Job ID = 10201972 sra ファイルのダウンロード中... Completed: 384374K bytes transferred in 12 seconds (243273K 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 21697486 spots for /home/okishinya/chipatlas/results/ce10/SRX2576641/SRR5272598.sra Written 21697486 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: 00:05:24 21697486 reads; of these: 21697486 (100.00%) were unpaired; of these: 2100613 (9.68%) aligned 0 times 16096996 (74.19%) aligned exactly 1 time 3499877 (16.13%) aligned >1 times 90.32% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 10156881 / 19596873 = 0.5183 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 13:18:18: # Command line: callpeak -t SRX2576641.bam -f BAM -g ce -n SRX2576641.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576641.05 # format = BAM # ChIP-seq file = ['SRX2576641.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 13:18:18: # Command line: callpeak -t SRX2576641.bam -f BAM -g ce -n SRX2576641.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576641.20 # format = BAM # ChIP-seq file = ['SRX2576641.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 13:18:18: # Command line: callpeak -t SRX2576641.bam -f BAM -g ce -n SRX2576641.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576641.10 # format = BAM # ChIP-seq file = ['SRX2576641.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 13:18:18: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:18:18: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:18:18: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:18:18: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:18:18: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:18:18: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:18:24: 1000000 INFO @ Mon, 13 Nov 2017 13:18:24: 1000000 INFO @ Mon, 13 Nov 2017 13:18:24: 1000000 INFO @ Mon, 13 Nov 2017 13:18:30: 2000000 INFO @ Mon, 13 Nov 2017 13:18:30: 2000000 INFO @ Mon, 13 Nov 2017 13:18:31: 2000000 INFO @ Mon, 13 Nov 2017 13:18:36: 3000000 INFO @ Mon, 13 Nov 2017 13:18:36: 3000000 INFO @ Mon, 13 Nov 2017 13:18:37: 3000000 INFO @ Mon, 13 Nov 2017 13:18:42: 4000000 INFO @ Mon, 13 Nov 2017 13:18:42: 4000000 INFO @ Mon, 13 Nov 2017 13:18:44: 4000000 INFO @ Mon, 13 Nov 2017 13:18:48: 5000000 INFO @ Mon, 13 Nov 2017 13:18:49: 5000000 INFO @ Mon, 13 Nov 2017 13:18:50: 5000000 INFO @ Mon, 13 Nov 2017 13:18:54: 6000000 INFO @ Mon, 13 Nov 2017 13:18:55: 6000000 INFO @ Mon, 13 Nov 2017 13:18:56: 6000000 INFO @ Mon, 13 Nov 2017 13:19:00: 7000000 INFO @ Mon, 13 Nov 2017 13:19:01: 7000000 INFO @ Mon, 13 Nov 2017 13:19:03: 7000000 INFO @ Mon, 13 Nov 2017 13:19:06: 8000000 INFO @ Mon, 13 Nov 2017 13:19:08: 8000000 INFO @ Mon, 13 Nov 2017 13:19:10: 8000000 INFO @ Mon, 13 Nov 2017 13:19:12: 9000000 INFO @ Mon, 13 Nov 2017 13:19:14: 9000000 INFO @ Mon, 13 Nov 2017 13:19:15: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:19:15: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:19:15: #1 total tags in treatment: 9439992 INFO @ Mon, 13 Nov 2017 13:19:15: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:19:15: #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 13:19:15: #1 tags after filtering in treatment: 9439992 INFO @ Mon, 13 Nov 2017 13:19:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:19:15: #1 finished! INFO @ Mon, 13 Nov 2017 13:19:15: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:19:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:19:16: #2 number of paired peaks: 565 WARNING @ Mon, 13 Nov 2017 13:19:16: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Mon, 13 Nov 2017 13:19:16: start model_add_line... INFO @ Mon, 13 Nov 2017 13:19:16: start X-correlation... INFO @ Mon, 13 Nov 2017 13:19:16: end of X-cor INFO @ Mon, 13 Nov 2017 13:19:16: #2 finished! INFO @ Mon, 13 Nov 2017 13:19:16: #2 predicted fragment length is 109 bps INFO @ Mon, 13 Nov 2017 13:19:16: #2 alternative fragment length(s) may be 109 bps INFO @ Mon, 13 Nov 2017 13:19:16: #2.2 Generate R script for model : SRX2576641.10_model.r INFO @ Mon, 13 Nov 2017 13:19:16: 9000000 INFO @ Mon, 13 Nov 2017 