Job ID = 10320327 sra ファイルのダウンロード中... Completed: 370218K bytes transferred in 8 seconds (344506K 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 16631460 spots for /home/okishinya/chipatlas/results/dm3/SRX2010897/SRR4017020.sra Written 16631460 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: 00:06:07 16631460 reads; of these: 16631460 (100.00%) were unpaired; of these: 499587 (3.00%) aligned 0 times 11823215 (71.09%) aligned exactly 1 time 4308658 (25.91%) aligned >1 times 97.00% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 2682757 / 16131873 = 0.1663 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 @ Thu, 11 Jan 2018 02:14:57: # Command line: callpeak -t SRX2010897.bam -f BAM -g dm -n SRX2010897.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2010897.20 # format = BAM # ChIP-seq file = ['SRX2010897.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 @ Thu, 11 Jan 2018 02:14:57: # Command line: callpeak -t SRX2010897.bam -f BAM -g dm -n SRX2010897.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2010897.10 # format = BAM # ChIP-seq file = ['SRX2010897.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 @ Thu, 11 Jan 2018 02:14:57: # Command line: callpeak -t SRX2010897.bam -f BAM -g dm -n SRX2010897.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2010897.05 # format = BAM # ChIP-seq file = ['SRX2010897.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 @ Thu, 11 Jan 2018 02:14:57: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:14:57: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:14:57: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:14:57: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:14:57: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:14:57: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:15:03: 1000000 INFO @ Thu, 11 Jan 2018 02:15:04: 1000000 INFO @ Thu, 11 Jan 2018 02:15:04: 1000000 INFO @ Thu, 11 Jan 2018 02:15:10: 2000000 INFO @ Thu, 11 Jan 2018 02:15:10: 2000000 INFO @ Thu, 11 Jan 2018 02:15:10: 2000000 INFO @ Thu, 11 Jan 2018 02:15:16: 3000000 INFO @ Thu, 11 Jan 2018 02:15:16: 3000000 INFO @ Thu, 11 Jan 2018 02:15:16: 3000000 INFO @ Thu, 11 Jan 2018 02:15:22: 4000000 INFO @ Thu, 11 Jan 2018 02:15:22: 4000000 INFO @ Thu, 11 Jan 2018 02:15:23: 4000000 INFO @ Thu, 11 Jan 2018 02:15:28: 5000000 INFO @ Thu, 11 Jan 2018 02:15:28: 5000000 INFO @ Thu, 11 Jan 2018 02:15:29: 5000000 INFO @ Thu, 11 Jan 2018 02:15:34: 6000000 INFO @ Thu, 11 Jan 2018 02:15:35: 6000000 INFO @ Thu, 11 Jan 2018 02:15:36: 6000000 INFO @ Thu, 11 Jan 2018 02:15:41: 7000000 INFO @ Thu, 11 Jan 2018 02:15:41: 7000000 INFO @ Thu, 11 Jan 2018 02:15:42: 7000000 INFO @ Thu, 11 Jan 2018 02:15:47: 8000000 INFO @ Thu, 11 Jan 2018 02:15:47: 8000000 INFO @ Thu, 11 Jan 2018 02:15:49: 8000000 INFO @ Thu, 11 Jan 2018 02:15:53: 9000000 INFO @ Thu, 11 Jan 2018 02:15:53: 9000000 INFO @ Thu, 11 Jan 2018 02:15:56: 9000000 INFO @ Thu, 11 Jan 2018 02:15:59: 10000000 INFO @ Thu, 11 Jan 2018 02:16:00: 10000000 INFO @ Thu, 11 Jan 2018 02:16:02: 10000000 INFO @ Thu, 11 Jan 2018 02:16:05: 11000000 INFO @ Thu, 11 Jan 2018 02:16:06: 11000000 INFO @ Thu, 11 Jan 2018 02:16:09: 11000000 INFO @ Thu, 11 Jan 2018 02:16:11: 12000000 INFO @ Thu, 11 Jan 2018 02:16:12: 12000000 INFO @ Thu, 11 Jan 2018 02:16:15: 12000000 INFO @ Thu, 11 Jan 2018 02:16:17: 13000000 INFO @ Thu, 11 Jan 2018 02:16:18: 13000000 INFO @ Thu, 11 Jan 2018 02:16:20: #1 tag size is determined as 49 bps INFO @ Thu, 11 Jan 2018 02:16:20: #1 tag size = 49 INFO @ Thu, 11 Jan 2018 02:16:20: #1 total tags in treatment: 13449116 INFO @ Thu, 11 Jan 2018 02:16:20: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:16:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:16:20: #1 tags after filtering in treatment: 13449116 INFO @ Thu, 11 Jan 2018 02:16:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:16:20: #1 finished! INFO @ Thu, 11 Jan 2018 02:16:20: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:16:21: #1 tag size is determined as 49 bps INFO @ Thu, 11 Jan 2018 02:16:21: #1 tag size = 49 INFO @ Thu, 11 Jan 2018 02:16:21: #1 total tags in treatment: 13449116 INFO @ Thu, 11 Jan 2018 02:16:21: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:16:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:16:21: #2 number of paired peaks: 945 WARNING @ Thu, 11 Jan 2018 02:16:21: Fewer paired peaks (945) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 945 pairs to build model! INFO @ Thu, 11 Jan 2018 