Job ID = 10450736 sra ファイルのダウンロード中... Completed: 540574K bytes transferred in 32 seconds (136067K 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 28602646 spots for /home/okishinya/chipatlas/results/dm3/SRX3404019/SRR6303496.sra Written 28602646 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:22:55 28602646 reads; of these: 28602646 (100.00%) were unpaired; of these: 721602 (2.52%) aligned 0 times 19544598 (68.33%) aligned exactly 1 time 8336446 (29.15%) aligned >1 times 97.48% overall alignment rate Time searching: 00:22:56 Overall time: 00:22:56 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 12 files... [bam_rmdupse_core] 4205119 / 27881044 = 0.1508 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 @ Wed, 07 Feb 2018 11:38:18: # Command line: callpeak -t SRX3404019.bam -f BAM -g dm -n SRX3404019.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404019.10 # format = BAM # ChIP-seq file = ['SRX3404019.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 @ Wed, 07 Feb 2018 11:38:18: #1 read tag files... INFO @ Wed, 07 Feb 2018 11:38:18: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 11:38:18: # Command line: callpeak -t SRX3404019.bam -f BAM -g dm -n SRX3404019.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404019.05 # format = BAM # ChIP-seq file = ['SRX3404019.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 @ Wed, 07 Feb 2018 11:38:18: #1 read tag files... INFO @ Wed, 07 Feb 2018 11:38:18: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 11:38:18: # Command line: callpeak -t SRX3404019.bam -f BAM -g dm -n SRX3404019.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404019.20 # format = BAM # ChIP-seq file = ['SRX3404019.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 @ Wed, 07 Feb 2018 11:38:18: #1 read tag files... INFO @ Wed, 07 Feb 2018 11:38:18: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 11:38:27: 1000000 INFO @ Wed, 07 Feb 2018 11:38:28: 1000000 INFO @ Wed, 07 Feb 2018 11:38:28: 1000000 INFO @ Wed, 07 Feb 2018 11:38:36: 2000000 INFO @ Wed, 07 Feb 2018 11:38:37: 2000000 INFO @ Wed, 07 Feb 2018 11:38:38: 2000000 INFO @ Wed, 07 Feb 2018 11:38:44: 3000000 INFO @ Wed, 07 Feb 2018 11:38:45: 3000000 INFO @ Wed, 07 Feb 2018 11:38:47: 3000000 INFO @ Wed, 07 Feb 2018 11:38:52: 4000000 INFO @ Wed, 07 Feb 2018 11:38:53: 4000000 INFO @ Wed, 07 Feb 2018 11:38:57: 4000000 INFO @ Wed, 07 Feb 2018 11:39:00: 5000000 INFO @ Wed, 07 Feb 2018 11:39:01: 5000000 INFO @ Wed, 07 Feb 2018 11:39:08: 5000000 INFO @ Wed, 07 Feb 2018 11:39:09: 6000000 INFO @ Wed, 07 Feb 2018 11:39:10: 6000000 INFO @ Wed, 07 Feb 2018 11:39:17: 6000000 INFO @ Wed, 07 Feb 2018 11:39:17: 7000000 INFO @ Wed, 07 Feb 2018 11:39:19: 7000000 INFO @ Wed, 07 Feb 2018 11:39:25: 7000000 INFO @ Wed, 07 Feb 2018 11:39:26: 8000000 INFO @ Wed, 07 Feb 2018 11:39:27: 8000000 INFO @ Wed, 07 Feb 2018 11:39:34: 9000000 INFO @ Wed, 07 Feb 2018 11:39:34: 8000000 INFO @ Wed, 07 Feb 2018 11:39:36: 9000000 INFO @ Wed, 07 Feb 2018 11:39:42: 9000000 INFO @ Wed, 07 Feb 2018 11:39:43: 10000000 INFO @ Wed, 07 Feb 2018 11:39:44: 10000000 INFO @ Wed, 07 Feb 2018 11:39:50: 11000000 INFO @ Wed, 07 Feb 2018 11:39:51: 10000000 INFO @ Wed, 07 Feb 2018 11:39:52: 11000000 INFO @ Wed, 07 Feb 2018 11:39:58: 12000000 INFO @ Wed, 07 Feb 2018 11:40:00: 11000000 INFO @ Wed, 07 Feb 2018 11:40:01: 12000000 INFO @ Wed, 07 Feb 2018 11:40:05: 13000000 INFO @ Wed, 07 Feb 2018 11:40:09: 