Job ID = 11171211 sra ファイルのダウンロード中... Completed: 327872K bytes transferred in 9 seconds (290358K 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 15644699 spots for /home/okishinya/chipatlas/results/dm3/SRX2618520/SRR5319074.sra Written 15644699 spots for /home/okishinya/chipatlas/results/dm3/SRX2618520/SRR5319074.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: 00:06:22 15644699 reads; of these: 15644699 (100.00%) were unpaired; of these: 862961 (5.52%) aligned 0 times 10906642 (69.71%) aligned exactly 1 time 3875096 (24.77%) aligned >1 times 94.48% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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] 1614350 / 14781738 = 0.1092 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 13:08:50: # Command line: callpeak -t SRX2618520.bam -f BAM -g dm -n SRX2618520.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618520.10 # format = BAM # ChIP-seq file = ['SRX2618520.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 13:08:50: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:08:50: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:08:50: # Command line: callpeak -t SRX2618520.bam -f BAM -g dm -n SRX2618520.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618520.20 # format = BAM # ChIP-seq file = ['SRX2618520.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 13:08:50: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:08:50: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:08:50: # Command line: callpeak -t SRX2618520.bam -f BAM -g dm -n SRX2618520.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618520.05 # format = BAM # ChIP-seq file = ['SRX2618520.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 13:08:50: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:08:50: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:08:57: 1000000 INFO @ Sat, 08 Sep 2018 13:08:57: 1000000 INFO @ Sat, 08 Sep 2018 13:08:57: 1000000 INFO @ Sat, 08 Sep 2018 13:09:05: 2000000 INFO @ Sat, 08 Sep 2018 13:09:05: 2000000 INFO @ Sat, 08 Sep 2018 13:09:05: 2000000 INFO @ Sat, 08 Sep 2018 13:09:12: 3000000 INFO @ Sat, 08 Sep 2018 13:09:12: 3000000 INFO @ Sat, 08 Sep 2018 13:09:12: 3000000 INFO @ Sat, 08 Sep 2018 13:09:19: 4000000 INFO @ Sat, 08 Sep 2018 13:09:19: 4000000 INFO @ Sat, 08 Sep 2018 13:09:19: 4000000 INFO @ Sat, 08 Sep 2018 13:09:27: 5000000 INFO @ Sat, 08 Sep 2018 13:09:27: 5000000 INFO @ Sat, 08 Sep 2018 13:09:27: 5000000 INFO @ Sat, 08 Sep 2018 13:09:34: 6000000 INFO @ Sat, 08 Sep 2018 13:09:34: 6000000 INFO @ Sat, 08 Sep 2018 13:09:34: 6000000 INFO @ Sat, 08 Sep 2018 13:09:41: 7000000 INFO @ Sat, 08 Sep 2018 13:09:41: 7000000 INFO @ Sat, 08 Sep 2018 13:09:41: 7000000 INFO @ Sat, 08 Sep 2018 13:09:48: 8000000 INFO @ Sat, 08 Sep 2018 13:09:48: 8000000 INFO @ Sat, 08 Sep 2018 13:09:48: 8000000 INFO @ Sat, 08 Sep 2018 13:09:56: 9000000 INFO @ Sat, 08 Sep 2018 13:09:56: 9000000 INFO @ Sat, 08 Sep 2018 13:09:56: 9000000 INFO @ Sat, 08 Sep 2018 13:10:03: 10000000 INFO @ Sat, 08 Sep 2018 13:10:03: 10000000 INFO @ Sat, 08 Sep 2018 13:10:03: 10000000 INFO @ Sat, 08 Sep 2018 13:10:10: 11000000 INFO @ Sat, 08 Sep 2018 13:10:10: 11000000 INFO @ Sat, 08 Sep 2018 13:10:10: 11000000 INFO @ Sat, 08 Sep 2018 13:10:18: 12000000 INFO @ Sat, 08 Sep 2018 13:10:18: 12000000 INFO @ Sat, 08 Sep 2018 13:10:18: 12000000 INFO @ Sat, 08 Sep 2018 13:10:25: 13000000 INFO @ Sat, 08 Sep 2018 13:10:25: 13000000 INFO @ Sat, 08 Sep 2018 13:10:25: 13000000 INFO @ Sat, 08 Sep 2018 13:10:26: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:10:26: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:10:26: #1 total tags in treatment: 13167388 INFO @ Sat, 08 Sep 2018 13:10:26: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:10:26: #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 13:10:26: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:10:26: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:10:26: #1 total tags in treatment: 13167388 INFO @ Sat, 08 Sep 2018 13:10:26: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:10:26: #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 13:10:26: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:10:26: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:10:26: #1 total tags in treatment: 