Job ID = 10251894 sra ファイルのダウンロード中... Completed: 66757K bytes transferred in 15 seconds (35782K 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 3952910 spots for /home/okishinya/chipatlas/results/ce10/SRX3411420/SRR6311151.sra Written 3952910 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:29 3952910 reads; of these: 3952910 (100.00%) were unpaired; of these: 2288875 (57.90%) aligned 0 times 1370025 (34.66%) aligned exactly 1 time 294010 (7.44%) aligned >1 times 42.10% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 398265 / 1664035 = 0.2393 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 @ Wed, 06 Dec 2017 07:34:28: # Command line: callpeak -t SRX3411420.bam -f BAM -g ce -n SRX3411420.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3411420.20 # format = BAM # ChIP-seq file = ['SRX3411420.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 06 Dec 2017 07:34:28: #1 read tag files... INFO @ Wed, 06 Dec 2017 07:34:28: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 07:34:28: # Command line: callpeak -t SRX3411420.bam -f BAM -g ce -n SRX3411420.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3411420.10 # format = BAM # ChIP-seq file = ['SRX3411420.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 06 Dec 2017 07:34:28: #1 read tag files... INFO @ Wed, 06 Dec 2017 07:34:28: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 07:34:28: # Command line: callpeak -t SRX3411420.bam -f BAM -g ce -n SRX3411420.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3411420.05 # format = BAM # ChIP-seq file = ['SRX3411420.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 06 Dec 2017 07:34:28: #1 read tag files... INFO @ Wed, 06 Dec 2017 07:34:28: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 07:34:34: 1000000 INFO @ Wed, 06 Dec 2017 07:34:34: 1000000 INFO @ Wed, 06 Dec 2017 07:34:34: 1000000 INFO @ Wed, 06 Dec 2017 07:34:36: #1 tag size is determined as 32 bps INFO @ Wed, 06 Dec 2017 07:34:36: #1 tag size = 32 INFO @ Wed, 06 Dec 2017 07:34:36: #1 total tags in treatment: 1265770 INFO @ Wed, 06 Dec 2017 07:34:36: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 07:34:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 07:34:36: #1 tags after filtering in treatment: 1265770 INFO @ Wed, 06 Dec 2017 07:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 07:34:36: #1 finished! INFO @ Wed, 06 Dec 2017 07:34:36: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 07:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 07:34:36: #1 tag size is determined as 32 bps INFO @ Wed, 06 Dec 2017 07:34:36: #1 tag size = 32 INFO @ Wed, 06 Dec 2017 07:34:36: #1 total tags in treatment: 1265770 INFO @ Wed, 06 Dec 2017 07:34:36: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 07:34:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 07:34:36: #1 tags after filtering in treatment: 1265770 INFO @ Wed, 06 Dec 2017 07:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 07:34:36: #1 finished! INFO @ Wed, 06 Dec 2017 07:34:36: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 07:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 07:34:36: #1 tag size is determined as 32 bps INFO @ Wed, 06 Dec 2017 07:34:36: #1 tag size = 32 INFO @ Wed, 06 Dec 2017 07:34:36: #1 total tags in treatment: 1265770 INFO @ Wed, 06 Dec 2017 07:34:36: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 07:34:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 07:34:36: #1 tags after filtering in treatment: 1265770 INFO @ Wed, 06 Dec 2017 07:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 07:34:36: #1 finished! INFO @ Wed, 06 Dec 2017 07:34:36: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 07:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 07:34:36: #2 number of paired peaks: 711 WARNING @ Wed, 06 Dec 2017 07:34:36: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Wed, 06 Dec 2017 07:34:36: start model_add_line... INFO @ Wed, 06 Dec 2017 07:34:36: start X-correlation... INFO @ Wed, 06 Dec 2017 07:34:36: end of X-cor INFO @ Wed, 06 Dec 2017 07:34:36: #2 finished! INFO @ Wed, 06 Dec 2017 07:34:36: #2 predicted fragment length is 81 bps INFO @ Wed, 06 Dec 2017 07:34:36: #2 alternative fragment length(s) may be 81 bps INFO @ Wed, 06 Dec 2017 07:34:36: #2.2 Generate R script for model : SRX3411420.10_model.r INFO @ Wed, 06 Dec 2017 07:34:36: #3 Call peaks... INFO @ Wed, 06 Dec 2017 07:34:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 07:34:36: #2 number of paired peaks: 711 WARNING @ Wed, 06 Dec 2017 07:34:36: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Wed, 06 Dec 2017 07:34:36: start model_add_line... INFO @ Wed, 06 Dec 2017 07:34:36: start X-correlation... INFO @ Wed, 06 Dec 2017 07:34:36: end of X-cor INFO @ Wed, 06 Dec 2017 07:34:36: #2 finished! INFO @ Wed, 06 Dec 2017 07:34:36: #2 predicted fragment length is 81 bps INFO @ Wed, 06 Dec 2017 07:34:36: #2 alternative fragment length(s) may be 81 bps INFO @ Wed, 06 Dec 2017 07:34:36: #2.2 Generate R script for model : SRX3411420.05_model.r INFO @ Wed, 06 Dec 2017 07:34:36: #3 Call peaks... INFO @ Wed, 06 Dec 2017 07:34:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 07:34:36: #2 number of paired peaks: 711 WARNING @ Wed, 06 Dec 2017 07:34:36: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Wed, 06 Dec 2017 07:34:36: start model_add_line... INFO @ Wed, 06 Dec 2017 07:34:36: start X-correlation... INFO @ Wed, 06 Dec 2017 07:34:36: end of X-cor INFO @ Wed, 06 Dec 2017 07:34:36: #2 finished! INFO @ Wed, 06 Dec 2017 07:34:36: #2 predicted fragment length is 81 bps INFO @ Wed, 06 Dec 2017 07:34:36: #2 alternative fragment length(s) may be 81 bps INFO @ Wed, 06 Dec 2017 07:34:36: #2.2 Generate R script for model : SRX3411420.20_model.r INFO @ Wed, 06 Dec 2017 07:34:36: #3 Call peaks... INFO @ Wed, 06 Dec 2017 07:34:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 07:34:39: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 07:34:39: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 07:34:39: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 07:34:41: #4 Write output xls file... SRX3411420.05_peaks.xls INFO @ Wed, 06 Dec 2017 07:34:41: #4 Write peak in narrowPeak format file... SRX3411420.05_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 07:34:41: #4 Write summits bed file... SRX3411420.05_summits.bed INFO @ Wed, 06 Dec 2017 07:34:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (438 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 06 Dec 2017 07:34:41: #4 Write output xls file... SRX3411420.20_peaks.xls INFO @ Wed, 06 Dec 2017 07:34:41: #4 Write output xls file... SRX3411420.10_peaks.xls INFO @ Wed, 06 Dec 2017 07:34:41: #4 Write peak in narrowPeak format file... SRX3411420.20_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 07:34:41: #4 Write summits bed file... SRX3411420.20_summits.bed INFO @ Wed, 06 Dec 2017 07:34:41: #4 Write peak in narrowPeak format file... SRX3411420.10_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 07:34:41: Done! INFO @ Wed, 06 Dec 2017 07:34:41: #4 Write summits bed file... SRX3411420.10_summits.bed INFO @ Wed, 06 Dec 2017 07:34:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (41 records, 4 fields): 2 millis pass1 - making usageList (7 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (136 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。