Job ID = 11240717 sra ファイルのダウンロード中... Completed: 715859K bytes transferred in 8 seconds (660851K 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 34362804 spots for /home/okishinya/chipatlas/results/dm3/SRX3630326/SRR6652848.sra Written 34362804 spots for /home/okishinya/chipatlas/results/dm3/SRX3630326/SRR6652848.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: 00:23:54 34362804 reads; of these: 34362804 (100.00%) were unpaired; of these: 699616 (2.04%) aligned 0 times 10993412 (31.99%) aligned exactly 1 time 22669776 (65.97%) aligned >1 times 97.96% overall alignment rate Time searching: 00:23:54 Overall time: 00:23:54 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] 10277262 / 33663188 = 0.3053 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 @ Sun, 07 Oct 2018 21:02:33: # Command line: callpeak -t SRX3630326.bam -f BAM -g dm -n SRX3630326.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3630326.20 # format = BAM # ChIP-seq file = ['SRX3630326.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 @ Sun, 07 Oct 2018 21:02:33: # Command line: callpeak -t SRX3630326.bam -f BAM -g dm -n SRX3630326.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3630326.05 # format = BAM # ChIP-seq file = ['SRX3630326.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 @ Sun, 07 Oct 2018 21:02:33: # Command line: callpeak -t SRX3630326.bam -f BAM -g dm -n SRX3630326.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3630326.10 # format = BAM # ChIP-seq file = ['SRX3630326.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 @ Sun, 07 Oct 2018 21:02:33: #1 read tag files... INFO @ Sun, 07 Oct 2018 21:02:33: #1 read tag files... INFO @ Sun, 07 Oct 2018 21:02:33: #1 read tag files... INFO @ Sun, 07 Oct 2018 21:02:33: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 21:02:33: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 21:02:33: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 21:02:39: 1000000 INFO @ Sun, 07 Oct 2018 21:02:40: 1000000 INFO @ Sun, 07 Oct 2018 21:02:40: 1000000 INFO @ Sun, 07 Oct 2018 21:02:46: 2000000 INFO @ Sun, 07 Oct 2018 21:02:46: 2000000 INFO @ Sun, 07 Oct 2018 21:02:46: 2000000 INFO @ Sun, 07 Oct 2018 21:02:53: 3000000 INFO @ Sun, 07 Oct 2018 21:02:53: 3000000 INFO @ Sun, 07 Oct 2018 21:02:53: 3000000 INFO @ Sun, 07 Oct 2018 21:03:00: 4000000 INFO @ Sun, 07 Oct 2018 21:03:00: 4000000 INFO @ Sun, 07 Oct 2018 21:03:00: 4000000 INFO @ Sun, 07 Oct 2018 21:03:07: 5000000 INFO @ Sun, 07 Oct 2018 21:03:07: 5000000 INFO @ Sun, 07 Oct 2018 21:03:07: 5000000 INFO @ Sun, 07 Oct 2018 21:03:13: 6000000 INFO @ Sun, 07 Oct 2018 21:03:14: 6000000 INFO @ Sun, 07 Oct 2018 21:03:14: 6000000 INFO @ Sun, 07 Oct 2018 21:03:20: 7000000 INFO @ Sun, 07 Oct 2018 21:03:21: 7000000 INFO @ Sun, 07 Oct 2018 21:03:21: 7000000 INFO @ Sun, 07 Oct 2018 21:03:27: 8000000 INFO @ Sun, 07 Oct 2018 21:03:28: 8000000 INFO @ Sun, 07 Oct 2018 21:03:28: 8000000 INFO @ Sun, 07 Oct 2018 21:03:34: 9000000 INFO @ Sun, 07 Oct 2018 21:03:34: 9000000 INFO @ Sun, 07 Oct 2018 21:03:35: 9000000 INFO @ Sun, 07 Oct 2018 21:03:41: 10000000 INFO @ Sun, 07 Oct 2018 21:03:41: 10000000 INFO @ Sun, 07 Oct 2018 21:03:41: 10000000 INFO @ Sun, 07 Oct 2018 21:03:48: 11000000 INFO @ Sun, 07 Oct 2018 21:03:48: 11000000 INFO @ Sun, 07 Oct 2018 21:03:49: 11000000 INFO @ Sun, 07 Oct 2018 21:03:54: 12000000 INFO @ Sun, 07 Oct 2018 21:03:55: 12000000 INFO @ Sun, 07 Oct 2018 21:03:55: 12000000 INFO @ Sun, 07 Oct 2018 21:04:01: 13000000 INFO @ Sun, 07 Oct 2018 21:04:02: 13000000 INFO @ Sun, 07 Oct 2018 21:04:02: 13000000 INFO @ Sun, 07 Oct 2018 21:04:08: 14000000 INFO @ Sun, 07 Oct 2018 21:04:09: 14000000 INFO @ Sun, 07 Oct 