Job ID = 9157391 sra ファイルのダウンロード中... Completed: 734067K bytes transferred in 10 seconds (587727K bits/sec), in 2 files, 3 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 11472991 spots for /home/okishinya/chipatlas/results/ce10/SRX1844114/SRR3665608.sra Written 11472991 spots total Written 12548621 spots for /home/okishinya/chipatlas/results/ce10/SRX1844114/SRR3665607.sra Written 12548621 spots total 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: 00:08:07 24021612 reads; of these: 24021612 (100.00%) were unpaired; of these: 5800878 (24.15%) aligned 0 times 15477171 (64.43%) aligned exactly 1 time 2743563 (11.42%) aligned >1 times 75.85% overall alignment rate Time searching: 00:08:07 Overall time: 00:08:07 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 8 files... [bam_rmdupse_core] 4926800 / 18220734 = 0.2704 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 11:52:21: # Command line: callpeak -t SRX1844114.bam -f BAM -g ce -n SRX1844114.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1844114.20 # format = BAM # ChIP-seq file = ['SRX1844114.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 11:52:21: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:52:21: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:52:21: # Command line: callpeak -t SRX1844114.bam -f BAM -g ce -n SRX1844114.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1844114.10 # format = BAM # ChIP-seq file = ['SRX1844114.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 11:52:21: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:52:21: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:52:21: # Command line: callpeak -t SRX1844114.bam -f BAM -g ce -n SRX1844114.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1844114.05 # format = BAM # ChIP-seq file = ['SRX1844114.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 11:52:21: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:52:21: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:52:28: 1000000 INFO @ Tue, 27 Jun 2017 11:52:30: 1000000 INFO @ Tue, 27 Jun 2017 11:52:30: 1000000 INFO @ Tue, 27 Jun 2017 11:52:36: 2000000 INFO @ Tue, 27 Jun 2017 11:52:39: 2000000 INFO @ Tue, 27 Jun 2017 11:52:39: 2000000 INFO @ Tue, 27 Jun 2017 11:52:43: 3000000 INFO @ Tue, 27 Jun 2017 11:52:47: 3000000 INFO @ Tue, 27 Jun 2017 11:52:47: 3000000 INFO @ Tue, 27 Jun 2017 11:52:51: 4000000 INFO @ Tue, 27 Jun 2017 11:52:56: 4000000 INFO @ Tue, 27 Jun 2017 11:52:56: 4000000 INFO @ Tue, 27 Jun 2017 11:53:00: 5000000 INFO @ Tue, 27 Jun 2017 11:53:05: 5000000 INFO @ Tue, 27 Jun 2017 11:53:05: 5000000 INFO @ Tue, 27 Jun 2017 11:53:07: 6000000 INFO @ Tue, 27 Jun 2017 11:53:13: 6000000 INFO @ Tue, 27 Jun 2017 11:53:13: 6000000 INFO @ Tue, 27 Jun 2017 11:53:15: 7000000 INFO @ Tue, 27 Jun 2017 11:53:21: 7000000 INFO @ Tue, 27 Jun 2017 11:53:22: 7000000 INFO @ Tue, 27 Jun 2017 11:53:22: 8000000 INFO @ Tue, 27 Jun 2017 11:53:30: 8000000 INFO @ Tue, 27 Jun 2017 11:53:30: 9000000 INFO @ Tue, 27 Jun 2017 11:53:30: 8000000 INFO @ Tue, 27 Jun 2017 11:53:37: 10000000 INFO @ Tue, 27 Jun 2017 11:53:38: 9000000 INFO @ Tue, 27 Jun 2017 11:53:39: 9000000 INFO @ Tue, 27 Jun 2017 11:53:45: 11000000 INFO @ Tue, 27 Jun 2017 11:53:47: 10000000 INFO @ Tue, 27 Jun 2017 11:53:47: 10000000 INFO @ Tue, 27 Jun 2017 11:53:52: 12000000 INFO @ Tue, 27 Jun 2017 11:53:55: 11000000 INFO @ Tue, 27 Jun 2017 11:53:55: 11000000 INFO @ Tue, 27 Jun 2017 11:54:00: 13000000 INFO @ Tue, 27 Jun 2017 11:54:02: #1 tag size is determined as 45 bps INFO @ Tue, 27 Jun 2017 11:54:02: #1 tag size = 45 INFO @ Tue, 27 Jun 2017 11:54:02: #1 total tags in treatment: 13293934 INFO @ Tue, 27 Jun 2017 11:54:02: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:54:02: #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 11:54:02: #1 tags after filtering in treatment: 13293934 INFO @ Tue, 27 Jun 2017 11:54:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:54:02: #1 finished! INFO @ Tue, 27 Jun 2017 11:54:02: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:54:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:54:03: 12000000 INFO @ Tue, 27 Jun 2017 11:54:03: #2 number of paired peaks: 122 WARNING @ Tue, 27 Jun 2017 11:54:03: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 27 Jun 2017 11:54:03: start model_add_line... INFO @ Tue, 27 Jun 2017 11:54:03: start X-correlation... INFO @ Tue, 27 Jun 2017 11:54:03: end of X-cor INFO @ Tue, 27 Jun 2017 11:54:03: #2 finished! INFO @ Tue, 27 Jun 2017 11:54:03: #2 predicted fragment length is 36 bps INFO @ Tue, 27 Jun 2017 11:54:03: #2 alternative fragment length(s) may be 3,36,113,197,244,436,474,494,598 bps INFO @ Tue, 27 Jun 2017 11:54:03: #2.2 Generate R script for model : SRX1844114.20_model.r WARNING @ Tue, 27 Jun 2017 11:54:03: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:54:03: #2 You may need to consider one of the other alternative d(s): 3,36,113,197,244,436,474,494,598 WARNING @ Tue, 27 Jun 2017 11:54:03: #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 11:54:03: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:54:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:54:04: 12000000 INFO @ Tue, 27 Jun 2017 11:54:11: 13000000 INFO @ Tue, 27 Jun 2017 11:54:12: 13000000 INFO @ Tue, 27 Jun 2017 11:54:14: #1 tag size is determined as 45 bps INFO @ Tue, 27 Jun 2017 11:54:14: #1 tag size = 45 INFO @ Tue, 27 Jun 2017 11:54:14: #1 total tags in treatment: 13293934 INFO @ Tue, 27 Jun 2017 11:54:14: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:54:14: #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 11:54:14: #1 tags after filtering in treatment: 13293934 INFO @ Tue, 27 Jun 2017 11:54:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:54:14: #1 finished! INFO @ Tue, 27 Jun 2017 11:54:14: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:54:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:54:14: #1 tag size is determined as 45 bps INFO @ Tue, 27 Jun 2017 11:54:14: #1 tag size = 45 INFO @ Tue, 27 Jun 2017 11:54:14: #1 total tags in treatment: 13293934 INFO @ Tue, 27 Jun 2017 11:54:14: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:54:14: #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 11:54:15: #1 tags after filtering in treatment: 13293934 INFO @ Tue, 27 Jun 2017 11:54:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:54:15: #1 finished! INFO @ Tue, 27 Jun 2017 11:54:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:54:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:54:15: #2 number of paired peaks: 122 WARNING @ Tue, 27 Jun 2017 11:54:15: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 27 Jun 2017 11:54:15: start model_add_line... INFO @ Tue, 27 Jun 2017 11:54:15: start X-correlation... INFO @ Tue, 27 Jun 2017 11:54:15: end of X-cor INFO @ Tue, 27 Jun 2017 11:54:15: #2 finished! INFO @ Tue, 27 Jun 2017 11:54:15: #2 predicted fragment length is 36 bps INFO @ Tue, 27 Jun 2017 11:54:15: #2 alternative fragment length(s) may be 3,36,113,197,244,436,474,494,598 bps INFO @ Tue, 27 Jun 2017 11:54:15: #2.2 Generate R script for model : SRX1844114.05_model.r WARNING @ Tue, 27 Jun 2017 11:54:15: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:54:15: #2 You may need to consider one of the other alternative d(s): 3,36,113,197,244,436,474,494,598 WARNING @ Tue, 27 Jun 2017 11:54:15: #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 11:54:15: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:54:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:54:16: #2 number of paired peaks: 122 WARNING @ Tue, 27 Jun 2017 11:54:16: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 27 Jun 2017 11:54:16: start model_add_line... INFO @ Tue, 27 Jun 2017 11:54:16: start X-correlation... INFO @ Tue, 27 Jun 2017 11:54:16: end of X-cor INFO @ Tue, 27 Jun 2017 11:54:16: #2 finished! INFO @ Tue, 27 Jun 2017 11:54:16: #2 predicted fragment length is 36 bps INFO @ Tue, 27 Jun 2017 11:54:16: #2 alternative fragment length(s) may be 3,36,113,197,244,436,474,494,598 bps INFO @ Tue, 27 Jun 2017 11:54:16: #2.2 Generate R script for model : SRX1844114.10_model.r WARNING @ Tue, 27 Jun 2017 11:54:16: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:54:16: #2 You may need to consider one of the other alternative d(s): 3,36,113,197,244,436,474,494,598 WARNING @ Tue, 27 Jun 2017 11:54:16: #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 11:54:16: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:54:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:54:29: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:54:41: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:54:42: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:54:43: #4 Write output xls file... SRX1844114.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:54:43: #4 Write peak in narrowPeak format file... SRX1844114.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:54:43: #4 Write summits bed file... SRX1844114.20_summits.bed INFO @ Tue, 27 Jun 2017 11:54:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (21 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:54:55: #4 Write output xls file... SRX1844114.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:54:55: #4 Write peak in narrowPeak format file... SRX1844114.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:54:55: #4 Write summits bed file... SRX1844114.05_summits.bed INFO @ Tue, 27 Jun 2017 11:54:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (597 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:54:56: #4 Write output xls file... SRX1844114.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:54:56: #4 Write peak in narrowPeak format file... SRX1844114.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:54:56: #4 Write summits bed file... SRX1844114.10_summits.bed INFO @ Tue, 27 Jun 2017 11:54:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (204 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。