12000000 INFO @ Wed, 07 Feb 2018 11:40:11: 13000000 INFO @ Wed, 07 Feb 2018 11:40:13: 14000000 INFO @ Wed, 07 Feb 2018 11:40:18: 13000000 INFO @ Wed, 07 Feb 2018 11:40:20: 14000000 INFO @ Wed, 07 Feb 2018 11:40:22: 15000000 INFO @ Wed, 07 Feb 2018 11:40:27: 14000000 INFO @ Wed, 07 Feb 2018 11:40:28: 15000000 INFO @ Wed, 07 Feb 2018 11:40:30: 16000000 INFO @ Wed, 07 Feb 2018 11:40:35: 15000000 INFO @ Wed, 07 Feb 2018 11:40:37: 16000000 INFO @ Wed, 07 Feb 2018 11:40:38: 17000000 INFO @ Wed, 07 Feb 2018 11:40:44: 16000000 INFO @ Wed, 07 Feb 2018 11:40:45: 17000000 INFO @ Wed, 07 Feb 2018 11:40:47: 18000000 INFO @ Wed, 07 Feb 2018 11:40:54: 17000000 INFO @ Wed, 07 Feb 2018 11:40:54: 18000000 INFO @ Wed, 07 Feb 2018 11:40:55: 19000000 INFO @ Wed, 07 Feb 2018 11:41:02: 19000000 INFO @ Wed, 07 Feb 2018 11:41:03: 20000000 INFO @ Wed, 07 Feb 2018 11:41:03: 18000000 INFO @ Wed, 07 Feb 2018 11:41:10: 20000000 INFO @ Wed, 07 Feb 2018 11:41:10: 21000000 INFO @ Wed, 07 Feb 2018 11:41:11: 19000000 INFO @ Wed, 07 Feb 2018 11:41:18: 21000000 INFO @ Wed, 07 Feb 2018 11:41:18: 22000000 INFO @ Wed, 07 Feb 2018 11:41:20: 20000000 INFO @ Wed, 07 Feb 2018 11:41:26: 23000000 INFO @ Wed, 07 Feb 2018 11:41:27: 22000000 INFO @ Wed, 07 Feb 2018 11:41:28: 21000000 INFO @ Wed, 07 Feb 2018 11:41:32: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 11:41:32: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 11:41:32: #1 total tags in treatment: 23675925 INFO @ Wed, 07 Feb 2018 11:41:32: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 11:41:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 11:41:32: #1 tags after filtering in treatment: 23675925 INFO @ Wed, 07 Feb 2018 11:41:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 11:41:32: #1 finished! INFO @ Wed, 07 Feb 2018 11:41:32: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 11:41:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 11:41:35: #2 number of paired peaks: 487 WARNING @ Wed, 07 Feb 2018 11:41:35: 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 @ Wed, 07 Feb 2018 11:41:35: start model_add_line... INFO @ Wed, 07 Feb 2018 11:41:35: 23000000 INFO @ Wed, 07 Feb 2018 11:41:35: start X-correlation... INFO @ Wed, 07 Feb 2018 11:41:35: end of X-cor INFO @ Wed, 07 Feb 2018 11:41:35: #2 finished! INFO @ Wed, 07 Feb 2018 11:41:35: #2 predicted fragment length is 164 bps INFO @ Wed, 07 Feb 2018 11:41:35: #2 alternative fragment length(s) may be 164 bps INFO @ Wed, 07 Feb 2018 11:41:35: #2.2 Generate R script for model : SRX3404019.20_model.r INFO @ Wed, 07 Feb 2018 11:41:35: #3 Call peaks... INFO @ Wed, 07 Feb 2018 11:41:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:41:36: 22000000 INFO @ Wed, 07 Feb 2018 11:41:40: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 11:41:40: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 11:41:40: #1 total tags in treatment: 23675925 INFO @ Wed, 07 Feb 2018 11:41:40: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 11:41:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 11:41:41: #1 tags after filtering in treatment: 23675925 INFO @ Wed, 07 Feb 2018 11:41:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 11:41:41: #1 finished! INFO @ Wed, 07 Feb 2018 11:41:41: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 11:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 11:41:43: #2 number of paired peaks: 487 WARNING @ Wed, 07 Feb 2018 11:41:43: 