Job ID = 11171197 sra ファイルのダウンロード中... Completed: 484620K bytes transferred in 21 seconds (186054K 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 24269055 spots for /home/okishinya/chipatlas/results/dm3/SRX2618510/SRR5319064.sra Written 24269055 spots for /home/okishinya/chipatlas/results/dm3/SRX2618510/SRR5319064.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: 00:00:01 Multiseed full-index search: 00:05:36 24269055 reads; of these: 24269055 (100.00%) were unpaired; of these: 8037631 (33.12%) aligned 0 times 14203142 (58.52%) aligned exactly 1 time 2028282 (8.36%) aligned >1 times 66.88% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 1815541 / 16231424 = 0.1119 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 12:57:01: # Command line: callpeak -t SRX2618510.bam -f BAM -g dm -n SRX2618510.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618510.05 # format = BAM # ChIP-seq file = ['SRX2618510.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 @ Sat, 08 Sep 2018 12:57:01: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:57:01: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:57:01: # Command line: callpeak -t SRX2618510.bam -f BAM -g dm -n SRX2618510.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618510.20 # format = BAM # ChIP-seq file = ['SRX2618510.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 @ Sat, 08 Sep 2018 12:57:01: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:57:01: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:57:01: # Command line: callpeak -t SRX2618510.bam -f BAM -g dm -n SRX2618510.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618510.10 # format = BAM # ChIP-seq file = ['SRX2618510.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 @ Sat, 08 Sep 2018 12:57:01: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:57:01: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:57:07: 1000000 INFO @ Sat, 08 Sep 2018 12:57:07: 1000000 INFO @ Sat, 08 Sep 2018 12:57:07: 1000000 INFO @ Sat, 08 Sep 2018 12:57:14: 2000000 INFO @ Sat, 08 Sep 2018 12:57:14: 2000000 INFO @ Sat, 08 Sep 2018 12:57:14: 2000000 INFO @ Sat, 08 Sep 2018 12:57:21: 3000000 INFO @ Sat, 08 Sep 2018 12:57:21: 3000000 INFO @ Sat, 08 Sep 2018 12:57:21: 3000000 INFO @ Sat, 08 Sep 2018 12:57:28: 4000000 INFO @ Sat, 08 Sep 2018 12:57:28: 4000000 INFO @ Sat, 08 Sep 2018 12:57:28: 4000000 INFO @ Sat, 08 Sep 2018 12:57:34: 5000000 INFO @ Sat, 08 Sep 2018 12:57:35: 5000000 INFO @ Sat, 08 Sep 2018 12:57:35: 5000000 INFO @ Sat, 08 Sep 2018 12:57:41: 6000000 INFO @ Sat, 08 Sep 2018 12:57:42: 6000000 INFO @ Sat, 08 Sep 2018 12:57:42: 6000000 INFO @ Sat, 08 Sep 2018 12:57:48: 7000000 INFO @ Sat, 08 Sep 2018 12:57:48: 7000000 INFO @ Sat, 08 Sep 2018 12:57:49: 7000000 INFO @ Sat, 08 Sep 2018 12:57:54: 8000000 INFO @ Sat, 08 Sep 2018 12:57:55: 8000000 INFO @ Sat, 08 Sep 2018 12:57:56: 8000000 INFO @ Sat, 08 Sep 2018 12:58:01: 9000000 INFO @ Sat, 08 Sep 2018 12:58:02: 9000000 INFO @ Sat, 08 Sep 2018 12:58:03: 9000000 INFO @ Sat, 08 Sep 2018 12:58:07: 10000000 INFO @ Sat, 08 Sep 2018 12:58:09: 10000000 INFO @ Sat, 08 Sep 2018 12:58:10: 10000000 INFO @ Sat, 08 Sep 2018 12:58:14: 11000000 INFO @ Sat, 08 Sep 2018 12:58:16: 11000000 INFO @ Sat, 08 Sep 2018 12:58:17: 11000000 INFO @ Sat, 08 Sep 2018 12:58:21: 12000000 INFO @ Sat, 08 Sep 2018 12:58:23: 12000000 INFO @ Sat, 08 Sep 2018 12:58:24: 12000000 INFO @ Sat, 08 Sep 2018 12:58:27: 13000000 INFO @ Sat, 08 Sep 2018 12:58:30: 13000000 INFO @ Sat, 08 Sep 2018 12:58:31: 13000000 INFO @ Sat, 08 Sep 2018 12:58:34: 14000000 INFO @ Sat, 08 Sep 2018 12:58:37: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:58:37: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:58:37: #1 total tags in treatment: 14415883 INFO @ Sat, 08 Sep 2018 12:58:37: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:58:37: #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 12:58:37: #1 tags after filtering in treatment: 14415883 INFO @ Sat, 08 Sep 2018 12:58:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:58:37: #1 finished! INFO @ Sat, 08 Sep 2018 12:58:37: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:58:37: 14000000 INFO @ Sat, 08 Sep 2018 12:58:38: #2 number of paired peaks: 925 WARNING @ Sat, 08 Sep 2018 12:58:38: Fewer paired peaks (925) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 925 pairs to build model! INFO @ Sat, 08 Sep 2018 12:58:38: start model_add_line... INFO @ Sat, 08 Sep 2018 12:58:38: 14000000 INFO @ Sat, 08 Sep 2018 12:58:38: start X-correlation... INFO @ Sat, 08 Sep 2018 12:58:38: end of X-cor INFO @ Sat, 08 Sep 2018 