Job ID = 9730509 sra ファイルのダウンロード中... Completed: 1214184K bytes transferred in 1010 seconds (9846K bits/sec), in 1 file, 2 directories. 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 48381350 spots for /home/okishinya/chipatlas/results/dm3/SRX3088629/SRR5928310.sra Written 48381350 spots total 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: 00:12:39 48381350 reads; of these: 48381350 (100.00%) were unpaired; of these: 19513993 (40.33%) aligned 0 times 19266597 (39.82%) aligned exactly 1 time 9600760 (19.84%) aligned >1 times 59.67% overall alignment rate Time searching: 00:12:39 Overall time: 00:12:39 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] 15777824 / 28867357 = 0.5466 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, 03 Sep 2017 01:35:01: # Command line: callpeak -t SRX3088629.bam -f BAM -g dm -n SRX3088629.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3088629.10 # format = BAM # ChIP-seq file = ['SRX3088629.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, 03 Sep 2017 01:35:01: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:35:01: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:35:01: # Command line: callpeak -t SRX3088629.bam -f BAM -g dm -n SRX3088629.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3088629.20 # format = BAM # ChIP-seq file = ['SRX3088629.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, 03 Sep 2017 01:35:01: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:35:01: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:35:01: # Command line: callpeak -t SRX3088629.bam -f BAM -g dm -n SRX3088629.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3088629.05 # format = BAM # ChIP-seq file = ['SRX3088629.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, 03 Sep 2017 01:35:01: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:35:01: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:35:08: 1000000 INFO @ Sun, 03 Sep 2017 01:35:08: 1000000 INFO @ Sun, 03 Sep 2017 01:35:08: 1000000 INFO @ Sun, 03 Sep 2017 01:35:15: 2000000 INFO @ Sun, 03 Sep 2017 01:35:16: 2000000 INFO @ Sun, 03 Sep 2017 01:35:16: 2000000 INFO @ Sun, 03 Sep 2017 01:35:21: 3000000 INFO @ Sun, 03 Sep 2017 01:35:23: 3000000 INFO @ Sun, 03 Sep 2017 01:35:23: 3000000 INFO @ Sun, 03 Sep 2017 01:35:28: 4000000 INFO @ Sun, 03 Sep 2017 01:35:30: 4000000 INFO @ Sun, 03 Sep 2017 01:35:30: 4000000 INFO @ Sun, 03 Sep 2017 01:35:35: 5000000 INFO @ Sun, 03 Sep 2017 01:35:37: 5000000 INFO @ Sun, 03 Sep 2017 01:35:37: 5000000 INFO @ Sun, 03 Sep 2017 01:35:41: 6000000 INFO @ Sun, 03 Sep 2017 01:35:44: 6000000 INFO @ Sun, 03 Sep 2017 01:35:44: 6000000 INFO @ Sun, 03 Sep 2017 01:35:48: 7000000 INFO @ Sun, 03 Sep 2017 01:35:51: 7000000 INFO @ Sun, 03 Sep 2017 01:35:52: 7000000 INFO @ Sun, 03 Sep 2017 01:35:56: 8000000 INFO @ Sun, 03 Sep 2017 01:35:57: 8000000 INFO @ Sun, 03 Sep 2017 01:35:59: 8000000 INFO @ Sun, 03 Sep 2017 01:36:03: 9000000 INFO @ Sun, 03 Sep 2017 01:36:04: 9000000 INFO @ Sun, 03 Sep 2017 01:36:06: 9000000 INFO @ Sun, 03 Sep 2017 01:36:09: 10000000 INFO @ Sun, 03 Sep 2017 01:36:11: 10000000 INFO @ Sun, 03 Sep 2017 01:36:13: 10000000 INFO @ Sun, 03 Sep 2017 01:36:16: 11000000 INFO @ Sun, 03 Sep 2017 01:36:18: 11000000 INFO @ Sun, 03 Sep 2017 01:36:20: 11000000 INFO @ Sun, 03 Sep 2017 01:36:23: 12000000 INFO @ Sun, 03 Sep 2017 01:36:25: 12000000 INFO @ Sun, 03 Sep 2017 01:36:27: 12000000 INFO @ Sun, 03 Sep 2017 01:36:30: 13000000 INFO @ Sun, 03 Sep 2017 01:36:31: #1 tag size is determined as 45 bps INFO @ Sun, 03 Sep 2017 01:36:31: #1 tag size = 45 INFO @ Sun, 03 Sep 2017 01:36:31: #1 total tags in treatment: 13089533 INFO @ Sun, 03 Sep 2017 01:36:31: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:36:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:36:31: #1 tags after filtering in treatment: 13089533 INFO @ Sun, 03 Sep 2017 01:36:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:36:31: #1 finished! INFO @ Sun, 03 Sep 2017 01:36:31: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:36:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:36:31: 13000000 INFO @ Sun, 03 Sep 2017 01:36:32: #2 number of paired peaks: 350 WARNING @ Sun, 03 Sep 2017 01:36:32: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Sun, 03 Sep 2017 01:36:32: start model_add_line... INFO @ Sun, 03 Sep 2017 01:36:32: #1 tag size is determined as 45 bps INFO @ Sun, 03 Sep 2017 01:36:32: #1 tag size = 45 INFO @ Sun, 03 Sep 2017 01:36:32: #1 total tags in treatment: 13089533 INFO @ Sun, 03 Sep 2017 01:36:32: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:36:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:36:32: start X-correlation... INFO @ Sun, 03 Sep 2017 01:36:32: end of X-cor