Job ID = 11170829 sra ファイルのダウンロード中... Completed: 742586K bytes transferred in 56 seconds (107284K 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 25772598 spots for /home/okishinya/chipatlas/results/ce10/SRX3043422/SRR5875906.sra Written 25772598 spots for /home/okishinya/chipatlas/results/ce10/SRX3043422/SRR5875906.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: 00:10:32 25772598 reads; of these: 25772598 (100.00%) were unpaired; of these: 1145115 (4.44%) aligned 0 times 20750290 (80.51%) aligned exactly 1 time 3877193 (15.04%) aligned >1 times 95.56% overall alignment rate Time searching: 00:10:32 Overall time: 00:10:32 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 12 files... [bam_rmdupse_core] 2623113 / 24627483 = 0.1065 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 11:44:24: # Command line: callpeak -t SRX3043422.bam -f BAM -g ce -n SRX3043422.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043422.05 # format = BAM # ChIP-seq file = ['SRX3043422.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 @ Sat, 08 Sep 2018 11:44:24: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:44:24: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:44:24: # Command line: callpeak -t SRX3043422.bam -f BAM -g ce -n SRX3043422.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043422.20 # format = BAM # ChIP-seq file = ['SRX3043422.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 @ Sat, 08 Sep 2018 11:44:24: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:44:24: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:44:24: # Command line: callpeak -t SRX3043422.bam -f BAM -g ce -n SRX3043422.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043422.10 # format = BAM # ChIP-seq file = ['SRX3043422.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 @ Sat, 08 Sep 2018 11:44:24: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:44:24: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:44:30: 1000000 INFO @ Sat, 08 Sep 2018 11:44:30: 1000000 INFO @ Sat, 08 Sep 2018 11:44:31: 1000000 INFO @ Sat, 08 Sep 2018 11:44:36: 2000000 INFO @ Sat, 08 Sep 2018 11:44:37: 2000000 INFO @ Sat, 08 Sep 2018 11:44:37: 2000000 INFO @ Sat, 08 Sep 2018 11:44:43: 3000000 INFO @ Sat, 08 Sep 2018 11:44:43: 3000000 INFO @ Sat, 08 Sep 2018 11:44:44: 3000000 INFO @ Sat, 08 Sep 2018 11:44:49: 4000000 INFO @ Sat, 08 Sep 2018 11:44:50: 4000000 INFO @ Sat, 08 Sep 2018 11:44:51: 4000000 INFO @ Sat, 08 Sep 2018 11:44:55: 5000000 INFO @ Sat, 08 Sep 2018 11:44:57: 5000000 INFO @ Sat, 08 Sep 2018 11:44:58: 5000000 INFO @ Sat, 08 Sep 2018 11:45:01: 6000000 INFO @ Sat, 08 Sep 2018 11:45:04: 6000000 INFO @ Sat, 08 Sep 2018 11:45:05: 6000000 INFO @ Sat, 08 Sep 2018 11:45:07: 7000000 INFO @ Sat, 08 Sep 2018 11:45:10: 7000000 INFO @ Sat, 08 Sep 2018 11:45:12: 7000000 INFO @ Sat, 08 Sep 2018 11:45:13: 8000000 INFO @ Sat, 08 Sep 2018 11:45:17: 8000000 INFO @ Sat, 08 Sep 2018 11:45:19: 8000000 INFO @ Sat, 08 Sep 2018 11:45:20: 9000000 INFO @ Sat, 08 Sep 2018 11:45:24: 9000000 INFO @ Sat, 08 Sep 2018 11:45:26: 10000000 INFO @ Sat, 08 Sep 2018 11:45:26: 9000000 INFO @ Sat, 08 Sep 2018 11:45:31: 10000000 INFO @ Sat, 08 Sep 2018 11:45:32: 11000000 INFO @ Sat, 08 Sep 2018 11:45:33: 10000000 INFO @ Sat, 08 Sep 2018 11:45:37: 11000000 INFO @ Sat, 08 Sep 2018 11:45:38: 12000000 INFO @ Sat, 08 Sep 2018 11:45:40: 11000000 INFO @ Sat, 08 Sep 2018 11:45:44: 12000000 INFO @ Sat, 08 Sep 2018 11:45:44: 13000000 INFO @ Sat, 08 Sep 2018 11:45:47: 12000000 INFO @ Sat, 08 Sep 2018 11:45:51: 14000000 INFO @ Sat, 08 Sep 2018 11:45:51: 