Job ID = 11171186 sra ファイルのダウンロード中... Completed: 865088K bytes transferred in 41 seconds (172842K 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 45288360 spots for /home/okishinya/chipatlas/results/dm3/SRX2618501/SRR5319055.sra Written 45288360 spots for /home/okishinya/chipatlas/results/dm3/SRX2618501/SRR5319055.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: 00:10:00 45288360 reads; of these: 45288360 (100.00%) were unpaired; of these: 21436992 (47.33%) aligned 0 times 20169106 (44.53%) aligned exactly 1 time 3682262 (8.13%) aligned >1 times 52.67% overall alignment rate Time searching: 00:10:00 Overall time: 00:10:00 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] 2871921 / 23851368 = 0.1204 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 12:52:36: # Command line: callpeak -t SRX2618501.bam -f BAM -g dm -n SRX2618501.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618501.20 # format = BAM # ChIP-seq file = ['SRX2618501.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 12:52:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:52:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:52:36: # Command line: callpeak -t SRX2618501.bam -f BAM -g dm -n SRX2618501.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618501.05 # format = BAM # ChIP-seq file = ['SRX2618501.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 12:52:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:52:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:52:36: # Command line: callpeak -t SRX2618501.bam -f BAM -g dm -n SRX2618501.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618501.10 # format = BAM # ChIP-seq file = ['SRX2618501.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 12:52:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:52:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:52:42: 1000000 INFO @ Sat, 08 Sep 2018 12:52:42: 1000000 INFO @ Sat, 08 Sep 2018 12:52:42: 1000000 INFO @ Sat, 08 Sep 2018 12:52:48: 2000000 INFO @ Sat, 08 Sep 2018 12:52:48: 2000000 INFO @ Sat, 08 Sep 2018 12:52:48: 2000000 INFO @ Sat, 08 Sep 2018 12:52:54: 3000000 INFO @ Sat, 08 Sep 2018 12:52:54: 3000000 INFO @ Sat, 08 Sep 2018 12:52:54: 3000000 INFO @ Sat, 08 Sep 2018 12:53:00: 4000000 INFO @ Sat, 08 Sep 2018 12:53:00: 4000000 INFO @ Sat, 08 Sep 2018 12:53:00: 4000000 INFO @ Sat, 08 Sep 2018 12:53:06: 5000000 INFO @ Sat, 08 Sep 2018 12:53:06: 5000000 INFO @ Sat, 08 Sep 2018 12:53:06: 5000000 INFO @ Sat, 08 Sep 2018 12:53:11: 6000000 INFO @ Sat, 08 Sep 2018 12:53:12: 6000000 INFO @ Sat, 08 Sep 2018 12:53:12: 6000000 INFO @ Sat, 08 Sep 2018 12:53:17: 7000000 INFO @ Sat, 08 Sep 2018 12:53:18: 7000000 INFO @ Sat, 08 Sep 2018 12:53:18: 7000000 INFO @ Sat, 08 Sep 2018 12:53:23: 8000000 INFO @ Sat, 08 Sep 2018 12:53:24: 8000000 INFO @ Sat, 08 Sep 2018 12:53:24: 8000000 INFO @ Sat, 08 Sep 2018 12:53:29: 9000000 INFO @ Sat, 08 Sep 2018 12:53:30: 9000000 INFO @ Sat, 08 Sep 2018 12:53:30: 9000000 INFO @ Sat, 08 Sep 2018 12:53:35: 10000000 INFO @ Sat, 08 Sep 2018 12:53:36: 10000000 INFO @ Sat, 08 Sep 2018 12:53:36: 10000000 INFO @ Sat, 08 Sep 2018 12:53:41: 11000000 INFO @ Sat, 08 Sep 2018 12:53:42: 11000000 INFO @ Sat, 08 Sep 2018 12:53:42: 11000000 INFO @ Sat, 08 Sep 2018 12:53:47: 12000000 INFO @ Sat, 08 Sep 2018 12:53:48: 12000000 INFO @ Sat, 08 Sep 2018 12:53:48: 12000000 INFO @ Sat, 08 Sep 2018 12:53:53: 13000000 INFO @ Sat, 08 Sep 2018 12:53:55: 13000000 INFO @ Sat, 08 Sep 2018 12:53:55: 13000000 INFO @ Sat, 08 Sep 2018 12:54:00: 14000000 INFO @ Sat, 08 Sep 2018 12:54:01: 14000000 INFO @ Sat, 08 Sep 2018 12:54:01: 14000000 INFO @ Sat, 08 Sep 2018 12:54:07: 15000000 INFO @ Sat, 08 Sep 2018 12:54:07: 15000000 INFO @ Sat, 08 Sep 2018 12:54:07: 15000000 INFO @ Sat, 08 Sep 2018 12:54:13: 16000000 INFO @ Sat, 08 Sep 2018 12:54:13: 16000000 INFO @ Sat, 08 Sep 2018 12:54:13: 16000000 INFO @ Sat, 08 Sep 2018 12:54:19: 17000000 INFO @ Sat, 08 Sep 2018 12:54:20: 17000000 INFO @ Sat, 08 Sep 2018 12:54:20: 17000000 INFO @ Sat, 08 Sep 2018 12:54:26: 18000000 INFO @ Sat, 08 Sep 2018 12:54:26: 18000000 INFO @ Sat, 08 Sep 2018 12:54:26: 18000000 INFO @ Sat, 08 Sep 2018 12:54:32: 19000000 INFO @ Sat, 08 Sep 2018 12:54:32: 19000000 INFO @ Sat, 08 Sep 2018 12:54:32: 19000000 INFO @ Sat, 08 Sep 2018 12:54:38: 20000000 INFO @ Sat, 08 Sep 2018 12:54:38: 20000000 INFO @ Sat, 08 Sep 2018 12:54:38: 20000000 INFO @ Sat, 08 Sep 2018 12:54:44: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:54:44: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:54:44: #1 total tags in treatment: 20979447 INFO @ Sat, 08 Sep 2018 12:54:44: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:54:44: #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 12:54:44: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:54:44: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:54:44: #1 total tags in treatment: 20979447 INFO @ Sat, 08 Sep 2018 12:54:44: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:54:44: #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 12:54:44: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:54:44: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:54:44: #1 total tags in treatment: 20979447 INFO @ Sat, 08 Sep 2018 12:54:44: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:54:44: #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 12:54:44: #1 tags after filtering in treatment: 20979447 INFO @ Sat, 08 Sep 2018 12:54:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:54:44: #1 finished! INFO @ Sat, 08 Sep 2018 12:54:44: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:54:45: #1 tags after filtering in treatment: 20979447 INFO @ Sat, 08 Sep 2018 12:54:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:54:45: #1 finished! INFO @ Sat, 08 Sep 2018 12:54:45: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:54:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:54:45: #1 tags after filtering in treatment: 20979447 INFO @ Sat, 08 Sep 2018 12:54:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:54:45: #1 finished! INFO @ Sat, 08 Sep 2018 12:54:45: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:54:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:54:46: #2 number of paired peaks: 286 WARNING @ Sat, 08 Sep 2018 12:54:46: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Sat, 08 Sep 2018 12:54:46: start model_add_line... INFO @ Sat, 08 Sep 2018 12:54:46: #2 number of paired peaks: 286 WARNING @ Sat, 08 Sep 2018 12:54:46: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Sat, 08 Sep 2018 12:54:46: start model_add_line... INFO @ Sat, 08 Sep 2018 12:54:46: start X-correlation... INFO @ Sat, 08 Sep 2018 12:54:46: end of X-cor INFO @ Sat, 08 Sep 2018 12:54:46: #2 finished! INFO @ Sat, 08 Sep 2018 12:54:46: #2 predicted fragment length is 154 bps INFO @ Sat, 08 Sep 2018 12:54:46: #2 alternative fragment length(s) may be 4,154,166 bps INFO @ Sat, 08 Sep 2018 12:54:46: #2.2 Generate R script for model : SRX2618501.10_model.r INFO @ Sat, 08 Sep 2018 12:54:46: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:54:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:54:46: start X-correlation... INFO @ Sat, 08 Sep 2018 12:54:46: end of X-cor INFO @ Sat, 08 Sep 2018 12:54:46: #2 finished! INFO @ Sat, 08 Sep 2018 12:54:46: #2 predicted fragment length is 154 bps INFO @ Sat, 08 Sep 2018 12:54:46: #2 alternative fragment length(s) may be 4,154,166 bps INFO @ Sat, 08 Sep 2018 12:54:46: #2.2 Generate R script for model : SRX2618501.20_model.r INFO @ Sat, 08 Sep 2018 12:54:46: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:54:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:54:46: #2 number of paired peaks: 286 WARNING @ Sat, 08 Sep 2018 12:54:46: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Sat, 08 Sep 2018 12:54:46: start model_add_line... INFO @ Sat, 08 Sep 2018 12:54:46: start X-correlation... INFO @ Sat, 08 Sep 2018 12:54:46: end of X-cor INFO @ Sat, 08 Sep 2018 12:54:46: #2 finished! INFO @ Sat, 08 Sep 2018 12:54:46: #2 predicted fragment length is 154 bps INFO @ Sat, 08 Sep 2018 12:54:46: #2 alternative fragment length(s) may be 4,154,166 bps INFO @ Sat, 08 Sep 2018 12:54:46: #2.2 Generate R script for model : SRX2618501.05_model.r INFO @ Sat, 08 Sep 2018 12:54:46: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:54:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:55:33: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:55:34: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:55:38: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:55:58: #4 Write output xls file... SRX2618501.10_peaks.xls INFO @ Sat, 08 Sep 2018 12:55:58: #4 Write peak in narrowPeak format file... SRX2618501.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:55:58: #4 Write summits bed file... SRX2618501.10_summits.bed INFO @ Sat, 08 Sep 2018 12:55:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4135 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:55:59: #4 Write output xls file... SRX2618501.05_peaks.xls INFO @ Sat, 08 Sep 2018 12:55:59: #4 Write peak in narrowPeak format file... SRX2618501.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:55:59: #4 Write summits bed file... SRX2618501.05_summits.bed INFO @ Sat, 08 Sep 2018 12:55:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7640 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:56:02: #4 Write output xls file... SRX2618501.20_peaks.xls INFO @ Sat, 08 Sep 2018 12:56:02: #4 Write peak in narrowPeak format file... SRX2618501.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:56:02: #4 Write summits bed file... SRX2618501.20_summits.bed INFO @ Sat, 08 Sep 2018 12:56:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1292 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。