Job ID = 10320314 sra ファイルのダウンロード中... Completed: 749237K bytes transferred in 105 seconds (57999K 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... Written 20483491 spots for /home/okishinya/chipatlas/results/ce10/SRX3043405/SRR5875889.sra Written 20483491 spots total 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: 00:07:17 20483491 reads; of these: 20483491 (100.00%) were unpaired; of these: 349499 (1.71%) aligned 0 times 16962639 (82.81%) aligned exactly 1 time 3171353 (15.48%) aligned >1 times 98.29% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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] 4187096 / 20133992 = 0.2080 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 @ Thu, 11 Jan 2018 02:20:01: # Command line: callpeak -t SRX3043405.bam -f BAM -g ce -n SRX3043405.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043405.10 # format = BAM # ChIP-seq file = ['SRX3043405.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 @ Thu, 11 Jan 2018 02:20:01: # Command line: callpeak -t SRX3043405.bam -f BAM -g ce -n SRX3043405.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043405.05 # format = BAM # ChIP-seq file = ['SRX3043405.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 @ Thu, 11 Jan 2018 02:20:01: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:20:01: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:20:01: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:20:01: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:20:01: # Command line: callpeak -t SRX3043405.bam -f BAM -g ce -n SRX3043405.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043405.20 # format = BAM # ChIP-seq file = ['SRX3043405.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 @ Thu, 11 Jan 2018 02:20:01: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:20:01: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:20:08: 1000000 INFO @ Thu, 11 Jan 2018 02:20:08: 1000000 INFO @ Thu, 11 Jan 2018 02:20:08: 1000000 INFO @ Thu, 11 Jan 2018 02:20:16: 2000000 INFO @ Thu, 11 Jan 2018 02:20:16: 2000000 INFO @ Thu, 11 Jan 2018 02:20:16: 2000000 INFO @ Thu, 11 Jan 2018 02:20:23: 3000000 INFO @ Thu, 11 Jan 2018 02:20:23: 3000000 INFO @ Thu, 11 Jan 2018 02:20:23: 3000000 INFO @ Thu, 11 Jan 2018 02:20:30: 4000000 INFO @ Thu, 11 Jan 2018 02:20:31: 4000000 INFO @ Thu, 11 Jan 2018 02:20:31: 4000000 INFO @ Thu, 11 Jan 2018 02:20:37: 5000000 INFO @ Thu, 11 Jan 2018 02:20:38: 5000000 INFO @ Thu, 11 Jan 2018 02:20:38: 5000000 INFO @ Thu, 11 Jan 2018 02:20:44: 6000000 INFO @ Thu, 11 Jan 2018 02:20:45: 6000000 INFO @ Thu, 11 Jan 2018 02:20:46: 6000000 INFO @ Thu, 11 Jan 2018 02:20:51: 7000000 INFO @ Thu, 11 Jan 2018 02:20:53: 7000000 INFO @ Thu, 11 Jan 2018 02:20:53: 7000000 INFO @ Thu, 11 Jan 2018 02:20:58: 8000000 INFO @ Thu, 11 Jan 2018 02:21:00: 8000000 INFO @ Thu, 11 Jan 2018 02:21:01: 8000000 INFO @ Thu, 11 Jan 2018 02:21:05: 9000000 INFO @ Thu, 11 Jan 2018 02:21:08: 9000000 INFO @ Thu, 11 Jan 2018 02:21:08: 9000000 INFO @ Thu, 11 Jan 2018 02:21:13: 10000000 INFO @ Thu, 11 Jan 2018 02:21:15: 10000000 INFO @ Thu, 11 Jan 2018 02:21:15: 10000000 INFO @ Thu, 11 Jan 2018 02:21:20: 11000000 INFO @ Thu, 11 Jan 2018 02:21:23: 11000000 INFO @ Thu, 11 Jan 2018 02:21:23: 11000000 INFO @ Thu, 11 Jan 2018 02:21:27: 12000000 INFO @ Thu, 11 Jan 2018 02:21:30: 12000000 INFO @ Thu, 11 Jan 2018 02:21:30: 12000000 INFO @ Thu, 11 Jan 2018 02:21:34: 13000000 INFO @ Thu, 11 Jan 2018 02:21:37: 13000000 INFO @ Thu, 11 Jan 2018 02:21:38: 13000000 INFO @ Thu, 11 Jan 2018 02:21:41: 14000000 INFO @ Thu, 11 Jan 2018 02:21:45: 14000000 INFO @ Thu, 11 Jan 2018 02:21:45: 14000000 INFO @ Thu, 11 Jan 2018 02:21:48: 15000000 INFO @ Thu, 11 Jan 2018 02:21:52: 15000000 INFO @ Thu, 11 Jan 2018 02:21:53: 15000000 INFO @ Thu, 11 Jan 2018 02:21:55: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:21:55: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:21:55: #1 total tags in treatment: 15946896 INFO @ Thu, 11 Jan 2018 02:21:55: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:21:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:21:55: #1 tags after filtering in treatment: 15946896 INFO @ Thu, 11 Jan 2018 02:21:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:21:55: #1 finished! INFO @ Thu, 11 Jan 2018 02:21:55: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:21:56: #2 number of paired peaks: 125 WARNING @ Thu, 11 Jan 2018 02:21:56: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Thu, 11 Jan 2018 02:21:56: start model_add_line... INFO @ Thu, 11 Jan 2018 02:21:57: start X-correlation... INFO @ Thu, 11 Jan 2018 02:21:57: end of X-cor INFO @ Thu, 11 Jan 2018 02:21:57: #2 finished! INFO @ Thu, 11 Jan 2018 02:21:57: #2 predicted fragment length is 54 bps INFO @ Thu, 11 Jan 2018 02:21:57: #2 alternative fragment length(s) may be 2,32,54,175,475,505,531,588,592 bps INFO @ Thu, 11 Jan 2018 02:21:57: #2.2 Generate R script for model : SRX3043405.05_model.r WARNING @ Thu, 11 Jan 2018 