Job ID = 9157428 sra ファイルのダウンロード中... Completed: 4159151K bytes transferred in 39 seconds (854859K 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 70355128 spots for /home/okishinya/chipatlas/results/ce10/SRX2163952/SRR4242867.sra Written 70355128 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: 00:27:06 70355128 reads; of these: 70355128 (100.00%) were unpaired; of these: 20848915 (29.63%) aligned 0 times 41548723 (59.06%) aligned exactly 1 time 7957490 (11.31%) aligned >1 times 70.37% overall alignment rate Time searching: 00:27:06 Overall time: 00:27:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 26579839 / 49506213 = 0.5369 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 @ Tue, 27 Jun 2017 12:41:53: # Command line: callpeak -t SRX2163952.bam -f BAM -g ce -n SRX2163952.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2163952.05 # format = BAM # ChIP-seq file = ['SRX2163952.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 12:41:53: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:41:53: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:41:53: # Command line: callpeak -t SRX2163952.bam -f BAM -g ce -n SRX2163952.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2163952.10 # format = BAM # ChIP-seq file = ['SRX2163952.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 12:41:53: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:41:53: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:41:53: # Command line: callpeak -t SRX2163952.bam -f BAM -g ce -n SRX2163952.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2163952.20 # format = BAM # ChIP-seq file = ['SRX2163952.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 12:41:53: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:41:53: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:42:03: 1000000 INFO @ Tue, 27 Jun 2017 12:42:03: 1000000 INFO @ Tue, 27 Jun 2017 12:42:03: 1000000 INFO @ Tue, 27 Jun 2017 12:42:12: 2000000 INFO @ Tue, 27 Jun 2017 12:42:13: 2000000 INFO @ Tue, 27 Jun 2017 12:42:13: 2000000 INFO @ Tue, 27 Jun 2017 12:42:22: 3000000 INFO @ Tue, 27 Jun 2017 12:42:22: 3000000 INFO @ Tue, 27 Jun 2017 12:42:22: 3000000 INFO @ Tue, 27 Jun 2017 12:42:31: 4000000 INFO @ Tue, 27 Jun 2017 12:42:31: 4000000 INFO @ Tue, 27 Jun 2017 12:42:31: 4000000 INFO @ Tue, 27 Jun 2017 12:42:41: 5000000 INFO @ Tue, 27 Jun 2017 12:42:41: 5000000 INFO @ Tue, 27 Jun 2017 12:42:41: 5000000 INFO @ Tue, 27 Jun 2017 12:42:50: 6000000 INFO @ Tue, 27 Jun 2017 12:42:50: 6000000 INFO @ Tue, 27 Jun 2017 12:42:50: 6000000 INFO @ Tue, 27 Jun 2017 12:42:59: 7000000 INFO @ Tue, 27 Jun 2017 12:43:00: 7000000 INFO @ Tue, 27 Jun 2017 12:43:00: 7000000 INFO @ Tue, 27 Jun 2017 12:43:09: 8000000 INFO @ Tue, 27 Jun 2017 12:43:09: 8000000 INFO @ Tue, 27 Jun 2017 12:43:09: 8000000 INFO @ Tue, 27 Jun 2017 12:43:18: 9000000 INFO @ Tue, 27 Jun 2017 12:43:19: 9000000 INFO @ Tue, 27 Jun 2017 12:43:19: 9000000 INFO @ Tue, 27 Jun 2017 12:43:27: 10000000 INFO @ Tue, 27 Jun 2017 12:43:28: 10000000 INFO @ Tue, 27 Jun 2017 12:43:28: 10000000 INFO @ Tue, 27 Jun 2017 12:43:37: 11000000 INFO @ Tue, 27 Jun 2017 12:43:38: 11000000 INFO @ Tue, 27 Jun 2017 12:43:38: 11000000 INFO @ Tue, 27 Jun 2017 12:43:46: 12000000 INFO @ Tue, 27 Jun 2017 12:43:47: 12000000 INFO @ Tue, 27 Jun 2017 12:43:47: 12000000 INFO @ Tue, 27 Jun 2017 12:43:56: 13000000 INFO @ Tue, 27 Jun 2017 12:43:57: 13000000 INFO @ Tue, 27 Jun 2017 12:43:57: 13000000 INFO @ Tue, 27 Jun 2017 12:44:05: 