Job ID = 10201983 sra ファイルのダウンロード中... Completed: 426982K bytes transferred in 14 seconds (241028K 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 17866724 spots for /home/okishinya/chipatlas/results/ce10/SRX2576652/SRR5272609.sra Written 17866724 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: 00:03:17 17866724 reads; of these: 17866724 (100.00%) were unpaired; of these: 643807 (3.60%) aligned 0 times 14254542 (79.78%) aligned exactly 1 time 2968375 (16.61%) aligned >1 times 96.40% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2806203 / 17222917 = 0.1629 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 @ Mon, 13 Nov 2017 13:16:17: # Command line: callpeak -t SRX2576652.bam -f BAM -g ce -n SRX2576652.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576652.20 # format = BAM # ChIP-seq file = ['SRX2576652.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 @ Mon, 13 Nov 2017 13:16:17: # Command line: callpeak -t SRX2576652.bam -f BAM -g ce -n SRX2576652.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576652.05 # format = BAM # ChIP-seq file = ['SRX2576652.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 @ Mon, 13 Nov 2017 13:16:17: # Command line: callpeak -t SRX2576652.bam -f BAM -g ce -n SRX2576652.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576652.10 # format = BAM # ChIP-seq file = ['SRX2576652.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 @ Mon, 13 Nov 2017 13:16:17: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:17: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:17: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:17: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:17: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:17: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:23: 1000000 INFO @ Mon, 13 Nov 2017 13:16:23: 1000000 INFO @ Mon, 13 Nov 2017 13:16:23: 1000000 INFO @ Mon, 13 Nov 2017 13:16:29: 2000000 INFO @ Mon, 13 Nov 2017 13:16:29: 2000000 INFO @ Mon, 13 Nov 2017 13:16:29: 2000000 INFO @ Mon, 13 Nov 2017 13:16:35: 3000000 INFO @ Mon, 13 Nov 2017 13:16:36: 3000000 INFO @ Mon, 13 Nov 2017 13:16:36: 3000000 INFO @ Mon, 13 Nov 2017 13:16:42: 4000000 INFO @ Mon, 13 Nov 2017 13:16:42: 4000000 INFO @ Mon, 13 Nov 2017 13:16:42: 4000000 INFO @ Mon, 13 Nov 2017 13:16:48: 5000000 INFO @ Mon, 13 Nov 2017 13:16:48: 5000000 INFO @ Mon, 13 Nov 2017 13:16:48: 5000000 INFO @ Mon, 13 Nov 2017 13:16:54: 6000000 INFO @ Mon, 13 Nov 2017 13:16:54: 6000000 INFO @ Mon, 13 Nov 2017 13:16:55: 6000000 INFO @ Mon, 13 Nov 2017 13:17:00: 7000000 INFO @ Mon, 13 Nov 2017 13:17:01: 7000000 INFO @ Mon, 13 Nov 2017 13:17:02: 7000000 INFO @ Mon, 13 Nov 2017 13:17:06: 8000000 INFO @ Mon, 13 Nov 2017 13:17:07: 8000000 INFO @ Mon, 13 Nov 2017 13:17:09: 8000000 INFO @ Mon, 13 Nov 2017 13:17:12: 9000000 INFO @ Mon, 13 Nov 2017 13:17:14: 9000000 INFO @ Mon, 13 Nov 2017 13:17:16: 9000000 INFO @ Mon, 13 Nov 2017 13:17:18: 10000000 INFO @ Mon, 13 Nov 2017 13:17:20: 10000000 INFO @ Mon, 13 Nov 2017 13:17:23: 10000000 INFO @ Mon, 13 Nov 2017 13:17:24: 11000000 INFO @ Mon, 13 Nov 2017 13:17:27: 11000000 INFO @ Mon, 13 Nov 2017 13:17:30: 12000000 INFO @ Mon, 13 Nov 2017 13:17:30: 11000000 INFO @ Mon, 13 Nov 2017 13:17:33: 12000000 INFO @ Mon, 13 Nov 2017 13:17:36: 13000000 INFO @ Mon, 13 Nov 2017 13:17:37: 12000000 INFO @ Mon, 13 Nov 2017 13:17:40: 13000000 INFO @ Mon, 13 Nov 2017 13:17:41: 14000000 INFO @ Mon, 13 Nov 2017 13:17:44: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:17:44: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:17:44: #1 total tags in treatment: 14416714 INFO @ Mon, 13 Nov 2017 13:17:44: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:17:44: #1 tags after filtering in treatment: 14416714 INFO @ Mon, 13 Nov 2017 13:17:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:44: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:44: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:45: 13000000 INFO @ Mon, 13 Nov 2017 13:17:45: #2 number of paired peaks: 531 WARNING @ Mon, 13 Nov 2017 13:17:45: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:45: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:46: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:46: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:46: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:46: #2 predicted fragment length is 142 bps INFO @ Mon, 13 Nov 2017 13:17:46: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 13 Nov 2017 13:17:46: #2.2 Generate R script for model : SRX2576652.20_model.r INFO @ Mon, 13 Nov 2017 13:17:46: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:47: 14000000 INFO @ Mon, 13 Nov 2017 13:17:50: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:17:50: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:17:50: #1 total tags in treatment: 14416714 INFO @ Mon, 13 Nov 2017 13:17:50: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:17:50: #1 tags after filtering in treatment: 14416714 INFO @ Mon, 13 Nov 2017 13:17:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:50: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:50: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:51: #2 number of paired peaks: 531 WARNING @ Mon, 13 Nov 2017 13:17:51: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:51: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:51: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:51: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:51: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:51: #2 predicted fragment length is 142 bps INFO @ Mon, 13 Nov 2017 13:17:51: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 13 Nov 2017 13:17:51: #2.2 Generate R script for model : SRX2576652.05_model.r INFO @ Mon, 13 Nov 2017 13:17:51: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:51: 14000000 INFO @ Mon, 13 Nov 2017 13:17:54: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:17:54: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:17:54: #1 total tags in treatment: 14416714 INFO @ Mon, 13 Nov 2017 13:17:54: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:17:54: #1 tags after filtering in treatment: 14416714 INFO @ Mon, 13 Nov 2017 13:17:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:54: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:54: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:55: #2 number of paired peaks: 531 WARNING @ Mon, 13 Nov 2017 13:17:55: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:55: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:55: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:55: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:55: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:55: #2 predicted fragment length is 142 bps INFO @ Mon, 13 Nov 2017 13:17:55: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 13 Nov 2017 13:17:55: #2.2 Generate R script for model : SRX2576652.10_model.r INFO @ Mon, 13 Nov 2017 13:17:55: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:18:17: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:23: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:30: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:33: #4 Write output xls file... SRX2576652.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:33: #4 Write peak in narrowPeak format file... SRX2576652.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:33: #4 Write summits bed file... SRX2576652.20_summits.bed INFO @ Mon, 13 Nov 2017 13:18:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1380 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:18:38: #4 Write output xls file... SRX2576652.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:38: #4 Write peak in narrowPeak format file... SRX2576652.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:38: #4 Write summits bed file... SRX2576652.05_summits.bed INFO @ Mon, 13 Nov 2017 13:18:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2791 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:18:45: #4 Write output xls file... SRX2576652.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:45: #4 Write peak in narrowPeak format file... SRX2576652.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:45: #4 Write summits bed file... SRX2576652.10_summits.bed INFO @ Mon, 13 Nov 2017 13:18:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1962 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。