Job ID = 11171188 sra ファイルのダウンロード中... Completed: 846839K bytes transferred in 20 seconds (337303K 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 43517163 spots for /home/okishinya/chipatlas/results/dm3/SRX2618503/SRR5319057.sra Written 43517163 spots for /home/okishinya/chipatlas/results/dm3/SRX2618503/SRR5319057.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: 00:10:27 43517163 reads; of these: 43517163 (100.00%) were unpaired; of these: 11525396 (26.48%) aligned 0 times 28568093 (65.65%) aligned exactly 1 time 3423674 (7.87%) aligned >1 times 73.52% overall alignment rate Time searching: 00:10:27 Overall time: 00:10:27 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 16 files... [bam_rmdupse_core] 5128021 / 31991767 = 0.1603 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 12:55:50: # Command line: callpeak -t SRX2618503.bam -f BAM -g dm -n SRX2618503.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618503.10 # format = BAM # ChIP-seq file = ['SRX2618503.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 12:55:50: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:55:50: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:55:50: # Command line: callpeak -t SRX2618503.bam -f BAM -g dm -n SRX2618503.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618503.05 # format = BAM # ChIP-seq file = ['SRX2618503.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 12:55:50: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:55:50: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:55:50: # Command line: callpeak -t SRX2618503.bam -f BAM -g dm -n SRX2618503.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618503.20 # format = BAM # ChIP-seq file = ['SRX2618503.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 12:55:50: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:55:50: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:55:57: 1000000 INFO @ Sat, 08 Sep 2018 12:55:57: 1000000 INFO @ Sat, 08 Sep 2018 12:55:58: 1000000 INFO @ Sat, 08 Sep 2018 12:56:04: 2000000 INFO @ Sat, 08 Sep 2018 12:56:05: 2000000 INFO @ Sat, 08 Sep 2018 12:56:05: 2000000 INFO @ Sat, 08 Sep 2018 12:56:11: 3000000 INFO @ Sat, 08 Sep 2018 12:56:12: 3000000 INFO @ Sat, 08 Sep 2018 12:56:12: 3000000 INFO @ Sat, 08 Sep 2018 12:56:18: 4000000 INFO @ Sat, 08 Sep 2018 12:56:19: 4000000 INFO @ Sat, 08 Sep 2018 12:56:20: 4000000 INFO @ Sat, 08 Sep 2018 12:56:24: 5000000 INFO @ Sat, 08 Sep 2018 12:56:26: 5000000 INFO @ Sat, 08 Sep 2018 12:56:28: 5000000 INFO @ Sat, 08 Sep 2018 12:56:31: 6000000 INFO @ Sat, 08 Sep 2018 12:56:34: 6000000 INFO @ Sat, 08 Sep 2018 12:56:35: 6000000 INFO @ Sat, 08 Sep 2018 12:56:38: 7000000 INFO @ Sat, 08 Sep 2018 12:56:41: 7000000 INFO @ Sat, 08 Sep 2018 12:56:43: 7000000 INFO @ Sat, 08 Sep 2018 12:56:45: 8000000 INFO @ Sat, 08 Sep 2018 12:56:49: 8000000 INFO @ Sat, 08 Sep 2018 12:56:51: 8000000 INFO @ Sat, 08 Sep 2018 12:56:52: 9000000 INFO @ Sat, 08 Sep 2018 12:56:56: 9000000 INFO @ Sat, 08 Sep 2018 12:56:58: 10000000 INFO @ Sat, 08 Sep 2018 12:56:59: 9000000 INFO @ Sat, 08 Sep 2018 12:57:03: 10000000 INFO @ Sat, 08 Sep 2018 12:57:05: 11000000 INFO @ Sat, 08 Sep 2018 12:57:06: 10000000 INFO @ Sat, 08 Sep 2018 12:57:10: 11000000 INFO @ Sat, 08 Sep 2018 12:57:12: 12000000 INFO @ Sat, 08 Sep 2018 12:57:14: 11000000 INFO @ Sat, 08 Sep 2018 12:57:18: 12000000 INFO @ Sat, 08 Sep 2018 12:57:19: 13000000 INFO @ Sat, 08 Sep 2018 12:57:21: 12000000 INFO @ Sat, 08 Sep 2018 12:57:25: 13000000 INFO @ Sat, 08 Sep 2018 12:57:25: 14000000 INFO @ Sat, 08 Sep 2018 12:57:29: 13000000 INFO @ Sat, 08 Sep 2018 12:57:32: 14000000 INFO @ Sat, 08 Sep 2018 12:57:32: 15000000 INFO @ Sat, 08 Sep 2018 12:57:36: 14000000 INFO @ Sat, 08 Sep 2018 12:57:39: 16000000 INFO @ Sat, 08 Sep 2018 12:57:39: 15000000 INFO @ Sat, 08 Sep 2018 12:57:44: 15000000 INFO @ Sat, 08 Sep 2018 12:57:46: 17000000 INFO @ Sat, 08 Sep 2018 12:57:46: 16000000 INFO @ Sat, 08 Sep 2018 12:57:52: 16000000 INFO @ Sat, 08 Sep 2018 12:57:52: 18000000 INFO @ Sat, 08 Sep 2018 12:57:54: 17000000 INFO @ Sat, 08 Sep 2018 12:57:59: 19000000 INFO @ Sat, 08 Sep 2018 12:57:59: 17000000 INFO @ Sat, 08 Sep 2018 12:58:01: 18000000 INFO @ Sat, 08 Sep 2018 12:58:06: 20000000 INFO @ Sat, 08 Sep 2018 12:58:07: 18000000 INFO @ Sat, 08 Sep 2018 12:58:08: 19000000 INFO @ Sat, 08 Sep 2018 12:58:12: 21000000 INFO @ Sat, 08 Sep 2018 12:58:14: 19000000 INFO @ Sat, 08 Sep 2018 12:58:15: 20000000 INFO @ Sat, 08 Sep 2018 12:58:19: 22000000 INFO @ Sat, 08 Sep 2018 12:58:22: 20000000 INFO @ Sat, 08 Sep 2018 12:58:22: 21000000 INFO @ Sat, 08 Sep 2018 12:58:26: 23000000 INFO @ Sat, 08 Sep 2018 12:58:29: 21000000 INFO @ Sat, 08 Sep 2018 12:58:30: 22000000 INFO @ Sat, 08 Sep 2018 12:58:33: 24000000 INFO @ Sat, 08 Sep 2018 12:58:37: 22000000 INFO @ Sat, 08 Sep 2018 12:58:37: 23000000 INFO @ Sat, 08 Sep 2018 12:58:39: 25000000 INFO @ Sat, 08 Sep 2018 12:58:44: 24000000 INFO @ Sat, 08 Sep 2018 12:58:44: 23000000 INFO @ Sat, 08 Sep 2018 12:58:46: 26000000 INFO @ Sat, 08 Sep 2018 12:58:51: 25000000 INFO @ Sat, 08 Sep 2018 12:58:52: 24000000 INFO @ Sat, 08 Sep 2018 12:58:52: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:58:52: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:58:52: #1 total tags in treatment: 26863746 INFO @ Sat, 08 Sep 2018 12:58:52: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:58:52: #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 12:58:53: #1 tags after filtering in treatment: 26863746 INFO @ Sat, 08 Sep 2018 12:58:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:58:53: #1 finished! INFO @ Sat, 08 Sep 2018 12:58:53: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:58:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:58:55: #2 number of paired peaks: 175 WARNING @ Sat, 08 Sep 2018 12:58:55: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 08 Sep 2018 12:58:55: start model_add_line... INFO @ Sat, 08 Sep 2018 12:58:55: start X-correlation... INFO @ Sat, 08 Sep 2018 12:58:55: end of X-cor INFO @ Sat, 08 Sep 2018 12:58:55: #2 finished! INFO @ Sat, 08 Sep 2018 12:58:55: #2 predicted fragment length is 121 bps INFO @ Sat, 08 Sep 2018 12:58:55: #2 alternative fragment length(s) may be 4,121 bps INFO @ Sat, 08 Sep 2018 12:58:55: #2.2 Generate R script for model : SRX2618503.05_model.r INFO @ Sat, 08 Sep 2018 12:58:55: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:58:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:58:58: 26000000 INFO @ Sat, 08 Sep 2018 12:58:59: 25000000 INFO @ Sat, 08 Sep 2018 12:59:04: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:59:04: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:59:04: #1 total tags in treatment: 26863746 INFO @ Sat, 08 Sep 2018 12:59:04: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:59:04: #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 12:59:05: #1 tags after filtering in treatment: 26863746 INFO @ Sat, 08 Sep 2018 12:59:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:59:05: #1 finished! INFO @ Sat, 08 Sep 2018 12:59:05: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:59:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:59:06: 