Job ID = 11240824 sra ファイルのダウンロード中... Completed: 531824K bytes transferred in 8 seconds (542851K 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... Read 14991244 spots for /home/okishinya/chipatlas/results/dm3/SRX4798871/SRR7965198.sra Written 14991244 spots for /home/okishinya/chipatlas/results/dm3/SRX4798871/SRR7965198.sra 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: 00:03:59 14991244 reads; of these: 14991244 (100.00%) were unpaired; of these: 2453805 (16.37%) aligned 0 times 10994394 (73.34%) aligned exactly 1 time 1543045 (10.29%) aligned >1 times 83.63% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4084395 / 12537439 = 0.3258 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 @ Sun, 07 Oct 2018 20:55:54: # Command line: callpeak -t SRX4798871.bam -f BAM -g dm -n SRX4798871.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798871.20 # format = BAM # ChIP-seq file = ['SRX4798871.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 @ Sun, 07 Oct 2018 20:55:54: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:55:54: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:55:54: # Command line: callpeak -t SRX4798871.bam -f BAM -g dm -n SRX4798871.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798871.05 # format = BAM # ChIP-seq file = ['SRX4798871.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 @ Sun, 07 Oct 2018 20:55:54: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:55:54: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:55:54: # Command line: callpeak -t SRX4798871.bam -f BAM -g dm -n SRX4798871.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798871.10 # format = BAM # ChIP-seq file = ['SRX4798871.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 @ Sun, 07 Oct 2018 20:55:54: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:55:54: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:56:00: 1000000 INFO @ Sun, 07 Oct 2018 20:56:01: 1000000 INFO @ Sun, 07 Oct 2018 20:56:01: 1000000 INFO @ Sun, 07 Oct 2018 20:56:07: 2000000 INFO @ Sun, 07 Oct 2018 20:56:08: 2000000 INFO @ Sun, 07 Oct 2018 20:56:08: 2000000 INFO @ Sun, 07 Oct 2018 20:56:14: 3000000 INFO @ Sun, 07 Oct 2018 20:56:16: 3000000 INFO @ Sun, 07 Oct 2018 20:56:16: 3000000 INFO @ Sun, 07 Oct 2018 20:56:20: 4000000 INFO @ Sun, 07 Oct 2018 20:56:23: 4000000 INFO @ Sun, 07 Oct 2018 20:56:23: 4000000 INFO @ Sun, 07 Oct 2018 20:56:27: 5000000 INFO @ Sun, 07 Oct 2018 20:56:30: 5000000 INFO @ Sun, 07 Oct 2018 20:56:30: 5000000 INFO @ Sun, 07 Oct 2018 20:56:34: 6000000 INFO @ Sun, 07 Oct 2018 20:56:38: 6000000 INFO @ Sun, 07 Oct 2018 20:56:38: 6000000 INFO @ Sun, 07 Oct 2018 20:56:41: 7000000 INFO @ Sun, 07 Oct 2018 20:56:45: 7000000 INFO @ Sun, 07 Oct 2018 20:56:45: 7000000 INFO @ Sun, 07 Oct 2018 20:56:47: 8000000 INFO @ Sun, 07 Oct 2018 20:56:50: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:56:50: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:56:50: #1 total tags in treatment: 8453044 INFO @ Sun, 07 Oct 2018 20:56:50: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:56:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:56:51: #1 tags after filtering in treatment: 8453044 INFO @ Sun, 07 Oct 2018 20:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:56:51: #1 finished! INFO @ Sun, 07 Oct 2018 20:56:51: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:56:51: #2 number of paired peaks: 233 WARNING @ Sun, 07 Oct 2018 20:56:51: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Sun, 07 Oct 2018 20:56:51: start model_add_line... INFO @ Sun, 07 Oct 2018 20:56:51: start X-correlation... INFO @ Sun, 07 Oct 2018 20:56:51: end of X-cor INFO @ Sun, 07 Oct 2018 20:56:51: #2 finished! INFO @ Sun, 07 Oct 2018 20:56:51: #2 predicted fragment length is 122 bps INFO @ Sun, 07 Oct 2018 20:56:51: #2 alternative fragment length(s) may be 122,587 bps INFO @ Sun, 07 Oct 2018 20:56:51: #2.2 Generate R script for model : SRX4798871.10_model.r INFO @ Sun, 07 Oct 2018 20:56:51: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:56:52: 