14000000 INFO @ Tue, 27 Jun 2017 12:44:06: 14000000 INFO @ Tue, 27 Jun 2017 12:44:06: 14000000 INFO @ Tue, 27 Jun 2017 12:44:14: 15000000 INFO @ Tue, 27 Jun 2017 12:44:16: 15000000 INFO @ Tue, 27 Jun 2017 12:44:16: 15000000 INFO @ Tue, 27 Jun 2017 12:44:23: 16000000 INFO @ Tue, 27 Jun 2017 12:44:25: 16000000 INFO @ Tue, 27 Jun 2017 12:44:25: 16000000 INFO @ Tue, 27 Jun 2017 12:44:33: 17000000 INFO @ Tue, 27 Jun 2017 12:44:35: 17000000 INFO @ Tue, 27 Jun 2017 12:44:35: 17000000 INFO @ Tue, 27 Jun 2017 12:44:42: 18000000 INFO @ Tue, 27 Jun 2017 12:44:44: 18000000 INFO @ Tue, 27 Jun 2017 12:44:44: 18000000 INFO @ Tue, 27 Jun 2017 12:44:51: 19000000 INFO @ Tue, 27 Jun 2017 12:44:54: 19000000 INFO @ Tue, 27 Jun 2017 12:44:54: 19000000 INFO @ Tue, 27 Jun 2017 12:45:00: 20000000 INFO @ Tue, 27 Jun 2017 12:45:03: 20000000 INFO @ Tue, 27 Jun 2017 12:45:03: 20000000 INFO @ Tue, 27 Jun 2017 12:45:10: 21000000 INFO @ Tue, 27 Jun 2017 12:45:13: 21000000 INFO @ Tue, 27 Jun 2017 12:45:13: 21000000 INFO @ Tue, 27 Jun 2017 12:45:19: 22000000 INFO @ Tue, 27 Jun 2017 12:45:22: 22000000 INFO @ Tue, 27 Jun 2017 12:45:22: 22000000 INFO @ Tue, 27 Jun 2017 12:45:27: #1 tag size is determined as 92 bps INFO @ Tue, 27 Jun 2017 12:45:27: #1 tag size = 92 INFO @ Tue, 27 Jun 2017 12:45:27: #1 total tags in treatment: 22926374 INFO @ Tue, 27 Jun 2017 12:45:27: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:45:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 12:45:28: #1 tags after filtering in treatment: 22926374 INFO @ Tue, 27 Jun 2017 12:45:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:45:28: #1 finished! INFO @ Tue, 27 Jun 2017 12:45:28: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:45:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:45:29: #2 number of paired peaks: 175 WARNING @ Tue, 27 Jun 2017 12:45:29: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Tue, 27 Jun 2017 12:45:29: start model_add_line... INFO @ Tue, 27 Jun 2017 12:45:30: start X-correlation... INFO @ Tue, 27 Jun 2017 12:45:30: end of X-cor INFO @ Tue, 27 Jun 2017 12:45:30: #2 finished! INFO @ Tue, 27 Jun 2017 12:45:30: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:45:30: #2 alternative fragment length(s) may be 1,49,70,589,597 bps INFO @ Tue, 27 Jun 2017 12:45:30: #2.2 Generate R script for model : SRX2163952.05_model.r WARNING @ Tue, 27 Jun 2017 12:45:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 12:45:30: #2 You may need to consider one of the other alternative d(s): 1,49,70,589,597 WARNING @ Tue, 27 Jun 2017 12:45:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 12:45:30: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:45:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:45:31: #1 tag size is determined as 92 bps INFO @ Tue, 27 Jun 2017 12:45:31: #1 tag size = 92 INFO @ Tue, 27 Jun 2017 12:45:31: #1 total tags in treatment: 22926374 INFO @ Tue, 27 Jun 2017 12:45:31: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:45:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 12:45:31: #1 tag size is determined as 92 bps INFO @ Tue, 27 Jun 2017 12:45:31: #1 tag size = 92 INFO @ Tue, 27 Jun 2017 12:45:31: #1 total tags in treatment: 22926374 INFO @ Tue, 27 Jun 2017 12:45:31: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:45:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 12:45:31: #1 tags after filtering in treatment: 22926374 INFO @ Tue, 27 Jun 2017 12:45:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:45:31: #1 finished! INFO @ Tue, 27 Jun 2017 12:45:31: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:45:31: #1 tags after filtering in treatment: 22926374 INFO @ Tue, 27 Jun 2017 12:45:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:45:31: #1 finished! INFO @ Tue, 27 Jun 2017 12:45:31: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:45:33: #2 number of paired peaks: 175 WARNING @ Tue, 27 Jun 2017 12:45:33: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Tue, 27 Jun 2017 12:45:33: start model_add_line... INFO @ Tue, 27 Jun 2017 12:45:33: start X-correlation... INFO @ Tue, 27 Jun 2017 12:45:33: end of X-cor INFO @ Tue, 27 Jun 2017 12:45:33: #2 finished! INFO @ Tue, 27 Jun 2017 12:45:33: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:45:33: #2 alternative fragment length(s) may be 1,49,70,589,597 bps INFO @ Tue, 27 Jun 2017 12:45:33: #2.2 Generate R script for model : SRX2163952.20_model.r WARNING @ Tue, 27 Jun 2017 12:45:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 12:45:33: #2 You may need to consider one of the other alternative d(s): 1,49,70,589,597 WARNING @ Tue, 27 Jun 2017 12:45:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 12:45:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:45:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:45:33: #2 number of paired peaks: 175 WARNING @ Tue, 27 Jun 2017 12:45:33: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Tue, 27 Jun 2017 12:45:33: start model_add_line... INFO @ Tue, 27 Jun 2017 12:45:33: start X-correlation... INFO @ Tue, 27 Jun 2017 12:45:33: end of X-cor INFO @ Tue, 27 Jun 2017 12:45:33: #2 finished! INFO @ Tue, 27 Jun 2017 12:45:33: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:45:33: #2 alternative fragment length(s) may be 1,49,70,589,597 bps INFO @ Tue, 27 Jun 2017 12:45:33: #2.2 Generate R script for model : SRX2163952.10_model.r WARNING @ Tue, 27 Jun 2017 12:45:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 12:45:33: #2 You may need to consider one of the other alternative d(s): 1,49,70,589,597 WARNING @ Tue, 27 Jun 2017 12:45:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 12:45:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:45:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:46:07: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:46:10: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:46:11: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:46:25: #4 Write output xls file... SRX2163952.05_peaks.xls INFO @ Tue, 27 Jun 2017 12:46:25: #4 Write peak in narrowPeak format file... SRX2163952.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:46:26: #4 Write summits bed file... SRX2163952.05_summits.bed INFO @ Tue, 27 Jun 2017 12:46:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:46:28: #4 Write output xls file... SRX2163952.10_peaks.xls INFO @ Tue, 27 Jun 2017 12:46:28: #4 Write peak in narrowPeak format file... SRX2163952.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:46:28: #4 Write summits bed file... SRX2163952.10_summits.bed INFO @ Tue, 27 Jun 2017 12:46:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:46:32: #4 Write output xls file... SRX2163952.20_peaks.xls INFO @ Tue, 27 Jun 2017 12:46:32: #4 Write peak in narrowPeak format file... SRX2163952.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:46:32: #4 Write summits bed file... SRX2163952.20_summits.bed INFO @ Tue, 27 Jun 2017 12:46:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。