Job ID = 10201992 sra ファイルのダウンロード中... Completed: 351469K bytes transferred in 11 seconds (240237K 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 14590761 spots for /home/okishinya/chipatlas/results/ce10/SRX2576661/SRR5272618.sra Written 14590761 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:43 14590761 reads; of these: 14590761 (100.00%) were unpaired; of these: 305739 (2.10%) aligned 0 times 11930837 (81.77%) aligned exactly 1 time 2354185 (16.13%) aligned >1 times 97.90% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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_rmdupse_core] 1255030 / 14285022 = 0.0879 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 @ Mon, 13 Nov 2017 13:15:07: # Command line: callpeak -t SRX2576661.bam -f BAM -g ce -n SRX2576661.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576661.10 # format = BAM # ChIP-seq file = ['SRX2576661.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 @ Mon, 13 Nov 2017 13:15:07: # Command line: callpeak -t SRX2576661.bam -f BAM -g ce -n SRX2576661.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576661.20 # format = BAM # ChIP-seq file = ['SRX2576661.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 @ Mon, 13 Nov 2017 13:15:07: # Command line: callpeak -t SRX2576661.bam -f BAM -g ce -n SRX2576661.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576661.05 # format = BAM # ChIP-seq file = ['SRX2576661.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 @ Mon, 13 Nov 2017 13:15:07: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:15:07: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:15:07: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:15:07: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:15:07: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:15:07: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:15:13: 1000000 INFO @ Mon, 13 Nov 2017 13:15:13: 1000000 INFO @ Mon, 13 Nov 2017 13:15:13: 1000000 INFO @ Mon, 13 Nov 2017 13:15:18: 2000000 INFO @ Mon, 13 Nov 2017 13:15:19: 2000000 INFO @ Mon, 13 Nov 2017 13:15:19: 2000000 INFO @ Mon, 13 Nov 2017 13:15:24: 3000000 INFO @ Mon, 13 Nov 2017 13:15:25: 3000000 INFO @ Mon, 13 Nov 2017 13:15:26: 3000000 INFO @ Mon, 13 Nov 2017 13:15:30: 4000000 INFO @ Mon, 13 Nov 2017 13:15:31: 4000000 INFO @ Mon, 13 Nov 2017 13:15:32: 4000000 INFO @ Mon, 13 Nov 2017 13:15:36: 5000000 INFO @ Mon, 13 Nov 2017 13:15:37: 5000000 INFO @ Mon, 13 Nov 2017 13:15:38: 5000000 INFO @ Mon, 13 Nov 2017 13:15:42: 6000000 INFO @ Mon, 13 Nov 2017 13:15:43: 6000000 INFO @ Mon, 13 Nov 2017 13:15:45: 6000000 INFO @ Mon, 13 Nov 2017 13:15:48: 7000000 INFO @ Mon, 13 Nov 2017 13:15:49: 7000000 INFO @ Mon, 13 Nov 2017 13:15:51: 7000000 INFO @ Mon, 13 Nov 2017 13:15:54: 8000000 INFO @ Mon, 13 Nov 2017 13:15:55: 8000000 INFO @ Mon, 13 Nov 2017 13:15:58: 8000000 INFO @ Mon, 13 Nov 2017 13:16:00: 9000000 INFO @ Mon, 13 Nov 2017 13:16:01: 9000000 INFO @ Mon, 13 Nov 2017 13:16:04: 9000000 INFO @ Mon, 13 Nov 2017 13:16:05: 10000000 INFO @ Mon, 13 Nov 2017 13:16:06: 10000000 INFO @ Mon, 13 Nov 2017 13:16:10: 10000000 INFO @ Mon, 13 Nov 2017 13:16:11: 11000000 INFO @ Mon, 13 Nov 2017 13:16:13: 11000000 INFO @ Mon, 13 Nov 2017 13:16:17: 11000000 INFO @ Mon, 13 Nov 2017 13:16:17: 12000000 INFO @ Mon, 13 Nov 2017 13:16:18: 12000000 INFO @ Mon, 13 Nov 2017 13:16:23: 12000000 INFO @ Mon, 13 Nov 2017 13:16:23: 13000000 INFO @ Mon, 13 Nov 2017 13:16:23: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:16:23: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:16:23: #1 total tags in treatment: 13029992 INFO @ Mon, 13 Nov 2017 13:16:23: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:16:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:16:23: #1 tags after filtering in treatment: 13029992 INFO @ Mon, 13 Nov 2017 13:16:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:16:23: #1 finished! INFO @ Mon, 13 Nov 2017 13:16:23: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:16:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:16:24: 13000000 INFO @ Mon, 13 Nov 2017 13:16:24: #2 number of paired peaks: 257 WARNING @ Mon, 13 Nov 2017 13:16:24: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Mon, 13 Nov 2017 13:16:24: start model_add_line... INFO @ Mon, 13 Nov 2017 13:16:25: start X-correlation... INFO @ Mon, 13 Nov 2017 13:16:25: end of X-cor INFO @ Mon, 13 Nov 2017 13:16:25: #2 finished! INFO @ Mon, 13 Nov 2017 13:16:25: #2 predicted fragment length is 34 bps INFO @ Mon, 13 Nov 2017 13:16:25: #2 alternative fragment length(s) may be 1,34,522,583 bps INFO @ Mon, 13 Nov 2017 13:16:25: #2.2 Generate R script for model : SRX2576661.20_model.r WARNING @ Mon, 13 Nov 2017 13:16:25: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:16:25: #2 You may need to consider one of the