13:19:16: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:19:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:19:17: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:19:17: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:19:17: #1 total tags in treatment: 9439992 INFO @ Mon, 13 Nov 2017 13:19:17: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:19:17: #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 13:19:17: #1 tags after filtering in treatment: 9439992 INFO @ Mon, 13 Nov 2017 13:19:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:19:17: #1 finished! INFO @ Mon, 13 Nov 2017 13:19:17: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:19:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:19:18: #2 number of paired peaks: 565 WARNING @ Mon, 13 Nov 2017 13:19:18: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Mon, 13 Nov 2017 13:19:18: start model_add_line... INFO @ Mon, 13 Nov 2017 13:19:18: start X-correlation... INFO @ Mon, 13 Nov 2017 13:19:18: end of X-cor INFO @ Mon, 13 Nov 2017 13:19:18: #2 finished! INFO @ Mon, 13 Nov 2017 13:19:18: #2 predicted fragment length is 109 bps INFO @ Mon, 13 Nov 2017 13:19:18: #2 alternative fragment length(s) may be 109 bps INFO @ Mon, 13 Nov 2017 13:19:18: #2.2 Generate R script for model : SRX2576641.20_model.r INFO @ Mon, 13 Nov 2017 13:19:18: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:19:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:19:19: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:19:19: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:19:19: #1 total tags in treatment: 9439992 INFO @ Mon, 13 Nov 2017 13:19:19: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:19:19: #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 13:19:19: #1 tags after filtering in treatment: 9439992 INFO @ Mon, 13 Nov 2017 13:19:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:19:19: #1 finished! INFO @ Mon, 13 Nov 2017 13:19:19: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:19:20: #2 number of paired peaks: 565 WARNING @ Mon, 13 Nov 2017 13:19:20: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Mon, 13 Nov 2017 13:19:20: start model_add_line... INFO @ Mon, 13 Nov 2017 13:19:20: start X-correlation... INFO @ Mon, 13 Nov 2017 13:19:20: end of X-cor INFO @ Mon, 13 Nov 2017 13:19:20: #2 finished! INFO @ Mon, 13 Nov 2017 13:19:20: #2 predicted fragment length is 109 bps INFO @ Mon, 13 Nov 2017 13:19:20: #2 alternative fragment length(s) may be 109 bps INFO @ Mon, 13 Nov 2017 13:19:20: #2.2 Generate R script for model : SRX2576641.05_model.r INFO @ Mon, 13 Nov 2017 13:19:20: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:19:37: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:19:39: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:19:41: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:19:48: #4 Write output xls file... SRX2576641.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:19:48: #4 Write peak in narrowPeak format file... SRX2576641.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:19:48: #4 Write summits bed file... SRX2576641.10_summits.bed INFO @ Mon, 13 Nov 2017 13:19:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1069 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:19:51: #4 Write output xls file... SRX2576641.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:19:51: #4 Write peak in narrowPeak format file... SRX2576641.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:19:51: #4 Write summits bed file... SRX2576641.20_summits.bed INFO @ Mon, 13 Nov 2017 13:19:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (600 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:19:52: #4 Write output xls file... SRX2576641.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:19:52: #4 Write peak in narrowPeak format file... SRX2576641.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:19:52: #4 Write summits bed file... SRX2576641.05_summits.bed INFO @ Mon, 13 Nov 2017 13:19:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1581 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。