Job ID = 10480708 sra ファイルのダウンロード中... Completed: 217657K bytes transferred in 19 seconds (91384K 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 7494587 spots for /home/okishinya/chipatlas/results/dm3/SRX3068979/SRR5907455.sra Written 7494587 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:37 7494587 reads; of these: 7494587 (100.00%) were unpaired; of these: 3819122 (50.96%) aligned 0 times 3078228 (41.07%) aligned exactly 1 time 597237 (7.97%) aligned >1 times 49.04% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 1400093 / 3675465 = 0.3809 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, 16 Mar 2018 07:43:56: # Command line: callpeak -t SRX3068979.bam -f BAM -g dm -n SRX3068979.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068979.20 # format = BAM # ChIP-seq file = ['SRX3068979.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:43:56: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:43:56: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:43:56: # Command line: callpeak -t SRX3068979.bam -f BAM -g dm -n SRX3068979.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068979.05 # format = BAM # ChIP-seq file = ['SRX3068979.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:43:56: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:43:56: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:43:56: # Command line: callpeak -t SRX3068979.bam -f BAM -g dm -n SRX3068979.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068979.10 # format = BAM # ChIP-seq file = ['SRX3068979.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:43:56: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:43:56: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:44:03: 1000000 INFO @ Fri, 16 Mar 2018 07:44:03: 1000000 INFO @ Fri, 16 Mar 2018 07:44:03: 1000000 INFO @ Fri, 16 Mar 2018 07:44:09: 2000000 INFO @ Fri, 16 Mar 2018 07:44:09: 2000000 INFO @ Fri, 16 Mar 2018 07:44:09: 2000000 INFO @ Fri, 16 Mar 2018 07:44:11: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:44:11: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:44:11: #1 total tags in treatment: 2275372 INFO @ Fri, 16 Mar 2018 07:44:11: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:44:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:44:11: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:44:11: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:44:11: #1 total tags in treatment: 2275372 INFO @ Fri, 16 Mar 2018 07:44:11: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:44:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:44:11: #1 tags after filtering in treatment: 2275372 INFO @ Fri, 16 Mar 2018 07:44:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:44:11: #1 finished! INFO @ Fri, 16 Mar 2018 07:44:11: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:44:11: #1 tags after filtering in treatment: 2275372 INFO @ Fri, 16 Mar 2018 07:44:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:44:11: #1 finished! INFO @ Fri, 16 Mar 2018 07:44:11: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:44:11: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:44:11: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:44:11: #1 total tags in treatment: 2275372 INFO @ Fri, 16 Mar 2018 07:44:11: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:44:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:44:11: #1 tags after filtering in treatment: 2275372 INFO @ Fri, 16 Mar 2018 07:44:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:44:11: #1 finished! INFO @ Fri, 16 Mar 2018 07:44:11: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:44:11: #2 number of paired peaks: 795 WARNING @ Fri, 16 Mar 2018 07:44:11: Fewer paired peaks (795) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 795 pairs to build model! INFO @ Fri, 16 Mar 2018 07:44:11: start model_add_line... INFO @ Fri, 16 Mar 2018 07:44:11: #2 number of paired peaks: 795 WARNING @ Fri, 16 Mar 2018 07:44:11: Fewer paired peaks (795) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 795 pairs to build model! INFO @ Fri, 16 Mar 2018 07:44:11: start model_add_line... INFO @ Fri, 16 Mar 2018 07:44:11: start X-correlation... INFO @ Fri, 16 Mar 2018 07:44:11: end of X-cor INFO @ Fri, 16 Mar 2018 07:44:11: #2 finished! INFO @ Fri, 16 Mar 2018 07:44:11: #2 predicted fragment length is 118 bps INFO @ Fri, 16 Mar 2018 07:44:11: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 16 Mar 2018 07:44:11: #2.2 Generate R script for model : SRX3068979.10_model.r INFO @ Fri, 16 Mar 2018 07:44:11: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:44:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:44:11: start X-correlation... INFO @ Fri, 16 Mar 2018 07:44:11: end of X-cor INFO @ Fri, 16 Mar 2018 07:44:11: #2 finished! INFO @ Fri, 16 Mar 2018 07:44:11: #2 predicted fragment length is 118 bps INFO @ Fri, 16 Mar 2018 07:44:11: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 16 Mar 2018 07:44:11: #2.2 Generate R script for model : SRX3068979.05_model.r INFO @ Fri, 16 Mar 2018 07:44:11: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:44:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:44:11: #2 number of paired peaks: 795 WARNING @ Fri, 16 Mar 2018 07:44:11: Fewer paired peaks (795) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 795 pairs to build model! INFO @ Fri, 16 Mar 2018 07:44:11: start model_add_line... INFO @ Fri, 16 Mar 2018 07:44:11: start X-correlation... INFO @ Fri, 16 Mar 2018 07:44:11: end of X-cor INFO @ Fri, 16 Mar 2018 07:44:11: #2 finished! INFO @ Fri, 16 Mar 2018 07:44:11: #2 predicted fragment length is 118 bps INFO @ Fri, 16 Mar 2018 07:44:11: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 16 Mar 2018 07:44:11: #2.2 Generate R script for model : SRX3068979.20_model.r INFO @ Fri, 16 Mar 2018 07:44:11: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:44:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:44:16: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:44:16: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:44:16: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:44:20: #4 Write output xls file... SRX3068979.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:44:20: #4 Write peak in narrowPeak format file... SRX3068979.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:44:20: #4 Write summits bed file... SRX3068979.05_summits.bed INFO @ Fri, 16 Mar 2018 07:44:20: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1271 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:44:20: #4 Write output xls file... SRX3068979.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:44:20: #4 Write peak in narrowPeak format file... SRX3068979.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:44:20: #4 Write summits bed file... SRX3068979.10_summits.bed INFO @ Fri, 16 Mar 2018 07:44:20: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (669 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:44:20: #4 Write output xls file... SRX3068979.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:44:20: #4 Write peak in narrowPeak format file... SRX3068979.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:44:20: #4 Write summits bed file... SRX3068979.20_summits.bed INFO @ Fri, 16 Mar 2018 07:44:20: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (313 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。