02:21:57: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:21:57: #2 You may need to consider one of the other alternative d(s): 2,32,54,175,475,505,531,588,592 WARNING @ Thu, 11 Jan 2018 02:21:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:21:57: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:21:59: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:21:59: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:21:59: #1 total tags in treatment: 15946896 INFO @ Thu, 11 Jan 2018 02:21:59: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:21:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:22:00: #1 tags after filtering in treatment: 15946896 INFO @ Thu, 11 Jan 2018 02:22:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:22:00: #1 finished! INFO @ Thu, 11 Jan 2018 02:22:00: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:22:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:22:00: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:22:00: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:22:00: #1 total tags in treatment: 15946896 INFO @ Thu, 11 Jan 2018 02:22:00: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:22:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:22:00: #1 tags after filtering in treatment: 15946896 INFO @ Thu, 11 Jan 2018 02:22:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:22:00: #1 finished! INFO @ Thu, 11 Jan 2018 02:22:00: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:22:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:22:01: #2 number of paired peaks: 125 WARNING @ Thu, 11 Jan 2018 02:22:01: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Thu, 11 Jan 2018 02:22:01: start model_add_line... INFO @ Thu, 11 Jan 2018 02:22:01: start X-correlation... INFO @ Thu, 11 Jan 2018 02:22:01: end of X-cor INFO @ Thu, 11 Jan 2018 02:22:01: #2 finished! INFO @ Thu, 11 Jan 2018 02:22:01: #2 predicted fragment length is 54 bps INFO @ Thu, 11 Jan 2018 02:22:01: #2 alternative fragment length(s) may be 2,32,54,175,475,505,531,588,592 bps INFO @ Thu, 11 Jan 2018 02:22:01: #2.2 Generate R script for model : SRX3043405.10_model.r WARNING @ Thu, 11 Jan 2018 02:22:01: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:22:01: #2 You may need to consider one of the other alternative d(s): 2,32,54,175,475,505,531,588,592 WARNING @ Thu, 11 Jan 2018 02:22:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:22:01: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:22:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:22:01: #2 number of paired peaks: 125 WARNING @ Thu, 11 Jan 2018 02:22:01: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Thu, 11 Jan 2018 02:22:01: start model_add_line... INFO @ Thu, 11 Jan 2018 02:22:01: start X-correlation... INFO @ Thu, 11 Jan 2018 02:22:01: end of X-cor INFO @ Thu, 11 Jan 2018 02:22:01: #2 finished! INFO @ Thu, 11 Jan 2018 02:22:01: #2 predicted fragment length is 54 bps INFO @ Thu, 11 Jan 2018 02:22:01: #2 alternative fragment length(s) may be 2,32,54,175,475,505,531,588,592 bps INFO @ Thu, 11 Jan 2018 02:22:01: #2.2 Generate R script for model : SRX3043405.20_model.r WARNING @ Thu, 11 Jan 2018 02:22:01: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:22:01: #2 You may need to consider one of the other alternative d(s): 2,32,54,175,475,505,531,588,592 WARNING @ Thu, 11 Jan 2018 02:22:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:22:01: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:22:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:22:27: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:22:33: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:22:35: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:22:44: #4 Write output xls file... SRX3043405.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:22:44: #4 Write peak in narrowPeak format file... SRX3043405.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:22:44: #4 Write summits bed file... SRX3043405.05_summits.bed INFO @ Thu, 11 Jan 2018 02:22:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (601 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:22:49: #4 Write output xls file... SRX3043405.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:22:49: #4 Write peak in narrowPeak format file... SRX3043405.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:22:49: #4 Write summits bed file... SRX3043405.10_summits.bed INFO @ Thu, 11 Jan 2018 02:22:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (310 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:22:54: #4 Write output xls file... SRX3043405.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:22:54: #4 Write peak in narrowPeak format file... SRX3043405.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:22:54: #4 Write summits bed file... SRX3043405.20_summits.bed INFO @ Thu, 11 Jan 2018 02:22:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (100 records, 4 fields): 88 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。