12:58:38: #2 finished! INFO @ Sat, 08 Sep 2018 12:58:38: #2 predicted fragment length is 155 bps INFO @ Sat, 08 Sep 2018 12:58:38: #2 alternative fragment length(s) may be 155 bps INFO @ Sat, 08 Sep 2018 12:58:38: #2.2 Generate R script for model : SRX2618510.20_model.r INFO @ Sat, 08 Sep 2018 12:58:38: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:58:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:58:40: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:58:40: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:58:40: #1 total tags in treatment: 14415883 INFO @ Sat, 08 Sep 2018 12:58:40: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:58:40: #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 12:58:40: #1 tags after filtering in treatment: 14415883 INFO @ Sat, 08 Sep 2018 12:58:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:58:40: #1 finished! INFO @ Sat, 08 Sep 2018 12:58:40: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:58:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:58:41: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:58:41: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:58:41: #1 total tags in treatment: 14415883 INFO @ Sat, 08 Sep 2018 12:58:41: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:58:41: #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 12:58:41: #2 number of paired peaks: 925 WARNING @ Sat, 08 Sep 2018 12:58:41: Fewer paired peaks (925) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 925 pairs to build model! INFO @ Sat, 08 Sep 2018 12:58:41: start model_add_line... INFO @ Sat, 08 Sep 2018 12:58:41: #1 tags after filtering in treatment: 14415883 INFO @ Sat, 08 Sep 2018 12:58:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:58:41: #1 finished! INFO @ Sat, 08 Sep 2018 12:58:41: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:58:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:58:41: start X-correlation... INFO @ Sat, 08 Sep 2018 12:58:41: end of X-cor INFO @ Sat, 08 Sep 2018 12:58:41: #2 finished! INFO @ Sat, 08 Sep 2018 12:58:41: #2 predicted fragment length is 155 bps INFO @ Sat, 08 Sep 2018 12:58:41: #2 alternative fragment length(s) may be 155 bps INFO @ Sat, 08 Sep 2018 12:58:41: #2.2 Generate R script for model : SRX2618510.05_model.r INFO @ Sat, 08 Sep 2018 12:58:41: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:58:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:58:42: #2 number of paired peaks: 925 WARNING @ Sat, 08 Sep 2018 12:58:42: Fewer paired peaks (925) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 925 pairs to build model! INFO @ Sat, 08 Sep 2018 12:58:42: start model_add_line... INFO @ Sat, 08 Sep 2018 12:58:43: start X-correlation... INFO @ Sat, 08 Sep 2018 12:58:43: end of X-cor INFO @ Sat, 08 Sep 2018 12:58:43: #2 finished! INFO @ Sat, 08 Sep 2018 12:58:43: #2 predicted fragment length is 155 bps INFO @ Sat, 08 Sep 2018 12:58:43: #2 alternative fragment length(s) may be 155 bps INFO @ Sat, 08 Sep 2018 12:58:43: #2.2 Generate R script for model : SRX2618510.10_model.r INFO @ Sat, 08 Sep 2018 12:58:43: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:58:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:59:08: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:59:14: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:59:15: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:59:26: #4 Write output xls file... SRX2618510.20_peaks.xls INFO @ Sat, 08 Sep 2018 12:59:26: #4 Write peak in narrowPeak format file... SRX2618510.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:59:26: #4 Write summits bed file... SRX2618510.20_summits.bed INFO @ Sat, 08 Sep 2018 12:59:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1752 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:59:32: #4 Write output xls file... SRX2618510.10_peaks.xls INFO @ Sat, 08 Sep 2018 12:59:32: #4 Write peak in narrowPeak format file... SRX2618510.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:59:32: #4 Write summits bed file... SRX2618510.10_summits.bed INFO @ Sat, 08 Sep 2018 12:59:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5142 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:59:35: #4 Write output xls file... SRX2618510.05_peaks.xls INFO @ Sat, 08 Sep 2018 12:59:35: #4 Write peak in narrowPeak format file... SRX2618510.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:59:35: #4 Write summits bed file... SRX2618510.05_summits.bed INFO @ Sat, 08 Sep 2018 12:59:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7757 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。