Job ID = 10450715 sra ファイルのダウンロード中... Completed: 489123K bytes transferred in 12 seconds (312523K 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 25437957 spots for /home/okishinya/chipatlas/results/dm3/SRX3404010/SRR6303487.sra Written 25437957 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: 00:09:50 25437957 reads; of these: 25437957 (100.00%) were unpaired; of these: 740192 (2.91%) aligned 0 times 17893427 (70.34%) aligned exactly 1 time 6804338 (26.75%) aligned >1 times 97.09% overall alignment rate Time searching: 00:09:50 Overall time: 00:09:50 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] 2442922 / 24697765 = 0.0989 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 10:38:09: # Command line: callpeak -t SRX3404010.bam -f BAM -g dm -n SRX3404010.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404010.05 # format = BAM # ChIP-seq file = ['SRX3404010.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 10:38:09: #1 read tag files... INFO @ Wed, 07 Feb 2018 10:38:09: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 10:38:09: # Command line: callpeak -t SRX3404010.bam -f BAM -g dm -n SRX3404010.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404010.10 # format = BAM # ChIP-seq file = ['SRX3404010.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 10:38:09: #1 read tag files... INFO @ Wed, 07 Feb 2018 10:38:09: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 10:38:09: # Command line: callpeak -t SRX3404010.bam -f BAM -g dm -n SRX3404010.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404010.20 # format = BAM # ChIP-seq file = ['SRX3404010.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 10:38:09: #1 read tag files... INFO @ Wed, 07 Feb 2018 10:38:09: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 10:38:16: 1000000 INFO @ Wed, 07 Feb 2018 10:38:16: 1000000 INFO @ Wed, 07 Feb 2018 10:38:16: 1000000 INFO @ Wed, 07 Feb 2018 10:38:23: 2000000 INFO @ Wed, 07 Feb 2018 10:38:23: 2000000 INFO @ Wed, 07 Feb 2018 10:38:23: 2000000 INFO @ Wed, 07 Feb 2018 10:38:30: 3000000 INFO @ Wed, 07 Feb 2018 10:38:30: 3000000 INFO @ Wed, 07 Feb 2018 10:38:30: 3000000 INFO @ Wed, 07 Feb 2018 10:38:36: 4000000 INFO @ Wed, 07 Feb 2018 10:38:36: 4000000 INFO @ Wed, 07 Feb 2018 10:38:37: 4000000 INFO @ Wed, 07 Feb 2018 10:38:43: 5000000 INFO @ Wed, 07 Feb 2018 10:38:43: 5000000 INFO @ Wed, 07 Feb 2018 10:38:44: 5000000 INFO @ Wed, 07 Feb 2018 10:38:50: 6000000 INFO @ Wed, 07 Feb 2018 10:38:50: 6000000 INFO @ Wed, 07 Feb 2018 10:38:51: 6000000 INFO @ Wed, 07 Feb 2018 10:38:57: 7000000 INFO @ Wed, 07 Feb 2018 10:38:57: 7000000 INFO @ Wed, 07 Feb 2018 10:38:58: 7000000 INFO @ Wed, 07 Feb 2018 10:39:04: 8000000 INFO @ Wed, 07 Feb 2018 10:39:04: 8000000 INFO @ Wed, 07 Feb 2018 10:39:04: 8000000 INFO @ Wed, 07 Feb 2018 10:39:11: 9000000 INFO @ Wed, 07 Feb 2018 10:39:11: 9000000 INFO @ Wed, 07 Feb 2018 10:39:11: 9000000 INFO @ Wed, 07 Feb 2018 10:39:18: 10000000 INFO @ Wed, 07 Feb 2018 10:39:18: 10000000 INFO @ Wed, 07 Feb 2018 10:39:18: 10000000 INFO @ Wed, 07 Feb 2018 10:39:25: 11000000 INFO @ Wed, 07 Feb 2018 10:39:25: 11000000 INFO @ Wed, 07 Feb 2018 10:39:25: 11000000 INFO @ Wed, 07 Feb 2018 10:39:31: 12000000 INFO @ Wed, 07 Feb 2018 10:39:31: 12000000 INFO @ Wed, 07 Feb 2018 10:39:32: 12000000 INFO @ Wed, 07 Feb 2018 10:39:38: 13000000 INFO @ Wed, 07 Feb 