Job ID = 11171182 sra ファイルのダウンロード中... Completed: 788087K bytes transferred in 37 seconds (170805K 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 41305931 spots for /home/okishinya/chipatlas/results/dm3/SRX2618497/SRR5319051.sra Written 41305931 spots for /home/okishinya/chipatlas/results/dm3/SRX2618497/SRR5319051.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: 00:11:03 41305931 reads; of these: 41305931 (100.00%) were unpaired; of these: 16599142 (40.19%) aligned 0 times 19223447 (46.54%) aligned exactly 1 time 5483342 (13.27%) aligned >1 times 59.81% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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] 3121882 / 24706789 = 0.1264 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 12:50:54: # Command line: callpeak -t SRX2618497.bam -f BAM -g dm -n SRX2618497.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618497.20 # format = BAM # ChIP-seq file = ['SRX2618497.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 12:50:54: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:50:54: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:50:54: # Command line: callpeak -t SRX2618497.bam -f BAM -g dm -n SRX2618497.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618497.05 # format = BAM # ChIP-seq file = ['SRX2618497.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 12:50:54: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:50:54: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:50:54: # Command line: callpeak -t SRX2618497.bam -f BAM -g dm -n SRX2618497.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618497.10 # format = BAM # ChIP-seq file = ['SRX2618497.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 12:50:54: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:50:54: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:51:02: 1000000 INFO @ Sat, 08 Sep 2018 12:51:02: 1000000 INFO @ Sat, 08 Sep 2018 12:51:02: 1000000 INFO @ Sat, 08 Sep 2018 12:51:09: 2000000 INFO @ Sat, 08 Sep 2018 12:51:09: 2000000 INFO @ Sat, 08 Sep 2018 12:51:09: 2000000 INFO @ Sat, 08 Sep 2018 12:51:17: 3000000 INFO @ Sat, 08 Sep 2018 12:51:17: 3000000 INFO @ Sat, 08 Sep 2018 12:51:17: 3000000 INFO @ Sat, 08 Sep 2018 12:51:24: 4000000 INFO @ Sat, 08 Sep 2018 12:51:25: 4000000 INFO @ Sat, 08 Sep 2018 12:51:25: 4000000 INFO @ Sat, 08 Sep 2018 12:51:32: 5000000 INFO @ Sat, 08 Sep 2018 12:51:32: 5000000 INFO @ Sat, 08 Sep 2018 12:51:32: 5000000 INFO @ Sat, 08 Sep 2018 12:51:39: 6000000 INFO @ Sat, 08 Sep 2018 12:51:40: 6000000 INFO @ Sat, 08 Sep 2018 12:51:40: 6000000 INFO @ Sat, 08 Sep 2018 12:51:47: 7000000 INFO @ Sat, 08 Sep 2018 12:51:47: 7000000 INFO @ Sat, 08 Sep 2018 12:51:47: 7000000 INFO @ Sat, 08 Sep 2018 12:51:54: 8000000 INFO @ Sat, 08 Sep 2018 12:51:55: 8000000 INFO @ Sat, 08 Sep 2018 12:51:55: 8000000 INFO @ Sat, 08 Sep 2018 12:52:02: 9000000 INFO @ Sat, 08 Sep 2018 12:52:03: 9000000 INFO @ Sat, 08 Sep 2018 12:52:03: 9000000 INFO @ Sat, 08 Sep 2018 12:52:09: 10000000 INFO @ Sat, 08 Sep 2018 12:52:10: 10000000 INFO @ Sat, 08 Sep 2018 12:52:10: 10000000 INFO @ Sat, 08 Sep 2018 12:52:17: 11000000 INFO @ Sat, 08 Sep 2018 12:52:18: 11000000 INFO @ Sat, 08 Sep 2018 12:52:18: 11000000 INFO @ Sat, 08 Sep 2018 12:52:25: 12000000 INFO @ Sat, 08 Sep 2018 12:52:25: 12000000 INFO @ Sat, 08 Sep 2018 12:52:25: 12000000 INFO @ Sat, 08 Sep 2018 12:52:32: 13000000 INFO @ Sat, 08 Sep 2018 12:52:33: 13000000 INFO @ Sat, 08 Sep 2018 12:52:33: 13000000 INFO @ Sat, 08 Sep 2018 12:52:40: 14000000 INFO @ Sat, 08 Sep 2018 12:52:40: 14000000 INFO @ Sat, 08 Sep 2018 12:52:40: 14000000 INFO @ Sat, 08 Sep 2018 12:52:47: 15000000 INFO @ Sat, 08 Sep 2018 12:52:48: 15000000 INFO @ Sat, 08 Sep 2018 12:52:48: 15000000 INFO @ Sat, 08 Sep 2018 12:52:55: 16000000 INFO @ Sat, 08 Sep 2018 12:52:56: 16000000 INFO @ Sat, 08 Sep 2018 12:52:56: 16000000 INFO @ Sat, 08 Sep 2018 12:53:02: 17000000 INFO @ Sat, 08 Sep 2018 12:53:03: 17000000 INFO @ Sat, 08 Sep 2018 12:53:03: 17000000 INFO @ Sat, 08 Sep 2018 12:53:10: 18000000 INFO @ Sat, 08 Sep 2018 12:53:11: 18000000 INFO @ Sat, 08 Sep 2018 12:53:11: 18000000 INFO @ Sat, 08 Sep 2018 12:53:18: 19000000 INFO @ Sat, 08 Sep 2018 12:53:19: 19000000 INFO @ Sat, 08 Sep 2018 12:53:19: 19000000 INFO @ Sat, 08 Sep 2018 12:53:25: 20000000 INFO @ Sat, 08 Sep 2018 12:53:26: 20000000 INFO @ Sat, 08 Sep 2018 12:53:26: 20000000 INFO @ Sat, 08 Sep 2018 12:53:33: 21000000 INFO @ Sat, 08 Sep 2018 12:53:34: 21000000 INFO @ Sat, 08 Sep 2018 12:53:34: 21000000 INFO @ Sat, 08 Sep 2018 12:53:37: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:53:37: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:53:37: #1 total tags in treatment: 21584907 INFO @ Sat, 08 Sep 2018 12:53:37: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:53:37: #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 12:53:38: #1 tags after filtering in treatment: 21584907 INFO @ Sat, 08 Sep 2018 