Job ID = 10201978 sra ファイルのダウンロード中... Completed: 470613K bytes transferred in 15 seconds (249700K 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 20063336 spots for /home/okishinya/chipatlas/results/ce10/SRX2576647/SRR5272604.sra Written 20063336 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: 00:10:36 20063336 reads; of these: 20063336 (100.00%) were unpaired; of these: 274057 (1.37%) aligned 0 times 16300375 (81.24%) aligned exactly 1 time 3488904 (17.39%) aligned >1 times 98.63% overall alignment rate Time searching: 00:10:36 Overall time: 00:10:36 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] 3717576 / 19789279 = 0.1879 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 13:27:28: # Command line: callpeak -t SRX2576647.bam -f BAM -g ce -n SRX2576647.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576647.10 # format = BAM # ChIP-seq file = ['SRX2576647.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 13:27:28: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:27:28: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:27:28: # Command line: callpeak -t SRX2576647.bam -f BAM -g ce -n SRX2576647.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576647.05 # format = BAM # ChIP-seq file = ['SRX2576647.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 13:27:28: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:27:28: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:27:28: # Command line: callpeak -t SRX2576647.bam -f BAM -g ce -n SRX2576647.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576647.20 # format = BAM # ChIP-seq file = ['SRX2576647.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 13:27:28: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:27:28: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:27:43: 1000000 INFO @ Mon, 13 Nov 2017 13:27:46: 1000000 INFO @ Mon, 13 Nov 2017 13:27:47: 1000000 INFO @ Mon, 13 Nov 2017 13:27:58: 2000000 INFO @ Mon, 13 Nov 2017 13:28:04: 2000000 INFO @ Mon, 13 Nov 2017 13:28:06: 2000000 INFO @ Mon, 13 Nov 2017 13:28:13: 3000000 INFO @ Mon, 13 Nov 2017 13:28:23: 3000000 INFO @ Mon, 13 Nov 2017 13:28:25: 3000000 INFO @ Mon, 13 Nov 2017 13:28:27: 4000000 INFO @ Mon, 13 Nov 2017 13:28:41: 4000000 INFO @ Mon, 13 Nov 2017 13:28:42: 5000000 INFO @ Mon, 13 Nov 2017 13:28:45: 4000000 INFO @ Mon, 13 Nov 2017 13:28:56: 6000000 INFO @ Mon, 13 Nov 2017 13:29:00: 5000000 INFO @ Mon, 13 Nov 2017 13:29:05: 5000000 INFO @ Mon, 13 Nov 2017 13:29:10: 7000000 INFO @ Mon, 13 Nov 2017 13:29:18: 6000000 INFO @ Mon, 13 Nov 2017 13:29:24: 6000000 INFO @ Mon, 13 Nov 2017 13:29:24: 8000000 INFO @ Mon, 13 Nov 2017 13:29:35: 7000000 INFO @ Mon, 13 Nov 2017 13:29:38: 9000000 INFO @ Mon, 13 Nov 2017 13:29:43: 7000000 INFO @ Mon, 13 Nov 2017 13:29:51: 10000000 INFO @ Mon, 13 Nov 2017 13:29:53: 8000000 INFO @ Mon, 13 Nov 2017 13:30:01: 11000000 INFO @ Mon, 13 Nov 2017 13:30:01: 8000000 INFO @ Mon, 13 Nov 2017 13:30:10: 9000000 INFO @ Mon, 13 Nov 2017 13:30:14: 12000000 INFO @ Mon, 13 Nov 2017 13:30:19: 9000000 INFO @ Mon, 13 Nov 2017 13:30:26: 10000000 INFO @ Mon, 13 Nov 2017 13:30:28: 13000000 INFO @ Mon, 13 Nov 2017 13:30:36: 10000000 INFO @ Mon, 13 Nov 2017 13:30:41: 14000000 INFO @ Mon, 13 Nov 2017 13:30:44: 11000000 INFO @ Mon, 13 Nov 2017 13:30:54: 11000000 INFO @ Mon, 13 Nov 2017 13:30:55: 15000000 INFO @ Mon, 13 Nov 2017 13:31:01: 12000000 INFO @ Mon, 13 Nov 2017 13:31:10: 16000000 INFO @ Mon, 13 Nov 2017 13:31:11: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:31:11: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:31:11: #1 total tags in treatment: 16071703 INFO @ Mon, 13 Nov 2017 13:31:11: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:31:11: #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 13:31:11: #1 tags after filtering in treatment: 16071703 INFO @ Mon, 13 Nov 2017 13:31:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:31:11: #1 finished! INFO @ Mon, 13 Nov 2017 13:31:11: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:31:12: 12000000 INFO @ Mon, 13 Nov 2017 13:31:13: #2 number of paired peaks: 487 WARNING @ Mon, 13 Nov 2017 13:31:13: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Mon, 13 Nov 2017 13:31:13: start model_add_line... INFO @ Mon, 13 Nov 2017 13:31:13: start X-correlation... INFO @ Mon, 13 Nov 2017 13:31:13: end of X-cor INFO @ Mon, 13 Nov 2017 13:31:13: #2 finished! INFO @ Mon, 13 Nov 2017 13:31:13: #2 predicted fragment length is 142 bps INFO @ Mon, 13 Nov 2017 13:31:13: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 13 Nov 2017 13:31:13: #2.2 Generate R script for model : SRX2576647.10_model.r INFO @ Mon, 13 Nov 2017 13:31:13: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:31:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:31:18: 13000000 INFO @ Mon, 13 Nov 2017 13:31:28: 13000000 INFO @ Mon, 13 Nov 2017 13:31:37: 14000000 INFO @ Mon, 13 Nov 2017 13:31:43: 14000000 INFO @ Mon, 13 Nov 2017 13:31:57: 15000000 INFO @ Mon, 13 Nov 2017 13:31:59: 15000000 INFO @ Mon, 13 Nov 2017 13:32:00: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:32:12: 16000000 INFO @ Mon, 13 Nov 2017 13:32:13: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:32:13: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:32:13: #1 total tags in treatment: 16071703 INFO @ Mon, 13 Nov 2017 13:32:13: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:32:13: #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 13:32:14: #1 tags after filtering in treatment: 16071703 INFO @ Mon, 13 Nov 2017 13:32:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:32:14: #1 finished! INFO @ Mon, 13 Nov 2017 13:32:14: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:32:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:32:15: #2 number of paired peaks: 487 WARNING @ Mon, 13 Nov 2017 13:32:15: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Mon, 13 Nov 2017 13:32:15: start model_add_line... INFO @ Mon, 13 Nov 2017 13:32:15: start X-correlation... INFO @ Mon, 13 Nov 2017 13:32:16: end of X-cor INFO @ Mon, 13 Nov 2017 13:32:16: #2 finished! INFO @ Mon, 13 Nov 2017 13:32:16: #2 predicted fragment length is 142 bps INFO @ Mon, 13 Nov 2017 13:32:16: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 13 Nov 2017 13:32:16: #2.2 Generate R script for model : SRX2576647.20_model.r INFO @ Mon, 13 Nov 2017 13:32:16: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:32:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:32:22: 16000000 INFO @ Mon, 13 Nov 2017 13:32:23: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:32:23: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:32:23: #1 total tags in treatment: 16071703 INFO @ Mon, 13 Nov 2017 13:32:23: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:32:23: #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 13:32:23: #4 Write output xls file... SRX2576647.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:32:23: #4 Write peak in narrowPeak format file... SRX2576647.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:32:23: #4 Write summits bed file... SRX2576647.10_summits.bed INFO @ Mon, 13 Nov 2017 13:32:23: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1985 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:32:24: #1 tags after filtering in treatment: 16071703 INFO @ Mon, 13 Nov 2017 13:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:32:24: #1 finished! INFO @ Mon, 13 Nov 2017 13:32:24: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:32:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:32:25: #2 number of paired peaks: 487 WARNING @ Mon, 13 Nov 2017 13:32:25: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Mon, 13 Nov 2017 13:32:25: start model_add_line... INFO @ Mon, 13 Nov 2017 13:32:25: start X-correlation... INFO @ Mon, 13 Nov 2017 13:32:25: end of X-cor INFO @ Mon, 13 Nov 2017 13:32:25: #2 finished! INFO @ Mon, 13 Nov 2017 13:32:25: #2 predicted fragment length is 142 bps INFO @ Mon, 13 Nov 2017 13:32:25: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 13 Nov 2017 13:32:25: #2.2 Generate R script for model : SRX2576647.05_model.r INFO @ Mon, 13 Nov 2017 13:32:25: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:32:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:33:02: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:33:13: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:33:24: #4 Write output xls file... SRX2576647.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:33:24: #4 Write peak in narrowPeak format file... SRX2576647.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:33:24: #4 Write summits bed file... SRX2576647.20_summits.bed INFO @ Mon, 13 Nov 2017 13:33:24: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1378 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:33:40: #4 Write output xls file... SRX2576647.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:33:40: #4 Write peak in narrowPeak format file... SRX2576647.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:33:40: #4 Write summits bed file... SRX2576647.05_summits.bed INFO @ Mon, 13 Nov 2017 13:33:40: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2748 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。