Job ID = 9370018 sra ファイルのダウンロード中... Completed: 2607344K bytes transferred in 144 seconds (147461K 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 53428231 spots for /home/okishinya/chipatlas/results/ce10/SRX2710279/SRR5418733.sra Written 53428231 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: 01:13:41 53428231 reads; of these: 53428231 (100.00%) were unpaired; of these: 5534748 (10.36%) aligned 0 times 28964289 (54.21%) aligned exactly 1 time 18929194 (35.43%) aligned >1 times 89.64% overall alignment rate Time searching: 01:13:41 Overall time: 01:13:41 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 20 files... [bam_rmdupse_core] 24834014 / 47893483 = 0.5185 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 @ Fri, 04 Aug 2017 13:41:42: # Command line: callpeak -t SRX2710279.bam -f BAM -g ce -n SRX2710279.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2710279.20 # format = BAM # ChIP-seq file = ['SRX2710279.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 @ Fri, 04 Aug 2017 13:41:42: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:41:42: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:41:42: # Command line: callpeak -t SRX2710279.bam -f BAM -g ce -n SRX2710279.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2710279.05 # format = BAM # ChIP-seq file = ['SRX2710279.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 @ Fri, 04 Aug 2017 13:41:42: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:41:42: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:41:42: # Command line: callpeak -t SRX2710279.bam -f BAM -g ce -n SRX2710279.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2710279.10 # format = BAM # ChIP-seq file = ['SRX2710279.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 @ Fri, 04 Aug 2017 13:41:42: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:41:42: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:42:03: 1000000 INFO @ Fri, 04 Aug 2017 13:42:03: 1000000 INFO @ Fri, 04 Aug 2017 13:42:06: 1000000 INFO @ Fri, 04 Aug 2017 13:42:24: 2000000 INFO @ Fri, 04 Aug 2017 13:42:29: 2000000 INFO @ Fri, 04 Aug 2017 13:42:35: 2000000 INFO @ Fri, 04 Aug 2017 13:42:46: 3000000 INFO @ Fri, 04 Aug 2017 13:42:51: 3000000 INFO @ Fri, 04 Aug 2017 13:42:59: 3000000 INFO @ Fri, 04 Aug 2017 13:43:10: 4000000 INFO @ Fri, 04 Aug 2017 13:43:11: 4000000 INFO @ Fri, 04 Aug 2017 13:43:20: 4000000 INFO @ Fri, 04 Aug 2017 13:43:33: 5000000 INFO @ Fri, 04 Aug 2017 13:43:37: 5000000 INFO @ Fri, 04 Aug 2017 13:43:40: 5000000 INFO @ Fri, 04 Aug 2017 13:43:53: 6000000 INFO @ Fri, 04 Aug 2017 13:43:55: 6000000 INFO @ Fri, 04 Aug 2017 13:43:59: 6000000 INFO @ Fri, 04 Aug 2017 13:44:11: 7000000 INFO @ Fri, 04 Aug 2017 13:44:16: 7000000 INFO @ Fri, 04 Aug 2017 13:44:18: 7000000 INFO @ Fri, 04 Aug 2017 13:44:28: 8000000 INFO @ Fri, 04 Aug 2017 13:44:36: 8000000 INFO @ Fri, 04 Aug 2017 13:44:38: 8000000 INFO @ Fri, 04 Aug 2017 13:44:49: 9000000 INFO @ Fri, 04 Aug 2017 13:44:59: 9000000 INFO @ Fri, 04 Aug 2017 13:45:06: 9000000 INFO @ Fri, 04 Aug 2017 13:45:10: 10000000 INFO @ Fri, 04 Aug 2017 13:45:25: 10000000 INFO @ Fri, 04 Aug 2017 13:45:27: 10000000 INFO @ Fri, 04 Aug 2017 13:45:33: 11000000 INFO @ Fri, 04 Aug 2017 13:45:49: 11000000 INFO @ Fri, 04 Aug 2017 13:45:54: 11000000 INFO @ Fri, 04 Aug 2017 13:45:56: 12000000 INFO @ Fri, 04 Aug 2017 13:46:09: 12000000 INFO @ Fri, 04 Aug 2017 13:46:13: 12000000 INFO @ Fri, 04 Aug 2017 13:46:20: 13000000 INFO @ Fri, 04 Aug 2017 13:46:27: 13000000 INFO @ Fri, 04 Aug 2017 13:46:40: 14000000 INFO @ Fri, 04 Aug 2017 13:46:41: 13000000 INFO @ Fri, 04 Aug 2017 