12:53:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:53:38: #1 finished! INFO @ Sat, 08 Sep 2018 12:53:38: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:53:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:53:39: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:53:39: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:53:39: #1 total tags in treatment: 21584907 INFO @ Sat, 08 Sep 2018 12:53:39: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:53:39: #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 12:53:39: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:53:39: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:53:39: #1 total tags in treatment: 21584907 INFO @ Sat, 08 Sep 2018 12:53:39: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:53:39: #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 12:53:39: #2 number of paired peaks: 107 WARNING @ Sat, 08 Sep 2018 12:53:39: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Sat, 08 Sep 2018 12:53:39: start model_add_line... INFO @ Sat, 08 Sep 2018 12:53:39: #1 tags after filtering in treatment: 21584907 INFO @ Sat, 08 Sep 2018 12:53:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:53:39: #1 finished! INFO @ Sat, 08 Sep 2018 12:53:39: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:53:39: #1 tags after filtering in treatment: 21584907 INFO @ Sat, 08 Sep 2018 12:53:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:53:39: #1 finished! INFO @ Sat, 08 Sep 2018 12:53:39: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:53:39: start X-correlation... INFO @ Sat, 08 Sep 2018 12:53:39: end of X-cor INFO @ Sat, 08 Sep 2018 12:53:39: #2 finished! INFO @ Sat, 08 Sep 2018 12:53:39: #2 predicted fragment length is 135 bps INFO @ Sat, 08 Sep 2018 12:53:39: #2 alternative fragment length(s) may be 4,51,88,135,577 bps INFO @ Sat, 08 Sep 2018 12:53:39: #2.2 Generate R script for model : SRX2618497.10_model.r INFO @ Sat, 08 Sep 2018 12:53:39: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:53:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:53:40: #2 number of paired peaks: 107 WARNING @ Sat, 08 Sep 2018 12:53:40: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Sat, 08 Sep 2018 12:53:40: start model_add_line... INFO @ Sat, 08 Sep 2018 12:53:41: #2 number of paired peaks: 107 WARNING @ Sat, 08 Sep 2018 12:53:41: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Sat, 08 Sep 2018 12:53:41: start model_add_line... INFO @ Sat, 08 Sep 2018 12:53:41: start X-correlation... INFO @ Sat, 08 Sep 2018 12:53:41: end of X-cor INFO @ Sat, 08 Sep 2018 12:53:41: #2 finished! INFO @ Sat, 08 Sep 2018 12:53:41: #2 predicted fragment length is 135 bps INFO @ Sat, 08 Sep 2018 12:53:41: #2 alternative fragment length(s) may be 4,51,88,135,577 bps INFO @ Sat, 08 Sep 2018 12:53:41: #2.2 Generate R script for model : SRX2618497.20_model.r INFO @ Sat, 08 Sep 2018 12:53:41: start X-correlation... INFO @ Sat, 08 Sep 2018 12:53:41: end of X-cor INFO @ Sat, 08 Sep 2018 12:53:41: #2 finished! INFO @ Sat, 08 Sep 2018 12:53:41: #2 predicted fragment length is 135 bps INFO @ Sat, 08 Sep 2018 12:53:41: #2 alternative fragment length(s) may be 4,51,88,135,577 bps INFO @ Sat, 08 Sep 2018 12:53:41: #2.2 Generate R script for model : SRX2618497.05_model.r INFO @ Sat, 08 Sep 2018 12:53:41: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:53:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:53:41: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:53:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:54:23: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:54:26: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:54:26: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:54:50: #4 Write output xls file... SRX2618497.10_peaks.xls INFO @ Sat, 08 Sep 2018 12:54:50: #4 Write peak in narrowPeak format file... SRX2618497.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:54:50: #4 Write summits bed file... SRX2618497.10_summits.bed INFO @ Sat, 08 Sep 2018 12:54:50: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3386 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:54:53: #4 Write output xls file... SRX2618497.05_peaks.xls INFO @ Sat, 08 Sep 2018 12:54:53: #4 Write peak in narrowPeak format file... SRX2618497.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:54:53: #4 Write summits bed file... SRX2618497.05_summits.bed INFO @ Sat, 08 Sep 2018 12:54:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6583 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:54:54: #4 Write output xls file... SRX2618497.20_peaks.xls INFO @ Sat, 08 Sep 2018 12:54:54: #4 Write peak in narrowPeak format file... SRX2618497.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:54:54: #4 Write summits bed file... SRX2618497.20_summits.bed INFO @ Sat, 08 Sep 2018 12:54:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1022 records, 4 fields): 57 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。