2018 21:04:09: 14000000 INFO @ Sun, 07 Oct 2018 21:04:15: 15000000 INFO @ Sun, 07 Oct 2018 21:04:16: 15000000 INFO @ Sun, 07 Oct 2018 21:04:16: 15000000 INFO @ Sun, 07 Oct 2018 21:04:22: 16000000 INFO @ Sun, 07 Oct 2018 21:04:22: 16000000 INFO @ Sun, 07 Oct 2018 21:04:23: 16000000 INFO @ Sun, 07 Oct 2018 21:04:29: 17000000 INFO @ Sun, 07 Oct 2018 21:04:29: 17000000 INFO @ Sun, 07 Oct 2018 21:04:30: 17000000 INFO @ Sun, 07 Oct 2018 21:04:35: 18000000 INFO @ Sun, 07 Oct 2018 21:04:36: 18000000 INFO @ Sun, 07 Oct 2018 21:04:36: 18000000 INFO @ Sun, 07 Oct 2018 21:04:42: 19000000 INFO @ Sun, 07 Oct 2018 21:04:43: 19000000 INFO @ Sun, 07 Oct 2018 21:04:43: 19000000 INFO @ Sun, 07 Oct 2018 21:04:49: 20000000 INFO @ Sun, 07 Oct 2018 21:04:50: 20000000 INFO @ Sun, 07 Oct 2018 21:04:50: 20000000 INFO @ Sun, 07 Oct 2018 21:04:56: 21000000 INFO @ Sun, 07 Oct 2018 21:04:57: 21000000 INFO @ Sun, 07 Oct 2018 21:04:57: 21000000 INFO @ Sun, 07 Oct 2018 21:05:03: 22000000 INFO @ Sun, 07 Oct 2018 21:05:04: 22000000 INFO @ Sun, 07 Oct 2018 21:05:04: 22000000 INFO @ Sun, 07 Oct 2018 21:05:10: 23000000 INFO @ Sun, 07 Oct 2018 21:05:11: 23000000 INFO @ Sun, 07 Oct 2018 21:05:11: 23000000 INFO @ Sun, 07 Oct 2018 21:05:12: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 21:05:12: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 21:05:12: #1 total tags in treatment: 23385926 INFO @ Sun, 07 Oct 2018 21:05:12: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:05:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 21:05:13: #1 tags after filtering in treatment: 23385926 INFO @ Sun, 07 Oct 2018 21:05:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:05:13: #1 finished! INFO @ Sun, 07 Oct 2018 21:05:13: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:05:13: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 21:05:13: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 21:05:13: #1 total tags in treatment: 23385926 INFO @ Sun, 07 Oct 2018 21:05:13: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:05:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 21:05:14: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 21:05:14: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 21:05:14: #1 total tags in treatment: 23385926 INFO @ Sun, 07 Oct 2018 21:05:14: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:05:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 21:05:14: #1 tags after filtering in treatment: 23385926 INFO @ Sun, 07 Oct 2018 21:05:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:05:14: #1 finished! INFO @ Sun, 07 Oct 2018 21:05:14: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:05:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:05:14: #1 tags after filtering in treatment: 23385926 INFO @ Sun, 07 Oct 2018 21:05:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:05:14: #1 finished! INFO @ Sun, 07 Oct 2018 21:05:14: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:05:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:05:15: #2 number of paired peaks: 633 WARNING @ Sun, 07 Oct 2018 21:05:15: Fewer paired peaks (633) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 633 pairs to build model! INFO @ Sun, 07 Oct 2018 21:05:15: start model_add_line... INFO @ Sun, 07 Oct 2018 21:05:15: start X-correlation... INFO @ Sun, 07 Oct 2018 21:05:15: end of X-cor INFO @ Sun, 07 Oct 2018 21:05:15: #2 finished! INFO @ Sun, 07 Oct 2018 21:05:15: #2 predicted fragment length is 44 bps INFO @ Sun, 07 Oct 2018 21:05:15: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 07 Oct 2018 21:05:15: #2.2 Generate R script for model : SRX3630326.20_model.r WARNING @ Sun, 07 Oct 2018 