13:46:51: 14000000 INFO @ Fri, 04 Aug 2017 13:47:05: 14000000 INFO @ Fri, 04 Aug 2017 13:47:06: 15000000 INFO @ Fri, 04 Aug 2017 13:47:14: 15000000 INFO @ Fri, 04 Aug 2017 13:47:19: 15000000 INFO @ Fri, 04 Aug 2017 13:47:22: 16000000 INFO @ Fri, 04 Aug 2017 13:47:29: 16000000 INFO @ Fri, 04 Aug 2017 13:47:39: 17000000 INFO @ Fri, 04 Aug 2017 13:47:40: 16000000 INFO @ Fri, 04 Aug 2017 13:47:52: 17000000 INFO @ Fri, 04 Aug 2017 13:47:57: 17000000 INFO @ Fri, 04 Aug 2017 13:47:58: 18000000 INFO @ Fri, 04 Aug 2017 13:48:15: 18000000 INFO @ Fri, 04 Aug 2017 13:48:18: 18000000 INFO @ Fri, 04 Aug 2017 13:48:21: 19000000 INFO @ Fri, 04 Aug 2017 13:48:38: 19000000 INFO @ Fri, 04 Aug 2017 13:48:41: 19000000 INFO @ Fri, 04 Aug 2017 13:48:43: 20000000 INFO @ Fri, 04 Aug 2017 13:48:56: 20000000 INFO @ Fri, 04 Aug 2017 13:49:08: 20000000 INFO @ Fri, 04 Aug 2017 13:49:09: 21000000 INFO @ Fri, 04 Aug 2017 13:49:28: 21000000 INFO @ Fri, 04 Aug 2017 13:49:30: 21000000 INFO @ Fri, 04 Aug 2017 13:49:31: 22000000 INFO @ Fri, 04 Aug 2017 13:49:50: 22000000 INFO @ Fri, 04 Aug 2017 13:49:54: 22000000 INFO @ Fri, 04 Aug 2017 13:49:59: 23000000 INFO @ Fri, 04 Aug 2017 13:50:00: #1 tag size is determined as 76 bps INFO @ Fri, 04 Aug 2017 13:50:00: #1 tag size = 76 INFO @ Fri, 04 Aug 2017 13:50:00: #1 total tags in treatment: 23059469 INFO @ Fri, 04 Aug 2017 13:50:00: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:50:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 13:50:01: #1 tags after filtering in treatment: 23059469 INFO @ Fri, 04 Aug 2017 13:50:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:50:01: #1 finished! INFO @ Fri, 04 Aug 2017 13:50:01: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:50:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:50:05: #2 number of paired peaks: 503 WARNING @ Fri, 04 Aug 2017 13:50:05: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Fri, 04 Aug 2017 13:50:05: start model_add_line... INFO @ Fri, 04 Aug 2017 13:50:05: start X-correlation... INFO @ Fri, 04 Aug 2017 13:50:05: end of X-cor INFO @ Fri, 04 Aug 2017 13:50:05: #2 finished! INFO @ Fri, 04 Aug 2017 13:50:05: #2 predicted fragment length is 2 bps INFO @ Fri, 04 Aug 2017 13:50:05: #2 alternative fragment length(s) may be 2,55 bps INFO @ Fri, 04 Aug 2017 13:50:05: #2.2 Generate R script for model : SRX2710279.05_model.r WARNING @ Fri, 04 Aug 2017 13:50:05: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 13:50:05: #2 You may need to consider one of the other alternative d(s): 2,55 WARNING @ Fri, 04 Aug 2017 13:50:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 13:50:05: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:50:12: 23000000 INFO @ Fri, 04 Aug 2017 13:50:14: #1 tag size is determined as 76 bps INFO @ Fri, 04 Aug 2017 13:50:14: #1 tag size = 76 INFO @ Fri, 04 Aug 2017 13:50:14: #1 total tags in treatment: 23059469 INFO @ Fri, 04 Aug 2017 13:50:14: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:50:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 13:50:15: #1 tags after filtering in treatment: 23059469 INFO @ Fri, 04 Aug 2017 13:50:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:50:15: #1 finished! INFO @ Fri, 04 Aug 2017 13:50:15: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:50:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:50:17: #2 number of paired peaks: 503 WARNING @ Fri, 04 Aug 2017 13:50:17: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Fri, 04 Aug 2017 13:50:17: start model_add_line... INFO @ Fri, 04 Aug 2017 13:50:18: start X-correlation... INFO @ Fri, 04 Aug 2017 13:50:18: end of