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 @ Wed, 07 Feb 2018 11:41:43: start model_add_line... INFO @ Wed, 07 Feb 2018 11:41:44: start X-correlation... INFO @ Wed, 07 Feb 2018 11:41:44: end of X-cor INFO @ Wed, 07 Feb 2018 11:41:44: #2 finished! INFO @ Wed, 07 Feb 2018 11:41:44: #2 predicted fragment length is 164 bps INFO @ Wed, 07 Feb 2018 11:41:44: #2 alternative fragment length(s) may be 164 bps INFO @ Wed, 07 Feb 2018 11:41:44: #2.2 Generate R script for model : SRX3404019.10_model.r INFO @ Wed, 07 Feb 2018 11:41:44: #3 Call peaks... INFO @ Wed, 07 Feb 2018 11:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:41:45: 23000000 INFO @ Wed, 07 Feb 2018 11:41:52: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 11:41:52: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 11:41:52: #1 total tags in treatment: 23675925 INFO @ Wed, 07 Feb 2018 11:41:52: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 11:41:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 11:41:53: #1 tags after filtering in treatment: 23675925 INFO @ Wed, 07 Feb 2018 11:41:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 11:41:53: #1 finished! INFO @ Wed, 07 Feb 2018 11:41:53: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 11:41:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 11:41:55: #2 number of paired peaks: 487 WARNING @ Wed, 07 Feb 2018 11:41:55: 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 @ Wed, 07 Feb 2018 11:41:55: start model_add_line... INFO @ Wed, 07 Feb 2018 11:41:56: start X-correlation... INFO @ Wed, 07 Feb 2018 11:41:56: end of X-cor INFO @ Wed, 07 Feb 2018 11:41:56: #2 finished! INFO @ Wed, 07 Feb 2018 11:41:56: #2 predicted fragment length is 164 bps INFO @ Wed, 07 Feb 2018 11:41:56: #2 alternative fragment length(s) may be 164 bps INFO @ Wed, 07 Feb 2018 11:41:56: #2.2 Generate R script for model : SRX3404019.05_model.r INFO @ Wed, 07 Feb 2018 11:41:56: #3 Call peaks... INFO @ Wed, 07 Feb 2018 11:41:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:42:50: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:42:58: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:43:10: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:43:30: #4 Write output xls file... SRX3404019.20_peaks.xls INFO @ Wed, 07 Feb 2018 11:43:30: #4 Write peak in narrowPeak format file... SRX3404019.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:43:30: #4 Write summits bed file... SRX3404019.20_summits.bed INFO @ Wed, 07 Feb 2018 11:43:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2957 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 11:43:36: #4 Write output xls file... SRX3404019.10_peaks.xls INFO @ Wed, 07 Feb 2018 11:43:36: #4 Write peak in narrowPeak format file... SRX3404019.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:43:37: #4 Write summits bed file... SRX3404019.10_summits.bed INFO @ Wed, 07 Feb 2018 11:43:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3998 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 11:43:47: #4 Write output xls file... SRX3404019.05_peaks.xls INFO @ Wed, 07 Feb 2018 11:43:47: #4 Write peak in narrowPeak format file... SRX3404019.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:43:47: #4 Write summits bed file... SRX3404019.05_summits.bed INFO @ Wed, 07 Feb 2018 11:43:48: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5206 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。