21:05:15: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 21:05:15: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 07 Oct 2018 21:05:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 21:05:15: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:05:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:05:16: #2 number of paired peaks: 633 WARNING @ Sun, 07 Oct 2018 21:05:16: Fewer paired peaks (633) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 633 pairs to build model! INFO @ Sun, 07 Oct 2018 21:05:16: start model_add_line... INFO @ Sun, 07 Oct 2018 21:05:16: #2 number of paired peaks: 633 WARNING @ Sun, 07 Oct 2018 21:05:16: Fewer paired peaks (633) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 633 pairs to build model! INFO @ Sun, 07 Oct 2018 21:05:16: start model_add_line... INFO @ Sun, 07 Oct 2018 21:05:16: start X-correlation... INFO @ Sun, 07 Oct 2018 21:05:16: end of X-cor INFO @ Sun, 07 Oct 2018 21:05:16: #2 finished! INFO @ Sun, 07 Oct 2018 21:05:16: #2 predicted fragment length is 44 bps INFO @ Sun, 07 Oct 2018 21:05:16: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 07 Oct 2018 21:05:16: #2.2 Generate R script for model : SRX3630326.05_model.r WARNING @ Sun, 07 Oct 2018 21:05:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 21:05:16: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 07 Oct 2018 21:05:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 21:05:16: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:05:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:05:16: start X-correlation... INFO @ Sun, 07 Oct 2018 21:05:16: end of X-cor INFO @ Sun, 07 Oct 2018 21:05:16: #2 finished! INFO @ Sun, 07 Oct 2018 21:05:16: #2 predicted fragment length is 44 bps INFO @ Sun, 07 Oct 2018 21:05:16: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 07 Oct 2018 21:05:16: #2.2 Generate R script for model : SRX3630326.10_model.r WARNING @ Sun, 07 Oct 2018 21:05:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 21:05:16: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 07 Oct 2018 21:05:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 21:05:16: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:05:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:05:57: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:06:00: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:06:01: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:06:21: #4 Write output xls file... SRX3630326.05_peaks.xls INFO @ Sun, 07 Oct 2018 21:06:21: #4 Write peak in narrowPeak format file... SRX3630326.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:06:22: #4 Write summits bed file... SRX3630326.05_summits.bed INFO @ Sun, 07 Oct 2018 21:06:22: Done! INFO @ Sun, 07 Oct 2018 21:06:22: #4 Write output xls file... SRX3630326.10_peaks.xls INFO @ Sun, 07 Oct 2018 21:06:22: #4 Write peak in narrowPeak format file... SRX3630326.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:06:22: #4 Write summits bed file... SRX3630326.10_summits.bed pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (13591 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 21:06:23: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4168 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 21:06:25: #4 Write output xls file... SRX3630326.20_peaks.xls INFO @ Sun, 07 Oct 2018 21:06:25: #4 Write peak in narrowPeak format file... SRX3630326.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:06:25: #4 Write summits bed file... SRX3630326.20_summits.bed INFO @ Sun, 07 Oct 2018 21:06:25: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1368 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。