Job ID = 10195003 sra ファイルのダウンロード中... Completed: 5201319K bytes transferred in 47 seconds (895904K 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 154586542 spots for /home/okishinya/chipatlas/results/rn6/SRX831353/SRR1743289.sra Written 154586542 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:02:11 154586542 reads; of these: 154586542 (100.00%) were unpaired; of these: 113970833 (73.73%) aligned 0 times 31612699 (20.45%) aligned exactly 1 time 9003010 (5.82%) aligned >1 times 26.27% overall alignment rate Time searching: 01:02:15 Overall time: 01:02:15 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 20 files... [bam_rmdupse_core] 34500937 / 40615709 = 0.8494 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 20:17:49: # Command line: callpeak -t SRX831353.bam -f BAM -g 2.15e9 -n SRX831353.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX831353.20 # format = BAM # ChIP-seq file = ['SRX831353.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 20:17:49: # Command line: callpeak -t SRX831353.bam -f BAM -g 2.15e9 -n SRX831353.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX831353.10 # format = BAM # ChIP-seq file = ['SRX831353.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 20:17:49: # Command line: callpeak -t SRX831353.bam -f BAM -g 2.15e9 -n SRX831353.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX831353.05 # format = BAM # ChIP-seq file = ['SRX831353.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 20:17:49: #1 read tag files... INFO @ Fri, 10 Nov 2017 20:17:49: #1 read tag files... INFO @ Fri, 10 Nov 2017 20:17:49: #1 read tag files... INFO @ Fri, 10 Nov 2017 20:17:49: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 20:17:49: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 20:17:49: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 20:17:56: 1000000 INFO @ Fri, 10 Nov 2017 20:17:56: 1000000 INFO @ Fri, 10 Nov 2017 20:17:56: 1000000 INFO @ Fri, 10 Nov 2017 20:18:03: 2000000 INFO @ Fri, 10 Nov 2017 20:18:03: 2000000 INFO @ Fri, 10 Nov 2017 20:18:03: 2000000 INFO @ Fri, 10 Nov 2017 20:18:10: 3000000 INFO @ Fri, 10 Nov 2017 20:18:10: 3000000 INFO @ Fri, 10 Nov 2017 20:18:11: 3000000 INFO @ Fri, 10 Nov 2017 20:18:17: 4000000 INFO @ Fri, 10 Nov 2017 20:18:17: 4000000 INFO @ Fri, 10 Nov 2017 20:18:18: 4000000 INFO @ Fri, 10 Nov 2017 20:18:23: 5000000 INFO @ Fri, 10 Nov 2017 20:18:25: 5000000 INFO @ Fri, 10 Nov 2017 20:18:25: 5000000 INFO @ Fri, 10 Nov 2017 20:18:30: 6000000 INFO @ Fri, 10 Nov 2017 20:18:31: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 20:18:31: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 20:18:31: #1 total tags in treatment: 6114772 INFO @ Fri, 10 Nov 2017 20:18:31: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 20:18:31: #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 20:18:32: #1 tags after filtering in treatment: 6114554 INFO @ Fri, 10 Nov 2017 20:18:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 20:18:32: #1 finished! INFO @ Fri, 10 Nov 2017 20:18:32: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 20:18:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 20:18:32: 6000000 INFO @ Fri, 10 Nov 2017 20:18:33: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 20:18:33: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 20:18:33: #1 total tags in treatment: 6114772 INFO @ Fri, 10 Nov 2017 20:18:33: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 20:18:33: #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 20:18:33: 6000000 INFO @ Fri, 10 Nov 2017 20:18:33: #1 tags after filtering in treatment: 6114554 INFO @ Fri, 10 Nov 2017 20:18:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 20:18:33: #1 finished! INFO @ Fri, 10 Nov 2017 20:18:33: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 20:18:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 20:18:34: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 20:18:34: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 20:18:34: #1 total tags in treatment: 6114772 INFO @ Fri, 10 Nov 2017 20:18:34: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 20:18:34: #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 20:18:34: #1 tags after filtering in treatment: 6114554 INFO @ Fri, 10 Nov 2017 