Job ID = 10194725 sra ファイルのダウンロード中... Completed: 3490841K bytes transferred in 42 seconds (671240K 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 58906651 spots for /home/okishinya/chipatlas/results/rn6/SRX1037560/SRR2039164.sra Written 58906651 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: 02:57:19 58906651 reads; of these: 58906651 (100.00%) were unpaired; of these: 3205210 (5.44%) aligned 0 times 43510826 (73.86%) aligned exactly 1 time 12190615 (20.69%) aligned >1 times 94.56% overall alignment rate Time searching: 02:57:23 Overall time: 02:57:23 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 24 files... [bam_rmdupse_core] 52917056 / 55701441 = 0.9500 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 @ Fri, 10 Nov 2017 22:35:39: # Command line: callpeak -t SRX1037560.bam -f BAM -g 2.15e9 -n SRX1037560.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1037560.20 # format = BAM # ChIP-seq file = ['SRX1037560.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 @ Fri, 10 Nov 2017 22:35:39: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:35:39: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:35:39: # Command line: callpeak -t SRX1037560.bam -f BAM -g 2.15e9 -n SRX1037560.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1037560.05 # format = BAM # ChIP-seq file = ['SRX1037560.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 @ Fri, 10 Nov 2017 22:35:39: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:35:39: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:35:39: # Command line: callpeak -t SRX1037560.bam -f BAM -g 2.15e9 -n SRX1037560.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1037560.10 # format = BAM # ChIP-seq file = ['SRX1037560.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 @ Fri, 10 Nov 2017 22:35:39: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:35:39: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:35:53: 1000000 INFO @ Fri, 10 Nov 2017 22:35:54: 1000000 INFO @ Fri, 10 Nov 2017 22:35:54: 1000000 INFO @ Fri, 10 Nov 2017 22:36:05: 2000000 INFO @ Fri, 10 Nov 2017 22:36:07: 2000000 INFO @ Fri, 10 Nov 2017 22:36:07: 2000000 INFO @ Fri, 10 Nov 2017 22:36:14: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 22:36:14: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 22:36:14: #1 total tags in treatment: 2784385 INFO @ Fri, 10 Nov 2017 22:36:14: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:36:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:36:14: #1 tags after filtering in treatment: 2784040 INFO @ Fri, 10 Nov 2017 22:36:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:36:14: #1 finished! INFO @ Fri, 10 Nov 2017 22:36:14: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:36:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:36:17: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 22:36:17: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 22:36:17: #1 total tags in treatment: 2784385 INFO @ Fri, 10 Nov 2017 22:36:17: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:36:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:36:17: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 22:36:17: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 22:36:17: #1 total tags in treatment: 2784385 INFO @ Fri, 10 Nov 2017 22:36:17: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:36:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:36:18: #1 tags after filtering in treatment: 2784040 INFO @ Fri, 10 Nov 2017 22:36:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:36:18: #1 finished! INFO @ Fri, 10 Nov 2017 22:36:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:36:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:36:18: #1 tags after filtering in treatment: 2784040 INFO @ Fri, 10 Nov 2017 22:36:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:36:18: #1 finished! INFO @ Fri, 10 Nov 2017 22:36:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:36:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:36:19: #2 number of paired peaks: 72203 INFO @ Fri, 10 Nov 2017 22:36:19: start model_add_line... INFO @ Fri, 10 Nov 2017 22:36:19: start X-correlation... INFO @ Fri, 10 Nov 2017 22:36:19: end of X-cor INFO @ Fri, 10 Nov 2017 22:36:19: #2 finished! INFO @ Fri, 10 Nov 2017 22:36:19: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Nov 2017 22:36:19: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Nov 2017 22:36:19: #2.2 Generate R script for model : SRX1037560.05_model.r WARNING @ Fri, 10 Nov 2017 22:36:19: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:36:19: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Nov 2017 22:36:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 22:36:19: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:36:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:36:22: #2 number of paired peaks: 72203 INFO @ Fri, 10 Nov 2017 22:36:22: start model_add_line... INFO @ Fri, 10 Nov 2017 22:36:22: start X-correlation... INFO @ Fri, 10 Nov 2017 22:36:22: #2 number of paired peaks: 72203 INFO @ Fri, 10 Nov 2017 22:36:22: start model_add_line... INFO @ Fri, 10 Nov 2017 22:36:22: end of X-cor INFO @ Fri, 10 Nov 2017 22:36:22: #2 finished! INFO @ Fri, 10 Nov 2017 22:36:22: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Nov 2017 22:36:22: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Nov 2017 22:36:22: #2.2 Generate R script for model : SRX1037560.20_model.r WARNING @ Fri, 10 Nov 2017 22:36:22: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:36:22: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Nov 2017 22:36:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 22:36:22: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:36:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:36:22: start X-correlation... INFO @ Fri, 10 Nov 2017 22:36:22: end of X-cor INFO @ Fri, 10 Nov 2017 22:36:22: #2 finished! INFO @ Fri, 10 Nov 2017 22:36:22: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Nov 2017 22:36:22: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Nov 2017 22:36:22: #2.2 Generate R script for model : SRX1037560.10_model.r WARNING @ Fri, 10 Nov 2017 22:36:22: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:36:22: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Nov 2017 22:36:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 22:36:22: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:36:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:36:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:36:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:36:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:36:34: #4 Write output xls file... SRX1037560.05_peaks.xls INFO @ Fri, 10 Nov 2017 22:36:34: #4 Write peak in narrowPeak format file... SRX1037560.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:36:34: #4 Write summits bed file... SRX1037560.05_summits.bed INFO @ Fri, 10 Nov 2017 22:36:34: Done! pass1 - making usageList (55 chroms): 2 millis pass2 - checking and writing primary data (2108 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:36:37: #4 Write output xls file... SRX1037560.20_peaks.xls INFO @ Fri, 10 Nov 2017 22:36:37: #4 Write peak in narrowPeak format file... SRX1037560.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:36:37: #4 Write summits bed file... SRX1037560.20_summits.bed INFO @ Fri, 10 Nov 2017 22:36:37: Done! pass1 - making usageList (24 chroms): 2 millis pass2 - checking and writing primary data (121 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:36:37: #4 Write output xls file... SRX1037560.10_peaks.xls INFO @ Fri, 10 Nov 2017 22:36:37: #4 Write peak in narrowPeak format file... SRX1037560.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:36:37: #4 Write summits bed file... SRX1037560.10_summits.bed INFO @ Fri, 10 Nov 2017 22:36:37: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (330 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。