 finished! INFO @ Sat, 11 Nov 2017 00:41:46: #2 predicted fragment length is 124 bps INFO @ Sat, 11 Nov 2017 00:41:46: #2 alternative fragment length(s) may be 124 bps INFO @ Sat, 11 Nov 2017 00:41:46: #2.2 Generate R script for model : SRX1037556.05_model.r WARNING @ Sat, 11 Nov 2017 00:41:46: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:41:46: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Sat, 11 Nov 2017 00:41:46: #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 00:41:46: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:41:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:42:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:42:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:42:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:42:17: #4 Write output xls file... SRX1037556.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:42:17: #4 Write peak in narrowPeak format file... SRX1037556.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:42:17: #4 Write summits bed file... SRX1037556.10_summits.bed INFO @ Sat, 11 Nov 2017 00:42:17: Done! pass1 - making usageList (50 chroms): 2 millis pass2 - checking and writing primary data (1779 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:42:18: #4 Write output xls file... SRX1037556.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:42:18: #4 Write peak in narrowPeak format file... SRX1037556.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:42:18: #4 Write summits bed file... SRX1037556.20_summits.bed INFO @ Sat, 11 Nov 2017 00:42:18: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (263 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:42:20: #4 Write output xls file... SRX1037556.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:42:20: #4 Write peak in narrowPeak format file... SRX1037556.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:42:20: #4 Write summits bed file... SRX1037556.05_summits.bed INFO @ Sat, 11 Nov 2017 00:42:20: Done! pass1 - making usageList (77 chroms): 10 millis pass2 - checking and writing primary data (13168 records, 4 fields): 32 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。