Job ID = 11171108 sra ファイルのダウンロード中... Completed: 482990K bytes transferred in 6 seconds (565566K 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 25508812 spots for /home/okishinya/chipatlas/results/dm3/SRX1794242/SRR3575286.sra Written 25508812 spots for /home/okishinya/chipatlas/results/dm3/SRX1794242/SRR3575286.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: 00:08:36 25508812 reads; of these: 25508812 (100.00%) were unpaired; of these: 5657774 (22.18%) aligned 0 times 13706187 (53.73%) aligned exactly 1 time 6144851 (24.09%) aligned >1 times 77.82% overall alignment rate Time searching: 00:08:36 Overall time: 00:08:36 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] 2492409 / 19851038 = 0.1256 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 12:02:41: # Command line: callpeak -t SRX1794242.bam -f BAM -g dm -n SRX1794242.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794242.05 # format = BAM # ChIP-seq file = ['SRX1794242.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 12:02:41: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:02:41: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:02:41: # Command line: callpeak -t SRX1794242.bam -f BAM -g dm -n SRX1794242.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794242.20 # format = BAM # ChIP-seq file = ['SRX1794242.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 12:02:41: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:02:41: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:02:41: # Command line: callpeak -t SRX1794242.bam -f BAM -g dm -n SRX1794242.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794242.10 # format = BAM # ChIP-seq file = ['SRX1794242.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 12:02:41: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:02:41: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:02:47: 1000000 INFO @ Sat, 08 Sep 2018 12:02:47: 1000000 INFO @ Sat, 08 Sep 2018 12:02:47: 1000000 INFO @ Sat, 08 Sep 2018 12:02:53: 2000000 INFO @ Sat, 08 Sep 2018 12:02:53: 2000000 INFO @ Sat, 08 Sep 2018 12:02:53: 2000000 INFO @ Sat, 08 Sep 2018 12:02:59: 3000000 INFO @ Sat, 08 Sep 2018 12:02:59: 3000000 INFO @ Sat, 08 Sep 2018 12:02:59: 3000000 INFO @ Sat, 08 Sep 2018 12:03:04: 4000000 INFO @ Sat, 08 Sep 2018 12:03:05: 4000000 INFO @ Sat, 08 Sep 2018 12:03:05: 4000000 INFO @ Sat, 08 Sep 2018 12:03:10: 5000000 INFO @ Sat, 08 Sep 2018 12:03:10: 5000000 INFO @ Sat, 08 Sep 2018 12:03:11: 5000000 INFO @ Sat, 08 Sep 2018 12:03:16: 6000000 INFO @ Sat, 08 Sep 2018 12:03:16: 6000000 INFO @ Sat, 08 Sep 2018 12:03:16: 6000000 INFO @ Sat, 08 Sep 2018 12:03:22: 7000000 INFO @ Sat, 08 Sep 2018 12:03:22: 7000000 INFO @ Sat, 08 Sep 2018 12:03:22: 7000000 INFO @ Sat, 08 Sep 2018 12:03:27: 8000000 INFO @ Sat, 08 Sep 2018 12:03:28: 8000000 INFO @ Sat, 08 Sep 2018 12:03:28: 8000000 INFO @ Sat, 08 Sep 2018 12:03:33: 9000000 INFO @ Sat, 08 Sep 2018 12:03:34: 9000000 INFO @ Sat, 08 Sep 2018 12:03:34: 9000000 INFO @ Sat, 08 Sep 2018 12:03:39: 10000000 INFO @ Sat, 08 Sep 2018 12:03:40: 10000000 INFO @ Sat, 08 Sep 2018 12:03:40: 10000000 INFO @ Sat, 08 Sep 2018 12:03:45: 11000000 INFO @ Sat, 08 Sep 2018 12:03:45: 11000000 INFO @ Sat, 08 Sep 2018 12:03:46: 11000000 INFO @ Sat, 08 Sep 2018 12:03:50: 12000000 INFO @ Sat, 08 Sep 2018 12:03:51: 12000000 INFO @ Sat, 08 Sep 2018 12:03:52: 12000000 INFO @ Sat, 08 Sep 2018 12:03:56: 13000000 INFO @ Sat, 08 Sep 2018 12:03:57: 13000000 INFO @ Sat, 08 Sep 2018 12:03:58: 13000000 INFO @ Sat, 08 Sep 2018 12:04:02: 14000000 INFO @ Sat, 08 Sep 2018 12:04:03: 14000000 INFO @ Sat, 08 Sep 2018 12:04:03: 14000000 INFO @ Sat, 08 Sep 2018 12:04:07: 15000000 INFO @ Sat, 08 Sep 2018 12:04:09: 15000000 INFO @ Sat, 08 Sep 2018 12:04:09: 15000000 INFO @ Sat, 08 Sep 2018 12:04:13: 16000000 INFO @ Sat, 08 Sep 2018 12:04:15: 16000000 INFO @ Sat, 08 Sep 2018 12:04:15: 16000000 INFO @ Sat, 08 Sep 2018 12:04:19: 17000000 INFO @ Sat, 08 Sep 2018 12:04:21: 17000000 INFO @ Sat, 08 Sep 2018 12:04:21: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:04:21: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:04:21: #1 total tags in treatment: 17358629 INFO @ Sat, 08 Sep 2018 12:04:21: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:04:21: #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 12:04:21: 17000000 INFO @ Sat, 08 Sep 2018 12:04:21: #1 tags after filtering in treatment: 17358629 INFO @ Sat, 08 Sep 2018 12:04:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:04:21: #1 finished! INFO @ Sat, 08 Sep 2018 12:04:21: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:04:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:04:23: #2 number of paired peaks: 135 WARNING @ Sat, 08 Sep 2018 12:04:23: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 08 Sep 2018 12:04:23: start model_add_line... INFO @ Sat, 08 Sep 2018 12:04:23: start X-correlation... INFO @ Sat, 08 Sep 2018 12:04:23: end of X-cor INFO @ Sat, 08 Sep 2018 12:04:23: #2 finished! INFO @ Sat, 08 Sep 2018 12:04:23: #2 predicted fragment length is 49 bps INFO @ Sat, 08 Sep 2018 12:04:23: #2 alternative fragment length(s) may be 3,19,49,508 bps INFO @ Sat, 08 Sep 2018 12:04:23: #2.2 Generate R script for model : SRX1794242.10_model.r WARNING @ Sat, 08 Sep 2018 12:04:23: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:04:23: #2 You may need to consider one of the other alternative d(s): 3,19,49,508 WARNING @ Sat, 08 Sep 2018 12:04:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 12:04:23: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:04:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:04:23: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:04:23: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:04:23: #1 total tags in treatment: 17358629 INFO @ Sat, 08 Sep 2018 12:04:23: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:04:23: #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 12:04:23: #1 tags after filtering in treatment: 17358629 INFO @ Sat, 08 Sep 2018 12:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:04:23: #1 finished! INFO @ Sat, 08 Sep 2018 12:04:23: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:04:24: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:04:24: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:04:24: #1 total tags in treatment: 17358629 INFO @ Sat, 08 Sep 2018 12:04:24: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:04:24: #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 12:04:24: #1 tags after filtering in treatment: 17358629 INFO @ Sat, 08 Sep 2018 12:04:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:04:24: #1 finished! INFO @ Sat, 08 Sep 2018 12:04:24: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:04:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:04:24: #2 number of paired peaks: 135 WARNING @ Sat, 08 Sep 2018 12:04:24: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 08 Sep 2018 12:04:24: start model_add_line... INFO @ Sat, 08 Sep 2018 12:04:25: start X-correlation... INFO @ Sat, 08 Sep 2018 12:04:25: end of X-cor INFO @ Sat, 08 Sep 2018 12:04:25: #2 finished! INFO @ Sat, 08 Sep 2018 12:04:25: #2 predicted fragment length is 49 bps INFO @ Sat, 08 Sep 2018 12:04:25: #2 alternative fragment length(s) may be 3,19,49,508 bps INFO @ Sat, 08 Sep 2018 12:04:25: #2.2 Generate R script for model : SRX1794242.20_model.r WARNING @ Sat, 08 Sep 2018 12:04:25: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:04:25: #2 You may need to consider one of the other alternative d(s): 3,19,49,508 WARNING @ Sat, 08 Sep 2018 12:04:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 12:04:25: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:04:25: #2 number of paired peaks: 135 WARNING @ Sat, 08 Sep 2018 12:04:25: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 08 Sep 2018 12:04:25: start model_add_line... INFO @ Sat, 08 Sep 2018 12:04:25: start X-correlation... INFO @ Sat, 08 Sep 2018 12:04:25: end of X-cor INFO @ Sat, 08 Sep 2018 12:04:25: #2 finished! INFO @ Sat, 08 Sep 2018 12:04:25: #2 predicted fragment length is 49 bps INFO @ Sat, 08 Sep 2018 12:04:25: #2 alternative fragment length(s) may be 3,19,49,508 bps INFO @ Sat, 08 Sep 2018 12:04:25: #2.2 Generate R script for model : SRX1794242.05_model.r WARNING @ Sat, 08 Sep 2018 12:04:25: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:04:25: #2 You may need to consider one of the other alternative d(s): 3,19,49,508 WARNING @ Sat, 08 Sep 2018 12:04:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 12:04:25: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:04:56: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:04:58: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:04:59: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:05:16: #4 Write output xls file... SRX1794242.10_peaks.xls INFO @ Sat, 08 Sep 2018 12:05:16: #4 Write peak in narrowPeak format file... SRX1794242.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:05:16: #4 Write summits bed file... SRX1794242.10_summits.bed INFO @ Sat, 08 Sep 2018 12:05:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1231 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:05:20: #4 Write output xls file... SRX1794242.20_peaks.xls INFO @ Sat, 08 Sep 2018 12:05:20: #4 Write peak in narrowPeak format file... SRX1794242.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:05:20: #4 Write summits bed file... SRX1794242.20_summits.bed INFO @ Sat, 08 Sep 2018 12:05:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:05:21: #4 Write output xls file... SRX1794242.05_peaks.xls INFO @ Sat, 08 Sep 2018 12:05:21: #4 Write peak in narrowPeak format file... SRX1794242.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:05:21: #4 Write summits bed file... SRX1794242.05_summits.bed INFO @ Sat, 08 Sep 2018 12:05:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2455 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。