02:16:21: start model_add_line... INFO @ Thu, 11 Jan 2018 02:16:21: #1 tags after filtering in treatment: 13449116 INFO @ Thu, 11 Jan 2018 02:16:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:16:21: #1 finished! INFO @ Thu, 11 Jan 2018 02:16:21: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:16:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:16:22: 13000000 INFO @ Thu, 11 Jan 2018 02:16:22: start X-correlation... INFO @ Thu, 11 Jan 2018 02:16:22: end of X-cor INFO @ Thu, 11 Jan 2018 02:16:22: #2 finished! INFO @ Thu, 11 Jan 2018 02:16:22: #2 predicted fragment length is 165 bps INFO @ Thu, 11 Jan 2018 02:16:22: #2 alternative fragment length(s) may be 165 bps INFO @ Thu, 11 Jan 2018 02:16:22: #2.2 Generate R script for model : SRX2010897.20_model.r INFO @ Thu, 11 Jan 2018 02:16:22: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:16:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:16:22: #2 number of paired peaks: 945 WARNING @ Thu, 11 Jan 2018 02:16:23: Fewer paired peaks (945) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 945 pairs to build model! INFO @ Thu, 11 Jan 2018 02:16:23: start model_add_line... INFO @ Thu, 11 Jan 2018 02:16:23: start X-correlation... INFO @ Thu, 11 Jan 2018 02:16:23: end of X-cor INFO @ Thu, 11 Jan 2018 02:16:23: #2 finished! INFO @ Thu, 11 Jan 2018 02:16:23: #2 predicted fragment length is 165 bps INFO @ Thu, 11 Jan 2018 02:16:23: #2 alternative fragment length(s) may be 165 bps INFO @ Thu, 11 Jan 2018 02:16:23: #2.2 Generate R script for model : SRX2010897.10_model.r INFO @ Thu, 11 Jan 2018 02:16:23: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:16:24: #1 tag size is determined as 49 bps INFO @ Thu, 11 Jan 2018 02:16:24: #1 tag size = 49 INFO @ Thu, 11 Jan 2018 02:16:24: #1 total tags in treatment: 13449116 INFO @ Thu, 11 Jan 2018 02:16:24: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:16:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:16:25: #1 tags after filtering in treatment: 13449116 INFO @ Thu, 11 Jan 2018 02:16:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:16:25: #1 finished! INFO @ Thu, 11 Jan 2018 02:16:25: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:16:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:16:26: #2 number of paired peaks: 945 WARNING @ Thu, 11 Jan 2018 02:16:26: Fewer paired peaks (945) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 945 pairs to build model! INFO @ Thu, 11 Jan 2018 02:16:26: start model_add_line... INFO @ Thu, 11 Jan 2018 02:16:26: start X-correlation... INFO @ Thu, 11 Jan 2018 02:16:26: end of X-cor INFO @ Thu, 11 Jan 2018 02:16:26: #2 finished! INFO @ Thu, 11 Jan 2018 02:16:26: #2 predicted fragment length is 165 bps INFO @ Thu, 11 Jan 2018 02:16:26: #2 alternative fragment length(s) may be 165 bps INFO @ Thu, 11 Jan 2018 02:16:26: #2.2 Generate R script for model : SRX2010897.05_model.r INFO @ Thu, 11 Jan 2018 02:16:26: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:16:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:16:52: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:16:54: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:16:55: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:17:08: #4 Write output xls file... SRX2010897.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:17:09: #4 Write peak in narrowPeak format file... SRX2010897.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:17:09: #4 Write summits bed file... SRX2010897.20_summits.bed INFO @ Thu, 11 Jan 2018 02:17:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2087 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:17:11: #4 Write output xls file... SRX2010897.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:17:11: #4 Write peak in narrowPeak format file... SRX2010897.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:17:11: #4 Write summits bed file... SRX2010897.10_summits.bed INFO @ Thu, 11 Jan 2018 02:17:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3173 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:17:13: #4 Write output xls file... SRX2010897.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:17:13: #4 Write peak in narrowPeak format file... SRX2010897.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:17:13: #4 Write summits bed file... SRX2010897.05_summits.bed INFO @ Thu, 11 Jan 2018 02:17:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4575 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。