20:18:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 20:18:34: #1 finished! INFO @ Fri, 10 Nov 2017 20:18:34: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 20:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 20:18:35: #2 number of paired peaks: 84857 INFO @ Fri, 10 Nov 2017 20:18:35: start model_add_line... INFO @ Fri, 10 Nov 2017 20:18:35: start X-correlation... INFO @ Fri, 10 Nov 2017 20:18:35: end of X-cor INFO @ Fri, 10 Nov 2017 20:18:35: #2 finished! INFO @ Fri, 10 Nov 2017 20:18:35: #2 predicted fragment length is 88 bps INFO @ Fri, 10 Nov 2017 20:18:35: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 10 Nov 2017 20:18:35: #2.2 Generate R script for model : SRX831353.05_model.r WARNING @ Fri, 10 Nov 2017 20:18:35: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 20:18:35: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 10 Nov 2017 20:18:35: #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 20:18:35: #3 Call peaks... INFO @ Fri, 10 Nov 2017 20:18:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 20:18:37: #2 number of paired peaks: 84857 INFO @ Fri, 10 Nov 2017 20:18:37: start model_add_line... INFO @ Fri, 10 Nov 2017 20:18:37: start X-correlation... INFO @ Fri, 10 Nov 2017 20:18:37: end of X-cor INFO @ Fri, 10 Nov 2017 20:18:37: #2 finished! INFO @ Fri, 10 Nov 2017 20:18:37: #2 predicted fragment length is 88 bps INFO @ Fri, 10 Nov 2017 20:18:37: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 10 Nov 2017 20:18:37: #2.2 Generate R script for model : SRX831353.20_model.r WARNING @ Fri, 10 Nov 2017 20:18:37: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 20:18:37: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 10 Nov 2017 20:18:37: #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 20:18:37: #3 Call peaks... INFO @ Fri, 10 Nov 2017 20:18:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 20:18:38: #2 number of paired peaks: 84857 INFO @ Fri, 10 Nov 2017 20:18:38: start model_add_line... INFO @ Fri, 10 Nov 2017 20:18:38: start X-correlation... INFO @ Fri, 10 Nov 2017 20:18:38: end of X-cor INFO @ Fri, 10 Nov 2017 20:18:38: #2 finished! INFO @ Fri, 10 Nov 2017 20:18:38: #2 predicted fragment length is 88 bps INFO @ Fri, 10 Nov 2017 20:18:38: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 10 Nov 2017 20:18:38: #2.2 Generate R script for model : SRX831353.10_model.r WARNING @ Fri, 10 Nov 2017 20:18:38: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 20:18:38: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 10 Nov 2017 20:18:38: #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 20:18:38: #3 Call peaks... INFO @ Fri, 10 Nov 2017 20:18:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 20:18:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 20:18:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 20:18:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 20:19:01: #4 Write output xls file... SRX831353.05_peaks.xls INFO @ Fri, 10 Nov 2017 20:19:01: #4 Write peak in narrowPeak format file... SRX831353.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 20:19:01: #4 Write summits bed file... SRX831353.05_summits.bed INFO @ Fri, 10 Nov 2017 20:19:01: Done! pass1 - making usageList (61 chroms): 9 millis pass2 - checking and writing primary data (1772 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 20:19:02: #4 Write output xls file... SRX831353.10_peaks.xls INFO @ Fri, 10 Nov 2017 20:19:02: #4 Write peak in narrowPeak format file... SRX831353.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 20:19:02: #4 Write summits bed file... SRX831353.10_summits.bed INFO @ Fri, 10 Nov 2017 20:19:02: Done! pass1 - making usageList (50 chroms): 0 millis pass2 - checking and writing primary data (685 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 20:19:03: #4 Write output xls file... SRX831353.20_peaks.xls INFO @ Fri, 10 Nov 2017 20:19:03: #4 Write peak in narrowPeak format file... SRX831353.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 20:19:03: #4 Write summits bed file... SRX831353.20_summits.bed INFO @ Fri, 10 Nov 2017 20:19:03: Done! pass1 - making usageList (44 chroms): 0 millis pass2 - checking and writing primary data (279 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。