2018 10:39:38: 13000000 INFO @ Wed, 07 Feb 2018 10:39:39: 13000000 INFO @ Wed, 07 Feb 2018 10:39:45: 14000000 INFO @ Wed, 07 Feb 2018 10:39:45: 14000000 INFO @ Wed, 07 Feb 2018 10:39:46: 14000000 INFO @ Wed, 07 Feb 2018 10:39:52: 15000000 INFO @ Wed, 07 Feb 2018 10:39:52: 15000000 INFO @ Wed, 07 Feb 2018 10:39:53: 15000000 INFO @ Wed, 07 Feb 2018 10:39:59: 16000000 INFO @ Wed, 07 Feb 2018 10:39:59: 16000000 INFO @ Wed, 07 Feb 2018 10:40:00: 16000000 INFO @ Wed, 07 Feb 2018 10:40:06: 17000000 INFO @ Wed, 07 Feb 2018 10:40:06: 17000000 INFO @ Wed, 07 Feb 2018 10:40:07: 17000000 INFO @ Wed, 07 Feb 2018 10:40:13: 18000000 INFO @ Wed, 07 Feb 2018 10:40:13: 18000000 INFO @ Wed, 07 Feb 2018 10:40:14: 18000000 INFO @ Wed, 07 Feb 2018 10:40:20: 19000000 INFO @ Wed, 07 Feb 2018 10:40:20: 19000000 INFO @ Wed, 07 Feb 2018 10:40:21: 19000000 INFO @ Wed, 07 Feb 2018 10:40:27: 20000000 INFO @ Wed, 07 Feb 2018 10:40:27: 20000000 INFO @ Wed, 07 Feb 2018 10:40:27: 20000000 INFO @ Wed, 07 Feb 2018 10:40:34: 21000000 INFO @ Wed, 07 Feb 2018 10:40:34: 21000000 INFO @ Wed, 07 Feb 2018 10:40:34: 21000000 INFO @ Wed, 07 Feb 2018 10:40:41: 22000000 INFO @ Wed, 07 Feb 2018 10:40:41: 22000000 INFO @ Wed, 07 Feb 2018 10:40:42: 22000000 INFO @ Wed, 07 Feb 2018 10:40:42: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 10:40:42: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 10:40:42: #1 total tags in treatment: 22254843 INFO @ Wed, 07 Feb 2018 10:40:42: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 10:40:42: #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 10:40:42: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 10:40:42: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 10:40:42: #1 total tags in treatment: 22254843 INFO @ Wed, 07 Feb 2018 10:40:42: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 10:40:42: #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 10:40:43: #1 tags after filtering in treatment: 22254843 INFO @ Wed, 07 Feb 2018 10:40:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 10:40:43: #1 finished! INFO @ Wed, 07 Feb 2018 10:40:43: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 10:40:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 10:40:43: #1 tags after filtering in treatment: 22254843 INFO @ Wed, 07 Feb 2018 10:40:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 10:40:43: #1 finished! INFO @ Wed, 07 Feb 2018 10:40:43: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 10:40:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 10:40:43: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 10:40:43: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 10:40:43: #1 total tags in treatment: 22254843 INFO @ Wed, 07 Feb 2018 10:40:43: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 10:40:43: #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 10:40:44: #1 tags after filtering in treatment: 22254843 INFO @ Wed, 07 Feb 2018 10:40:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 10:40:44: #1 finished! INFO @ Wed, 07 Feb 2018 10:40:44: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 10:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 10:40:45: #2 number of paired peaks: 392 WARNING @ Wed, 07 Feb 2018 10:40:45: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Wed, 07 Feb 2018 10:40:45: start model_add_line... INFO @ Wed, 07 