INFO @ Sun, 03 Sep 2017 01:36:32: #2 finished! INFO @ Sun, 03 Sep 2017 01:36:32: #2 predicted fragment length is 42 bps INFO @ Sun, 03 Sep 2017 01:36:32: #2 alternative fragment length(s) may be 42 bps INFO @ Sun, 03 Sep 2017 01:36:32: #2.2 Generate R script for model : SRX3088629.10_model.r WARNING @ Sun, 03 Sep 2017 01:36:32: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:36:32: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Sun, 03 Sep 2017 01:36:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:36:32: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:36:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:36:32: #1 tags after filtering in treatment: 13089533 INFO @ Sun, 03 Sep 2017 01:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:36:32: #1 finished! INFO @ Sun, 03 Sep 2017 01:36:32: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:36:33: #2 number of paired peaks: 350 WARNING @ Sun, 03 Sep 2017 01:36:33: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Sun, 03 Sep 2017 01:36:33: start model_add_line... INFO @ Sun, 03 Sep 2017 01:36:33: start X-correlation... INFO @ Sun, 03 Sep 2017 01:36:33: end of X-cor INFO @ Sun, 03 Sep 2017 01:36:33: #2 finished! INFO @ Sun, 03 Sep 2017 01:36:33: #2 predicted fragment length is 42 bps INFO @ Sun, 03 Sep 2017 01:36:33: #2 alternative fragment length(s) may be 42 bps INFO @ Sun, 03 Sep 2017 01:36:33: #2.2 Generate R script for model : SRX3088629.20_model.r WARNING @ Sun, 03 Sep 2017 01:36:33: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:36:33: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Sun, 03 Sep 2017 01:36:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:36:33: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:36:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:36:34: 13000000 INFO @ Sun, 03 Sep 2017 01:36:35: #1 tag size is determined as 45 bps INFO @ Sun, 03 Sep 2017 01:36:35: #1 tag size = 45 INFO @ Sun, 03 Sep 2017 01:36:35: #1 total tags in treatment: 13089533 INFO @ Sun, 03 Sep 2017 01:36:35: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:36:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:36:35: #1 tags after filtering in treatment: 13089533 INFO @ Sun, 03 Sep 2017 01:36:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:36:35: #1 finished! INFO @ Sun, 03 Sep 2017 01:36:35: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:36:36: #2 number of paired peaks: 350 WARNING @ Sun, 03 Sep 2017 01:36:36: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Sun, 03 Sep 2017 01:36:36: start model_add_line... INFO @ Sun, 03 Sep 2017 01:36:36: start X-correlation... INFO @ Sun, 03 Sep 2017 01:36:36: end of X-cor INFO @ Sun, 03 Sep 2017 01:36:36: #2 finished! INFO @ Sun, 03 Sep 2017 01:36:36: #2 predicted fragment length is 42 bps INFO @ Sun, 03 Sep 2017 01:36:36: #2 alternative fragment length(s) may be 42 bps INFO @ Sun, 03 Sep 2017 01:36:36: #2.2 Generate R script for model : SRX3088629.05_model.r WARNING @ Sun, 03 Sep 2017 01:36:36: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:36:36: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Sun, 03 Sep 2017 01:36:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:36:36: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:37:00: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:37:02: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:37:04: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:37:14: #4 Write output xls file... SRX3088629.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:37:14: #4 Write peak in narrowPeak format file... SRX3088629.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:37:14: #4 Write summits bed file... SRX3088629.10_summits.bed INFO @ Sun, 03 Sep 2017 01:37:14: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (2413 records, 4 fields): 99 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:37:18: #4 Write output xls file... SRX3088629.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:37:18: #4 Write peak in narrowPeak format file... SRX3088629.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:37:18: #4 Write summits bed file... SRX3088629.20_summits.bed INFO @ Sun, 03 Sep 2017 01:37:18: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1183 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:37:19: #4 Write output xls file... SRX3088629.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:37:19: #4 Write peak in narrowPeak format file... SRX3088629.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:37:19: #4 Write summits bed file... SRX3088629.05_summits.bed INFO @ Sun, 03 Sep 2017 01:37:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6344 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。