other alternative d(s): 1,34,522,583 WARNING @ Mon, 13 Nov 2017 13:16:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:16:25: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:16:25: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:16:25: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:16:25: #1 total tags in treatment: 13029992 INFO @ Mon, 13 Nov 2017 13:16:25: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:16:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:16:25: #1 tags after filtering in treatment: 13029992 INFO @ Mon, 13 Nov 2017 13:16:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:16:25: #1 finished! INFO @ Mon, 13 Nov 2017 13:16:25: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:16:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:16:26: #2 number of paired peaks: 257 WARNING @ Mon, 13 Nov 2017 13:16:26: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Mon, 13 Nov 2017 13:16:26: start model_add_line... INFO @ Mon, 13 Nov 2017 13:16:26: start X-correlation... INFO @ Mon, 13 Nov 2017 13:16:26: end of X-cor INFO @ Mon, 13 Nov 2017 13:16:26: #2 finished! INFO @ Mon, 13 Nov 2017 13:16:26: #2 predicted fragment length is 34 bps INFO @ Mon, 13 Nov 2017 13:16:26: #2 alternative fragment length(s) may be 1,34,522,583 bps INFO @ Mon, 13 Nov 2017 13:16:26: #2.2 Generate R script for model : SRX2576661.05_model.r WARNING @ Mon, 13 Nov 2017 13:16:26: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:16:26: #2 You may need to consider one of the other alternative d(s): 1,34,522,583 WARNING @ Mon, 13 Nov 2017 13:16:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:16:26: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:16:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:16:29: 13000000 INFO @ Mon, 13 Nov 2017 13:16:29: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:16:29: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:16:29: #1 total tags in treatment: 13029992 INFO @ Mon, 13 Nov 2017 13:16:29: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:16:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:16:30: #1 tags after filtering in treatment: 13029992 INFO @ Mon, 13 Nov 2017 13:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:16:30: #1 finished! INFO @ Mon, 13 Nov 2017 13:16:30: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:16:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:16:30: #2 number of paired peaks: 257 WARNING @ Mon, 13 Nov 2017 13:16:30: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Mon, 13 Nov 2017 13:16:30: start model_add_line... INFO @ Mon, 13 Nov 2017 13:16:31: start X-correlation... INFO @ Mon, 13 Nov 2017 13:16:31: end of X-cor INFO @ Mon, 13 Nov 2017 13:16:31: #2 finished! INFO @ Mon, 13 Nov 2017 13:16:31: #2 predicted fragment length is 34 bps INFO @ Mon, 13 Nov 2017 13:16:31: #2 alternative fragment length(s) may be 1,34,522,583 bps INFO @ Mon, 13 Nov 2017 13:16:31: #2.2 Generate R script for model : SRX2576661.10_model.r WARNING @ Mon, 13 Nov 2017 13:16:31: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:16:31: #2 You may need to consider one of the other alternative d(s): 1,34,522,583 WARNING @ Mon, 13 Nov 2017 13:16:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:16:31: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:16:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:16:50: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:16:52: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:16:57: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:17:03: #4 Write output xls file... SRX2576661.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:17:03: #4 Write peak in narrowPeak format file... SRX2576661.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:17:03: #4 Write summits bed file... SRX2576661.20_summits.bed INFO @ Mon, 13 Nov 2017 13:17:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (64 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:17:05: #4 Write output xls file... SRX2576661.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:17:05: #4 Write peak in narrowPeak format file... SRX2576661.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:17:05: #4 Write summits bed file... SRX2576661.05_summits.bed INFO @ Mon, 13 Nov 2017 13:17:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (550 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:17:12: #4 Write output xls file... SRX2576661.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:17:12: #4 Write peak in narrowPeak format file... SRX2576661.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:17:12: #4 Write summits bed file... SRX2576661.10_summits.bed INFO @ Mon, 13 Nov 2017 13:17:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (272 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。