X-cor INFO @ Fri, 04 Aug 2017 13:50:18: #2 finished! INFO @ Fri, 04 Aug 2017 13:50:18: #2 predicted fragment length is 2 bps INFO @ Fri, 04 Aug 2017 13:50:18: #2 alternative fragment length(s) may be 2,55 bps INFO @ Fri, 04 Aug 2017 13:50:18: #2.2 Generate R script for model : SRX2710279.20_model.r WARNING @ Fri, 04 Aug 2017 13:50:18: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 13:50:18: #2 You may need to consider one of the other alternative d(s): 2,55 WARNING @ Fri, 04 Aug 2017 13:50:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 13:50:18: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:50:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:50:20: 23000000 INFO @ Fri, 04 Aug 2017 13:50:21: #1 tag size is determined as 76 bps INFO @ Fri, 04 Aug 2017 13:50:21: #1 tag size = 76 INFO @ Fri, 04 Aug 2017 13:50:21: #1 total tags in treatment: 23059469 INFO @ Fri, 04 Aug 2017 13:50:21: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:50:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 13:50:22: #1 tags after filtering in treatment: 23059469 INFO @ Fri, 04 Aug 2017 13:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:50:22: #1 finished! INFO @ Fri, 04 Aug 2017 13:50:22: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:50:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:50:24: #2 number of paired peaks: 503 WARNING @ Fri, 04 Aug 2017 13:50:24: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Fri, 04 Aug 2017 13:50:24: start model_add_line... INFO @ Fri, 04 Aug 2017 13:50:25: start X-correlation... INFO @ Fri, 04 Aug 2017 13:50:25: end of X-cor INFO @ Fri, 04 Aug 2017 13:50:25: #2 finished! INFO @ Fri, 04 Aug 2017 13:50:25: #2 predicted fragment length is 2 bps INFO @ Fri, 04 Aug 2017 13:50:25: #2 alternative fragment length(s) may be 2,55 bps INFO @ Fri, 04 Aug 2017 13:50:25: #2.2 Generate R script for model : SRX2710279.10_model.r WARNING @ Fri, 04 Aug 2017 13:50:25: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 13:50:25: #2 You may need to consider one of the other alternative d(s): 2,55 WARNING @ Fri, 04 Aug 2017 13:50:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 13:50:25: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:50:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:51:10: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:51:22: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:51:27: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:51:44: #4 Write output xls file... SRX2710279.05_peaks.xls INFO @ Fri, 04 Aug 2017 13:51:44: #4 Write peak in narrowPeak format file... SRX2710279.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:51:44: #4 Write summits bed file... SRX2710279.05_summits.bed INFO @ Fri, 04 Aug 2017 13:51:44: Done! pass1 - making usageList (0 chroms): 12 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 13:51:56: #4 Write output xls file... SRX2710279.20_peaks.xls INFO @ Fri, 04 Aug 2017 13:51:56: #4 Write peak in narrowPeak format file... SRX2710279.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:51:56: #4 Write summits bed file... SRX2710279.20_summits.bed INFO @ Fri, 04 Aug 2017 13:51:56: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 13:52:01: #4 Write output xls file... SRX2710279.10_peaks.xls INFO @ Fri, 04 Aug 2017 13:52:01: #4 Write peak in narrowPeak format file... SRX2710279.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:52:01: #4 Write summits bed file... SRX2710279.10_summits.bed INFO @ Fri, 04 Aug 2017 13:52:01: Done! pass1 - making usageList (0 chroms): 3 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。