13000000 INFO @ Sat, 08 Sep 2018 11:45:54: 13000000 INFO @ Sat, 08 Sep 2018 11:45:57: 15000000 INFO @ Sat, 08 Sep 2018 11:45:57: 14000000 INFO @ Sat, 08 Sep 2018 11:46:01: 14000000 INFO @ Sat, 08 Sep 2018 11:46:03: 16000000 INFO @ Sat, 08 Sep 2018 11:46:04: 15000000 INFO @ Sat, 08 Sep 2018 11:46:08: 15000000 INFO @ Sat, 08 Sep 2018 11:46:09: 17000000 INFO @ Sat, 08 Sep 2018 11:46:10: 16000000 INFO @ Sat, 08 Sep 2018 11:46:15: 16000000 INFO @ Sat, 08 Sep 2018 11:46:16: 18000000 INFO @ Sat, 08 Sep 2018 11:46:16: 17000000 INFO @ Sat, 08 Sep 2018 11:46:22: 17000000 INFO @ Sat, 08 Sep 2018 11:46:23: 18000000 INFO @ Sat, 08 Sep 2018 11:46:23: 19000000 INFO @ Sat, 08 Sep 2018 11:46:29: 19000000 INFO @ Sat, 08 Sep 2018 11:46:29: 20000000 INFO @ Sat, 08 Sep 2018 11:46:30: 18000000 INFO @ Sat, 08 Sep 2018 11:46:35: 20000000 INFO @ Sat, 08 Sep 2018 11:46:36: 21000000 INFO @ Sat, 08 Sep 2018 11:46:37: 19000000 INFO @ Sat, 08 Sep 2018 11:46:41: 21000000 INFO @ Sat, 08 Sep 2018 11:46:42: 22000000 INFO @ Sat, 08 Sep 2018 11:46:43: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:46:43: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:46:43: #1 total tags in treatment: 22004370 INFO @ Sat, 08 Sep 2018 11:46:43: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:46:43: #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 11:46:43: #1 tags after filtering in treatment: 22004370 INFO @ Sat, 08 Sep 2018 11:46:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:46:43: #1 finished! INFO @ Sat, 08 Sep 2018 11:46:43: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:46:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:46:44: 20000000 INFO @ Sat, 08 Sep 2018 11:46:44: #2 number of paired peaks: 159 WARNING @ Sat, 08 Sep 2018 11:46:44: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 08 Sep 2018 11:46:44: start model_add_line... INFO @ Sat, 08 Sep 2018 11:46:45: start X-correlation... INFO @ Sat, 08 Sep 2018 11:46:45: end of X-cor INFO @ Sat, 08 Sep 2018 11:46:45: #2 finished! INFO @ Sat, 08 Sep 2018 11:46:45: #2 predicted fragment length is 1 bps INFO @ Sat, 08 Sep 2018 11:46:45: #2 alternative fragment length(s) may be 1,12,41,587 bps INFO @ Sat, 08 Sep 2018 11:46:45: #2.2 Generate R script for model : SRX3043422.05_model.r WARNING @ Sat, 08 Sep 2018 11:46:45: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:46:45: #2 You may need to consider one of the other alternative d(s): 1,12,41,587 WARNING @ Sat, 08 Sep 2018 11:46:45: #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 11:46:45: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:46:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:46:47: 22000000 INFO @ Sat, 08 Sep 2018 11:46:48: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:46:48: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:46:48: #1 total tags in treatment: 22004370 INFO @ Sat, 08 Sep 2018 11:46:48: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:46:48: #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 11:46:48: #1 tags after filtering in treatment: 22004370 INFO @ Sat, 08 Sep 2018 11:46:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:46:48: #1 finished! INFO @ Sat, 08 Sep 2018 11:46:48: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:46:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:46:50: #2 number of paired peaks: 159 WARNING @ Sat, 08 Sep 2018 11:46:50: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 08 Sep 2018 11:46:50: start model_add_line... INFO @ Sat, 08 Sep 2018 11:46:50: start X-correlation... INFO @ Sat, 08 Sep 2018 11:46:50: end of X-cor INFO @ Sat, 08 Sep 2018 11:46:50: #2 finished! INFO @ Sat, 08 Sep 2018 11:46:50: #2 predicted fragment length is 1 bps INFO @ Sat, 08 Sep 2018 11:46:50: #2 alternative fragment length(s) may be 1,12,41,587 bps INFO @ Sat, 08 Sep 2018 11:46:50: #2.2 Generate R script for model : SRX3043422.10_model.r WARNING @ Sat, 08 Sep 2018 11:46:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:46:50: #2 You may need to consider one of the other alternative d(s): 1,12,41,587 WARNING @ Sat, 08 Sep 2018 11:46:50: #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 11:46:50: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:46:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:46:50: 21000000 INFO @ Sat, 08 Sep 2018 11:46:57: 22000000 INFO @ Sat, 08 Sep 2018 11:46:57: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:46:57: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:46:57: #1 total tags in treatment: 22004370 INFO @ Sat, 08 Sep 2018 11:46:57: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:46:57: #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 11:46:58: #1 tags after filtering in treatment: 22004370 INFO @ Sat, 08 Sep 2018 11:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:46:58: #1 finished! INFO @ Sat, 08 Sep 2018 11:46:58: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:46:59: #2 number of paired peaks: 159 WARNING @ Sat, 08 Sep 2018 11:46:59: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 08 Sep 2018 11:46:59: start model_add_line... INFO @ Sat, 08 Sep 2018 11:46:59: start X-correlation... INFO @ Sat, 08 Sep 2018 11:46:59: end of X-cor INFO @ Sat, 08 Sep 2018 11:46:59: #2 finished! INFO @ Sat, 08 Sep 2018 11:46:59: #2 predicted fragment length is 1 bps INFO @ Sat, 08 Sep 2018 11:46:59: #2 alternative fragment length(s) may be 1,12,41,587 bps INFO @ Sat, 08 Sep 2018 11:46:59: #2.2 Generate R script for model : SRX3043422.20_model.r WARNING @ Sat, 08 Sep 2018 11:46:59: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:46:59: #2 You may need to consider one of the other alternative d(s): 1,12,41,587 WARNING @ Sat, 08 Sep 2018 11:46:59: #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 11:46:59: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:46:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:47:20: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:47:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:47:34: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:47:37: #4 Write output xls file... SRX3043422.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:47:37: #4 Write peak in narrowPeak format file... SRX3043422.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:47:37: #4 Write summits bed file... SRX3043422.05_summits.bed INFO @ Sat, 08 Sep 2018 11:47:37: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:47:47: #4 Write output xls file... SRX3043422.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:47:47: #4 Write peak in narrowPeak format file... SRX3043422.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:47:47: #4 Write summits bed file... SRX3043422.10_summits.bed INFO @ Sat, 08 Sep 2018 11:47:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:47:53: #4 Write output xls file... SRX3043422.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:47:53: #4 Write peak in narrowPeak format file... SRX3043422.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:47:53: #4 Write summits bed file... SRX3043422.20_summits.bed INFO @ Sat, 08 Sep 2018 11:47:53: 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。