Feb 2018 10:40:45: #2 number of paired peaks: 392 WARNING @ Wed, 07 Feb 2018 10:40:45: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Wed, 07 Feb 2018 10:40:45: start model_add_line... INFO @ Wed, 07 Feb 2018 10:40:45: start X-correlation... INFO @ Wed, 07 Feb 2018 10:40:45: end of X-cor INFO @ Wed, 07 Feb 2018 10:40:45: #2 finished! INFO @ Wed, 07 Feb 2018 10:40:45: #2 predicted fragment length is 143 bps INFO @ Wed, 07 Feb 2018 10:40:45: #2 alternative fragment length(s) may be 143 bps INFO @ Wed, 07 Feb 2018 10:40:45: #2.2 Generate R script for model : SRX3404010.10_model.r INFO @ Wed, 07 Feb 2018 10:40:45: #3 Call peaks... INFO @ Wed, 07 Feb 2018 10:40:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 10:40:45: start X-correlation... INFO @ Wed, 07 Feb 2018 10:40:45: end of X-cor INFO @ Wed, 07 Feb 2018 10:40:45: #2 finished! INFO @ Wed, 07 Feb 2018 10:40:45: #2 predicted fragment length is 143 bps INFO @ Wed, 07 Feb 2018 10:40:45: #2 alternative fragment length(s) may be 143 bps INFO @ Wed, 07 Feb 2018 10:40:45: #2.2 Generate R script for model : SRX3404010.05_model.r INFO @ Wed, 07 Feb 2018 10:40:45: #3 Call peaks... INFO @ Wed, 07 Feb 2018 10:40:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 10:40:45: #2 number of paired peaks: 392 WARNING @ Wed, 07 Feb 2018 10:40:45: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Wed, 07 Feb 2018 10:40:45: start model_add_line... INFO @ Wed, 07 Feb 2018 10:40:46: start X-correlation... INFO @ Wed, 07 Feb 2018 10:40:46: end of X-cor INFO @ Wed, 07 Feb 2018 10:40:46: #2 finished! INFO @ Wed, 07 Feb 2018 10:40:46: #2 predicted fragment length is 143 bps INFO @ Wed, 07 Feb 2018 10:40:46: #2 alternative fragment length(s) may be 143 bps INFO @ Wed, 07 Feb 2018 10:40:46: #2.2 Generate R script for model : SRX3404010.20_model.r INFO @ Wed, 07 Feb 2018 10:40:46: #3 Call peaks... INFO @ Wed, 07 Feb 2018 10:40:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 10:41:34: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 10:41:35: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 10:41:35: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 10:41:59: #4 Write output xls file... SRX3404010.20_peaks.xls INFO @ Wed, 07 Feb 2018 10:41:59: #4 Write output xls file... SRX3404010.05_peaks.xls INFO @ Wed, 07 Feb 2018 10:41:59: #4 Write peak in narrowPeak format file... SRX3404010.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 10:41:59: #4 Write summits bed file... SRX3404010.20_summits.bed INFO @ Wed, 07 Feb 2018 10:41:59: #4 Write peak in narrowPeak format file... SRX3404010.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 10:41:59: Done! INFO @ Wed, 07 Feb 2018 10:41:59: #4 Write summits bed file... SRX3404010.05_summits.bed INFO @ Wed, 07 Feb 2018 10:42:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2094 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4724 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 10:42:00: #4 Write output xls file... SRX3404010.10_peaks.xls INFO @ Wed, 07 Feb 2018 10:42:00: #4 Write peak in narrowPeak format file... SRX3404010.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 10:42:00: #4 Write summits bed file... SRX3404010.10_summits.bed INFO @ Wed, 07 Feb 2018 10:42:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3320 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。