Job ID = 10480754 sra ファイルのダウンロード中... Completed: 531351K bytes transferred in 13 seconds (312814K 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 21842262 spots for /home/okishinya/chipatlas/results/dm3/SRX3380813/SRR6278176.sra Written 21842262 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: 00:06:29 21842262 reads; of these: 21842262 (100.00%) were unpaired; of these: 2797293 (12.81%) aligned 0 times 16105618 (73.74%) aligned exactly 1 time 2939351 (13.46%) aligned >1 times 87.19% overall alignment rate Time searching: 00:06:29 Overall time: 00:06:29 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] 2438519 / 19044969 = 0.1280 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 @ Fri, 16 Mar 2018 08:00:23: # Command line: callpeak -t SRX3380813.bam -f BAM -g dm -n SRX3380813.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380813.10 # format = BAM # ChIP-seq file = ['SRX3380813.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 @ Fri, 16 Mar 2018 08:00:23: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:00:23: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:00:23: # Command line: callpeak -t SRX3380813.bam -f BAM -g dm -n SRX3380813.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380813.20 # format = BAM # ChIP-seq file = ['SRX3380813.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 @ Fri, 16 Mar 2018 08:00:23: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:00:23: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:00:23: # Command line: callpeak -t SRX3380813.bam -f BAM -g dm -n SRX3380813.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380813.05 # format = BAM # ChIP-seq file = ['SRX3380813.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 @ Fri, 16 Mar 2018 08:00:23: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:00:23: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:00:29: 1000000 INFO @ Fri, 16 Mar 2018 08:00:29: 1000000 INFO @ Fri, 16 Mar 2018 08:00:29: 1000000 INFO @ Fri, 16 Mar 2018 08:00:35: 2000000 INFO @ Fri, 16 Mar 2018 08:00:35: 2000000 INFO @ Fri, 16 Mar 2018 08:00:35: 2000000 INFO @ Fri, 16 Mar 2018 08:00:41: 3000000 INFO @ Fri, 16 Mar 2018 08:00:41: 3000000 INFO @ Fri, 16 Mar 2018 08:00:41: 3000000 INFO @ Fri, 16 Mar 2018 08:00:46: 4000000 INFO @ Fri, 16 Mar 2018 08:00:46: 4000000 INFO @ Fri, 16 Mar 2018 08:00:46: 4000000 INFO @ Fri, 16 Mar 2018 08:00:52: 5000000 INFO @ Fri, 16 Mar 2018 08:00:52: 5000000 INFO @ Fri, 16 Mar 2018 08:00:52: 5000000 INFO @ Fri, 16 Mar 2018 08:00:58: 6000000 INFO @ Fri, 16 Mar 2018 08:00:58: 6000000 INFO @ Fri, 16 Mar 2018 08:00:58: 6000000 INFO @ Fri, 16 Mar 2018 08:01:04: 7000000 INFO @ Fri, 16 Mar 2018 08:01:04: 7000000 INFO @ Fri, 16 Mar 2018 08:01:04: 7000000 INFO @ Fri, 16 Mar 2018 08:01:10: 8000000 INFO @ Fri, 16 Mar 2018 08:01:10: 8000000 INFO @ Fri, 16 Mar 2018 08:01:10: 8000000 INFO @ Fri, 16 Mar 2018 08:01:16: 9000000 INFO @ Fri, 16 Mar 2018 08:01:16: 9000000 INFO @ Fri, 16 Mar 2018 08:01:16: 9000000 INFO @ Fri, 16 Mar 2018 08:01:22: 10000000 INFO @ Fri, 16 Mar 2018 08:01:22: 10000000 INFO @ Fri, 16 Mar 2018 08:01:22: 10000000 INFO @ Fri, 16 Mar 2018 08:01:27: 11000000 INFO @ Fri, 16 Mar 2018 08:01:27: 11000000 INFO @ Fri, 16 Mar 2018 08:01:28: 11000000 INFO @ Fri, 16 Mar 2018 08:01:33: 12000000 INFO @ Fri, 16 Mar 2018 08:01:33: 12000000 INFO @ Fri, 16 Mar 2018 08:01:34: 12000000 INFO @ Fri, 16 Mar 2018 08:01:39: 13000000 INFO @ Fri, 16 Mar 2018 08:01:39: 13000000 INFO @ Fri, 16 Mar 2018 08:01:39: 13000000 INFO @ Fri, 16 Mar 2018 08:01:45: 14000000 INFO @ Fri, 16 Mar 2018 08:01:45: 14000000 INFO @ Fri, 16 Mar 2018 08:01:46: 14000000 INFO @ Fri, 16 Mar 2018 08:01:51: 15000000 INFO @ Fri, 16 Mar 2018 08:01:51: 15000000 INFO @ Fri, 16 Mar 2018 08:01:51: 15000000 INFO @ Fri, 16 Mar 2018 08:01:57: 16000000 INFO @ Fri, 16 Mar 2018 08:01:57: 16000000 INFO @ Fri, 16 Mar 2018 08:01:58: 16000000 INFO @ Fri, 16 Mar 2018 08:02:01: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 08:02:01: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 08:02:01: #1 total tags in treatment: 16606450 INFO @ Fri, 16 Mar 2018 08:02:01: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:02:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:02:01: #1 tags after filtering in treatment: 16606450 INFO @ Fri, 16 Mar 2018 08:02:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:02:01: #1 finished! INFO @ Fri, 16 Mar 2018 08:02:01: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:02:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:02:01: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 08:02:01: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 08:02:01: #1 total tags in treatment: 16606450 INFO @ Fri, 16 Mar 2018 