26000000 INFO @ Sat, 08 Sep 2018 12:59:06: #2 number of paired peaks: 175 WARNING @ Sat, 08 Sep 2018 12:59:06: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 08 Sep 2018 12:59:06: start model_add_line... INFO @ Sat, 08 Sep 2018 12:59:07: start X-correlation... INFO @ Sat, 08 Sep 2018 12:59:07: end of X-cor INFO @ Sat, 08 Sep 2018 12:59:07: #2 finished! INFO @ Sat, 08 Sep 2018 12:59:07: #2 predicted fragment length is 121 bps INFO @ Sat, 08 Sep 2018 12:59:07: #2 alternative fragment length(s) may be 4,121 bps INFO @ Sat, 08 Sep 2018 12:59:07: #2.2 Generate R script for model : SRX2618503.10_model.r INFO @ Sat, 08 Sep 2018 12:59:07: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:59:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:59:12: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:59:12: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:59:12: #1 total tags in treatment: 26863746 INFO @ Sat, 08 Sep 2018 12:59:12: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:59:12: #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 12:59:13: #1 tags after filtering in treatment: 26863746 INFO @ Sat, 08 Sep 2018 12:59:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:59:13: #1 finished! INFO @ Sat, 08 Sep 2018 12:59:13: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:59:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:59:14: #2 number of paired peaks: 175 WARNING @ Sat, 08 Sep 2018 12:59:14: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 08 Sep 2018 12:59:14: start model_add_line... INFO @ Sat, 08 Sep 2018 12:59:15: start X-correlation... INFO @ Sat, 08 Sep 2018 12:59:15: end of X-cor INFO @ Sat, 08 Sep 2018 12:59:15: #2 finished! INFO @ Sat, 08 Sep 2018 12:59:15: #2 predicted fragment length is 121 bps INFO @ Sat, 08 Sep 2018 12:59:15: #2 alternative fragment length(s) may be 4,121 bps INFO @ Sat, 08 Sep 2018 12:59:15: #2.2 Generate R script for model : SRX2618503.20_model.r INFO @ Sat, 08 Sep 2018 12:59:15: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:59:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:59:50: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:59:59: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:00:07: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:00:19: #4 Write output xls file... SRX2618503.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:00:19: #4 Write peak in narrowPeak format file... SRX2618503.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:00:19: #4 Write summits bed file... SRX2618503.05_summits.bed INFO @ Sat, 08 Sep 2018 13:00:19: Done! pass1 - making usageList (15 chroms): 11 millis pass2 - checking and writing primary data (9838 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:00:28: #4 Write output xls file... SRX2618503.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:00:28: #4 Write peak in narrowPeak format file... SRX2618503.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:00:28: #4 Write summits bed file... SRX2618503.10_summits.bed INFO @ Sat, 08 Sep 2018 13:00:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5402 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:00:36: #4 Write output xls file... SRX2618503.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:00:36: #4 Write peak in narrowPeak format file... SRX2618503.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:00:36: #4 Write summits bed file... SRX2618503.20_summits.bed INFO @ Sat, 08 Sep 2018 13:00:36: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1543 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。