13167388 INFO @ Sat, 08 Sep 2018 13:10:26: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:10:26: #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 13:10:27: #1 tags after filtering in treatment: 13167388 INFO @ Sat, 08 Sep 2018 13:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:10:27: #1 finished! INFO @ Sat, 08 Sep 2018 13:10:27: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:10:27: #1 tags after filtering in treatment: 13167388 INFO @ Sat, 08 Sep 2018 13:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:10:27: #1 finished! INFO @ Sat, 08 Sep 2018 13:10:27: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:10:27: #1 tags after filtering in treatment: 13167388 INFO @ Sat, 08 Sep 2018 13:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:10:27: #1 finished! INFO @ Sat, 08 Sep 2018 13:10:27: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:10:27: #2 number of paired peaks: 189 WARNING @ Sat, 08 Sep 2018 13:10:27: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Sat, 08 Sep 2018 13:10:27: start model_add_line... INFO @ Sat, 08 Sep 2018 13:10:27: #2 number of paired peaks: 189 WARNING @ Sat, 08 Sep 2018 13:10:27: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Sat, 08 Sep 2018 13:10:27: start model_add_line... INFO @ Sat, 08 Sep 2018 13:10:27: #2 number of paired peaks: 189 WARNING @ Sat, 08 Sep 2018 13:10:27: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Sat, 08 Sep 2018 13:10:27: start model_add_line... INFO @ Sat, 08 Sep 2018 13:10:28: start X-correlation... INFO @ Sat, 08 Sep 2018 13:10:28: end of X-cor INFO @ Sat, 08 Sep 2018 13:10:28: #2 finished! INFO @ Sat, 08 Sep 2018 13:10:28: #2 predicted fragment length is 141 bps INFO @ Sat, 08 Sep 2018 13:10:28: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 08 Sep 2018 13:10:28: #2.2 Generate R script for model : SRX2618520.05_model.r INFO @ Sat, 08 Sep 2018 13:10:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:10:28: start X-correlation... INFO @ Sat, 08 Sep 2018 13:10:28: end of X-cor INFO @ Sat, 08 Sep 2018 13:10:28: #2 finished! INFO @ Sat, 08 Sep 2018 13:10:28: #2 predicted fragment length is 141 bps INFO @ Sat, 08 Sep 2018 13:10:28: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 08 Sep 2018 13:10:28: #2.2 Generate R script for model : SRX2618520.10_model.r INFO @ Sat, 08 Sep 2018 13:10:28: start X-correlation... INFO @ Sat, 08 Sep 2018 13:10:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:10:28: end of X-cor INFO @ Sat, 08 Sep 2018 13:10:28: #2 finished! INFO @ Sat, 08 Sep 2018 13:10:28: #2 predicted fragment length is 141 bps INFO @ Sat, 08 Sep 2018 13:10:28: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 08 Sep 2018 13:10:28: #2.2 Generate R script for model : SRX2618520.20_model.r INFO @ Sat, 08 Sep 2018 13:10:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:10:56: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:10:56: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:10:57: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:11:12: #4 Write output xls file... SRX2618520.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:11:12: #4 Write peak in narrowPeak format file... SRX2618520.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:11:12: #4 Write summits bed file... SRX2618520.05_summits.bed INFO @ Sat, 08 Sep 2018 13:11:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5953 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:11:13: #4 Write output xls file... SRX2618520.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:11:13: #4 Write peak in narrowPeak format file... SRX2618520.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:11:13: #4 Write summits bed file... SRX2618520.10_summits.bed INFO @ Sat, 08 Sep 2018 13:11:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3555 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:11:14: #4 Write output xls file... SRX2618520.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:11:14: #4 Write peak in narrowPeak format file... SRX2618520.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:11:14: #4 Write summits bed file... SRX2618520.20_summits.bed INFO @ Sat, 08 Sep 2018 13:11:14: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1511 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。