08:02:01: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:02:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:02:01: #1 tags after filtering in treatment: 16606450 INFO @ Fri, 16 Mar 2018 08:02:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:02:01: #1 finished! INFO @ Fri, 16 Mar 2018 08:02:01: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:02:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:02:02: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 08:02:02: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 08:02:02: #1 total tags in treatment: 16606450 INFO @ Fri, 16 Mar 2018 08:02:02: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:02:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:02:02: #1 tags after filtering in treatment: 16606450 INFO @ Fri, 16 Mar 2018 08:02:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:02:02: #1 finished! INFO @ Fri, 16 Mar 2018 08:02:02: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:02:02: #2 number of paired peaks: 500 WARNING @ Fri, 16 Mar 2018 08:02:02: Fewer paired peaks (500) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 500 pairs to build model! INFO @ Fri, 16 Mar 2018 08:02:02: start model_add_line... INFO @ Fri, 16 Mar 2018 08:02:02: start X-correlation... INFO @ Fri, 16 Mar 2018 08:02:02: end of X-cor INFO @ Fri, 16 Mar 2018 08:02:02: #2 finished! INFO @ Fri, 16 Mar 2018 08:02:02: #2 predicted fragment length is 153 bps INFO @ Fri, 16 Mar 2018 08:02:02: #2 alternative fragment length(s) may be 4,153 bps INFO @ Fri, 16 Mar 2018 08:02:02: #2.2 Generate R script for model : SRX3380813.05_model.r INFO @ Fri, 16 Mar 2018 08:02:02: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:02:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:02:03: #2 number of paired peaks: 500 WARNING @ Fri, 16 Mar 2018 08:02:03: Fewer paired peaks (500) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 500 pairs to build model! INFO @ Fri, 16 Mar 2018 08:02:03: start model_add_line... INFO @ Fri, 16 Mar 2018 08:02:03: start X-correlation... INFO @ Fri, 16 Mar 2018 08:02:03: end of X-cor INFO @ Fri, 16 Mar 2018 08:02:03: #2 finished! INFO @ Fri, 16 Mar 2018 08:02:03: #2 predicted fragment length is 153 bps INFO @ Fri, 16 Mar 2018 08:02:03: #2 alternative fragment length(s) may be 4,153 bps INFO @ Fri, 16 Mar 2018 08:02:03: #2.2 Generate R script for model : SRX3380813.10_model.r INFO @ Fri, 16 Mar 2018 08:02:03: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:02:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:02:03: #2 number of paired peaks: 500 WARNING @ Fri, 16 Mar 2018 08:02:03: Fewer paired peaks (500) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 500 pairs to build model! INFO @ Fri, 16 Mar 2018 08:02:03: start model_add_line... INFO @ Fri, 16 Mar 2018 08:02:03: start X-correlation... INFO @ Fri, 16 Mar 2018 08:02:03: end of X-cor INFO @ Fri, 16 Mar 2018 08:02:03: #2 finished! INFO @ Fri, 16 Mar 2018 08:02:03: #2 predicted fragment length is 153 bps INFO @ Fri, 16 Mar 2018 08:02:03: #2 alternative fragment length(s) may be 4,153 bps INFO @ Fri, 16 Mar 2018 08:02:03: #2.2 Generate R script for model : SRX3380813.20_model.r INFO @ Fri, 16 Mar 2018 08:02:03: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:02:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:02:39: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:02:40: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:02:43: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:02:59: #4 Write output xls file... SRX3380813.05_peaks.xls INFO @ Fri, 16 Mar 2018 08:02:59: #4 Write peak in narrowPeak format file... SRX3380813.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:02:59: #4 Write summits bed file... SRX3380813.05_summits.bed INFO @ Fri, 16 Mar 2018 08:02:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6501 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:02:59: #4 Write output xls file... SRX3380813.10_peaks.xls INFO @ Fri, 16 Mar 2018 08:02:59: #4 Write peak in narrowPeak format file... SRX3380813.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:02:59: #4 Write summits bed file... SRX3380813.10_summits.bed INFO @ Fri, 16 Mar 2018 08:02:59: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4161 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:03:04: #4 Write output xls file... SRX3380813.20_peaks.xls INFO @ Fri, 16 Mar 2018 08:03:04: #4 Write peak in narrowPeak format file... SRX3380813.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:03:04: #4 Write summits bed file... SRX3380813.20_summits.bed INFO @ Fri, 16 Mar 2018 08:03:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1333 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。