Job ID = 11170840 sra ファイルのダウンロード中... Completed: 963960K bytes transferred in 122 seconds (64331K 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 33757140 spots for /home/okishinya/chipatlas/results/ce10/SRX3583340/SRR6493996.sra Written 33757140 spots for /home/okishinya/chipatlas/results/ce10/SRX3583340/SRR6493996.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: 00:12:11 33757140 reads; of these: 33757140 (100.00%) were unpaired; of these: 757204 (2.24%) aligned 0 times 28926476 (85.69%) aligned exactly 1 time 4073460 (12.07%) aligned >1 times 97.76% overall alignment rate Time searching: 00:12:11 Overall time: 00:12:11 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 16 files... [bam_rmdupse_core] 6677238 / 32999936 = 0.2023 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 @ Sat, 08 Sep 2018 11:49:32: # Command line: callpeak -t SRX3583340.bam -f BAM -g ce -n SRX3583340.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3583340.10 # format = BAM # ChIP-seq file = ['SRX3583340.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 @ Sat, 08 Sep 2018 11:49:32: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:49:32: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:49:32: # Command line: callpeak -t SRX3583340.bam -f BAM -g ce -n SRX3583340.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3583340.05 # format = BAM # ChIP-seq file = ['SRX3583340.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 @ Sat, 08 Sep 2018 11:49:32: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:49:32: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:49:32: # Command line: callpeak -t SRX3583340.bam -f BAM -g ce -n SRX3583340.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3583340.20 # format = BAM # ChIP-seq file = ['SRX3583340.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 @ Sat, 08 Sep 2018 11:49:32: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:49:32: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:49:38: 1000000 INFO @ Sat, 08 Sep 2018 11:49:38: 1000000 INFO @ Sat, 08 Sep 2018 11:49:38: 1000000 INFO @ Sat, 08 Sep 2018 11:49:45: 2000000 INFO @ Sat, 08 Sep 2018 11:49:45: 2000000 INFO @ Sat, 08 Sep 2018 11:49:45: 2000000 INFO @ Sat, 08 Sep 2018 11:49:51: 3000000 INFO @ Sat, 08 Sep 2018 11:49:51: 3000000 INFO @ Sat, 08 Sep 2018 11:49:51: 3000000 INFO @ Sat, 08 Sep 2018 11:49:57: 4000000 INFO @ Sat, 08 Sep 2018 11:49:57: 4000000 INFO @ Sat, 08 Sep 2018 11:49:57: 4000000 INFO @ Sat, 08 Sep 2018 11:50:03: 5000000 INFO @ Sat, 08 Sep 2018 11:50:03: 5000000 INFO @ Sat, 08 Sep 2018 11:50:04: 5000000 INFO @ Sat, 08 Sep 2018 11:50:09: 6000000 INFO @ Sat, 08 Sep 2018 11:50:09: 6000000 INFO @ Sat, 08 Sep 2018 11:50:10: 6000000 INFO @ Sat, 08 Sep 2018 11:50:15: 7000000 INFO @ Sat, 08 Sep 2018 11:50:16: 7000000 INFO @ Sat, 08 Sep 2018 11:50:16: 7000000 INFO @ Sat, 08 Sep 2018 11:50:21: 8000000 INFO @ Sat, 08 Sep 2018 11:50:22: 8000000 INFO @ Sat, 08 Sep 2018 11:50:23: 8000000 INFO @ Sat, 08 Sep 2018 11:50:28: 9000000 INFO @ Sat, 08 Sep 2018 11:50:28: 9000000 INFO @ Sat, 08 Sep 2018 11:50:29: 9000000 INFO @ Sat, 08 Sep 2018 11:50:34: 10000000 INFO @ Sat, 08 Sep 2018 11:50:35: 10000000 INFO @ Sat, 08 Sep 2018 11:50:35: 10000000 INFO @ Sat, 08 Sep 2018 11:50:40: 11000000 INFO @ Sat, 08 Sep 2018 11:50:41: 11000000 INFO @ Sat, 08 Sep 2018 11:50:42: 11000000 INFO @ Sat, 08 Sep 2018 11:50:46: 12000000 INFO @ Sat, 08 Sep 2018 11:50:47: 12000000 INFO @ Sat, 08 Sep 2018 11:50:48: 12000000 INFO @ Sat, 08 Sep 2018 11:50:52: 