8000000 INFO @ Sun, 07 Oct 2018 20:56:52: 8000000 INFO @ Sun, 07 Oct 2018 20:56:56: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:56:56: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:56:56: #1 total tags in treatment: 8453044 INFO @ Sun, 07 Oct 2018 20:56:56: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:56:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:56:56: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:56:56: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:56:56: #1 total tags in treatment: 8453044 INFO @ Sun, 07 Oct 2018 20:56:56: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:56:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:56:56: #1 tags after filtering in treatment: 8453044 INFO @ Sun, 07 Oct 2018 20:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:56:56: #1 finished! INFO @ Sun, 07 Oct 2018 20:56:56: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:56:56: #1 tags after filtering in treatment: 8453044 INFO @ Sun, 07 Oct 2018 20:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:56:56: #1 finished! INFO @ Sun, 07 Oct 2018 20:56:56: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:56:57: #2 number of paired peaks: 233 INFO @ Sun, 07 Oct 2018 20:56:57: #2 number of paired peaks: 233 WARNING @ Sun, 07 Oct 2018 20:56:57: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! WARNING @ Sun, 07 Oct 2018 20:56:57: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Sun, 07 Oct 2018 20:56:57: start model_add_line... INFO @ Sun, 07 Oct 2018 20:56:57: start model_add_line... INFO @ Sun, 07 Oct 2018 20:56:57: start X-correlation... INFO @ Sun, 07 Oct 2018 20:56:57: start X-correlation... INFO @ Sun, 07 Oct 2018 20:56:57: end of X-cor INFO @ Sun, 07 Oct 2018 20:56:57: end of X-cor INFO @ Sun, 07 Oct 2018 20:56:57: #2 finished! INFO @ Sun, 07 Oct 2018 20:56:57: #2 finished! INFO @ Sun, 07 Oct 2018 20:56:57: #2 predicted fragment length is 122 bps INFO @ Sun, 07 Oct 2018 20:56:57: #2 predicted fragment length is 122 bps INFO @ Sun, 07 Oct 2018 20:56:57: #2 alternative fragment length(s) may be 122,587 bps INFO @ Sun, 07 Oct 2018 20:56:57: #2 alternative fragment length(s) may be 122,587 bps INFO @ Sun, 07 Oct 2018 20:56:57: #2.2 Generate R script for model : SRX4798871.05_model.r INFO @ Sun, 07 Oct 2018 20:56:57: #2.2 Generate R script for model : SRX4798871.20_model.r INFO @ Sun, 07 Oct 2018 20:56:57: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:56:57: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:56:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:56:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:57:11: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:57:16: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:57:17: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:57:21: #4 Write output xls file... SRX4798871.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:57:21: #4 Write peak in narrowPeak format file... SRX4798871.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:57:21: #4 Write summits bed file... SRX4798871.10_summits.bed INFO @ Sun, 07 Oct 2018 20:57:21: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (265 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:57:26: #4 Write output xls file... SRX4798871.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:57:26: #4 Write peak in narrowPeak format file... SRX4798871.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:57:26: #4 Write summits bed file... SRX4798871.20_summits.bed INFO @ Sun, 07 Oct 2018 20:57:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:57:27: #4 Write output xls file... SRX4798871.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:57:27: #4 Write peak in narrowPeak format file... SRX4798871.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:57:27: #4 Write summits bed file... SRX4798871.05_summits.bed INFO @ Sun, 07 Oct 2018 20:57:27: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (421 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。