13000000 INFO @ Sat, 08 Sep 2018 11:50:53: 13000000 INFO @ Sat, 08 Sep 2018 11:50:55: 13000000 INFO @ Sat, 08 Sep 2018 11:50:58: 14000000 INFO @ Sat, 08 Sep 2018 11:51:00: 14000000 INFO @ Sat, 08 Sep 2018 11:51:01: 14000000 INFO @ Sat, 08 Sep 2018 11:51:04: 15000000 INFO @ Sat, 08 Sep 2018 11:51:06: 15000000 INFO @ Sat, 08 Sep 2018 11:51:08: 15000000 INFO @ Sat, 08 Sep 2018 11:51:10: 16000000 INFO @ Sat, 08 Sep 2018 11:51:12: 16000000 INFO @ Sat, 08 Sep 2018 11:51:14: 16000000 INFO @ Sat, 08 Sep 2018 11:51:16: 17000000 INFO @ Sat, 08 Sep 2018 11:51:19: 17000000 INFO @ Sat, 08 Sep 2018 11:51:21: 17000000 INFO @ Sat, 08 Sep 2018 11:51:22: 18000000 INFO @ Sat, 08 Sep 2018 11:51:25: 18000000 INFO @ Sat, 08 Sep 2018 11:51:27: 18000000 INFO @ Sat, 08 Sep 2018 11:51:28: 19000000 INFO @ Sat, 08 Sep 2018 11:51:31: 19000000 INFO @ Sat, 08 Sep 2018 11:51:34: 19000000 INFO @ Sat, 08 Sep 2018 11:51:34: 20000000 INFO @ Sat, 08 Sep 2018 11:51:38: 20000000 INFO @ Sat, 08 Sep 2018 11:51:40: 20000000 INFO @ Sat, 08 Sep 2018 11:51:40: 21000000 INFO @ Sat, 08 Sep 2018 11:51:44: 21000000 INFO @ Sat, 08 Sep 2018 11:51:46: 22000000 INFO @ Sat, 08 Sep 2018 11:51:47: 21000000 INFO @ Sat, 08 Sep 2018 11:51:50: 22000000 INFO @ Sat, 08 Sep 2018 11:51:53: 23000000 INFO @ Sat, 08 Sep 2018 11:51:53: 22000000 INFO @ Sat, 08 Sep 2018 11:51:57: 23000000 INFO @ Sat, 08 Sep 2018 11:51:59: 24000000 INFO @ Sat, 08 Sep 2018 11:52:00: 23000000 INFO @ Sat, 08 Sep 2018 11:52:03: 24000000 INFO @ Sat, 08 Sep 2018 11:52:05: 25000000 INFO @ Sat, 08 Sep 2018 11:52:06: 24000000 INFO @ Sat, 08 Sep 2018 11:52:09: 25000000 INFO @ Sat, 08 Sep 2018 11:52:11: 26000000 INFO @ Sat, 08 Sep 2018 11:52:13: 25000000 INFO @ Sat, 08 Sep 2018 11:52:13: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:52:13: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:52:13: #1 total tags in treatment: 26322698 INFO @ Sat, 08 Sep 2018 11:52:13: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:52:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:52:13: #1 tags after filtering in treatment: 26322698 INFO @ Sat, 08 Sep 2018 11:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:52:14: #1 finished! INFO @ Sat, 08 Sep 2018 11:52:14: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:52:16: #2 number of paired peaks: 591 WARNING @ Sat, 08 Sep 2018 11:52:16: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Sat, 08 Sep 2018 11:52:16: start model_add_line... INFO @ Sat, 08 Sep 2018 11:52:16: 26000000 INFO @ Sat, 08 Sep 2018 11:52:16: start X-correlation... INFO @ Sat, 08 Sep 2018 11:52:16: end of X-cor INFO @ Sat, 08 Sep 2018 11:52:16: #2 finished! INFO @ Sat, 08 Sep 2018 11:52:16: #2 predicted fragment length is 168 bps INFO @ Sat, 08 Sep 2018 11:52:16: #2 alternative fragment length(s) may be 3,168 bps INFO @ Sat, 08 Sep 2018 11:52:16: #2.2 Generate R script for model : SRX3583340.10_model.r INFO @ Sat, 08 Sep 2018 11:52:16: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:52:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:52:18: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:52:18: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:52:18: #1 total tags in treatment: 26322698 INFO @ Sat, 08 Sep 2018 11:52:18: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:52:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:52:18: #1 tags after filtering in treatment: 26322698 INFO @ Sat, 08 Sep 2018 11:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:52:18: #1 finished! INFO @ Sat, 08 Sep 2018 11:52:18: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:52:19: 26000000 INFO @ Sat, 08 Sep 2018 11:52:20: #2 number of paired peaks: 591 WARNING @ Sat, 08 Sep 2018 11:52:20: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Sat, 08 Sep 2018 11:52:20: start model_add_line... INFO @ Sat, 08 Sep 2018 11:52:21: start X-correlation... INFO @ Sat, 08 Sep 2018 11:52:21: end of X-cor INFO @ Sat, 08 Sep 2018 11:52:21: #2 finished! INFO @ Sat, 08 Sep 2018 11:52:21: #2 predicted fragment length is 168 bps INFO @ Sat, 08 Sep 2018 11:52:21: #2 alternative fragment length(s) may be 3,168 bps INFO @ Sat, 08 Sep 2018 11:52:21: #2.2 Generate R script for model : SRX3583340.20_model.r INFO @ Sat, 08 Sep 2018 11:52:21: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:52:21: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:52:21: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:52:21: #1 total tags in treatment: 26322698 INFO @ Sat, 08 Sep 2018 11:52:21: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:52:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:52:22: #1 tags after filtering in treatment: 26322698 INFO @ Sat, 08 Sep 2018 11:52:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:52:22: #1 finished! INFO @ Sat, 08 Sep 2018 11:52:22: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:52:24: #2 number of paired peaks: 591 WARNING @ Sat, 08 Sep 2018 11:52:24: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Sat, 08 Sep 2018 11:52:24: start model_add_line... INFO @ Sat, 08 Sep 2018 11:52:24: start X-correlation... INFO @ Sat, 08 Sep 2018 11:52:24: end of X-cor INFO @ Sat, 08 Sep 2018 11:52:24: #2 finished! INFO @ Sat, 08 Sep 2018 11:52:24: #2 predicted fragment length is 168 bps INFO @ Sat, 08 Sep 2018 11:52:24: #2 alternative fragment length(s) may be 3,168 bps INFO @ Sat, 08 Sep 2018 11:52:24: #2.2 Generate R script for model : SRX3583340.05_model.r INFO @ Sat, 08 Sep 2018 11:52:24: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:52:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:53:13: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:53:19: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:53:22: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:53:38: #4 Write output xls file... SRX3583340.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:53:38: #4 Write peak in narrowPeak format file... SRX3583340.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:53:38: #4 Write summits bed file... SRX3583340.10_summits.bed INFO @ Sat, 08 Sep 2018 11:53:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4435 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:53:44: #4 Write output xls file... SRX3583340.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:53:45: #4 Write peak in narrowPeak format file... SRX3583340.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:53:45: #4 Write summits bed file... SRX3583340.20_summits.bed INFO @ Sat, 08 Sep 2018 11:53:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3287 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:53:47: #4 Write output xls file... SRX3583340.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:53:47: #4 Write peak in narrowPeak format file... SRX3583340.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:53:47: #4 Write summits bed file... SRX3583340.05_summits.bed INFO @ Sat, 08 Sep 2018 11:53:47: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5925 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。