Job ID = 9159814 sra ファイルのダウンロード中... Completed: 797868K bytes transferred in 10 seconds (646667K 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: PAIRED fastq に変換中... Written 3465784 spots for /home/okishinya/chipatlas/results/dm3/SRX699108/SRR1573147.sra Written 3465784 spots total Written 3508850 spots for /home/okishinya/chipatlas/results/dm3/SRX699108/SRR1573148.sra Written 3508850 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: 00:24:52 6974634 reads; of these: 6974634 (100.00%) were paired; of these: 1001695 (14.36%) aligned concordantly 0 times 4422294 (63.41%) aligned concordantly exactly 1 time 1550645 (22.23%) aligned concordantly >1 times ---- 1001695 pairs aligned concordantly 0 times; of these: 92745 (9.26%) aligned discordantly 1 time ---- 908950 pairs aligned 0 times concordantly or discordantly; of these: 1817900 mates make up the pairs; of these: 1563611 (86.01%) aligned 0 times 117662 (6.47%) aligned exactly 1 time 136627 (7.52%) aligned >1 times 88.79% overall alignment rate Time searching: 00:24:52 Overall time: 00:24:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 4882808 / 6042491 = 0.8081 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 @ Wed, 28 Jun 2017 00:16:43: # Command line: callpeak -t SRX699108.bam -f BAM -g dm -n SRX699108.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX699108.10 # format = BAM # ChIP-seq file = ['SRX699108.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Wed, 28 Jun 2017 00:16:43: # Command line: callpeak -t SRX699108.bam -f BAM -g dm -n SRX699108.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX699108.05 # format = BAM # ChIP-seq file = ['SRX699108.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Wed, 28 Jun 2017 00:16:43: # Command line: callpeak -t SRX699108.bam -f BAM -g dm -n SRX699108.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX699108.20 # format = BAM # ChIP-seq file = ['SRX699108.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Wed, 28 Jun 2017 00:16:43: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:16:43: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:16:43: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:16:43: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:16:43: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:16:43: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:16:51: 1000000 INFO @ Wed, 28 Jun 2017 00:16:52: 1000000 INFO @ Wed, 28 Jun 2017 00:16:52: 1000000 INFO @ Wed, 28 Jun 2017 00:16:59: 2000000 INFO @ Wed, 28 Jun 2017 00:17:00: 2000000 INFO @ Wed, 28 Jun 2017 00:17:00: 2000000 INFO @ Wed, 28 Jun 2017 00:17:04: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 00:17:04: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 00:17:04: #1 total tags in treatment: 1168973 INFO @ Wed, 28 Jun 2017 00:17:04: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:17:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:17:04: #1 tags after filtering in treatment: 1025053 INFO @ Wed, 28 Jun 2017 00:17:04: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 28 Jun 2017 00:17:04: #1 finished! INFO @ Wed, 28 Jun 2017 00:17:04: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:17:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:17:05: #2 number of paired peaks: 3121 INFO @ Wed, 28 Jun 2017 00:17:05: start model_add_line... INFO @ Wed, 28 Jun 2017 00:17:05: start X-correlation... INFO @ Wed, 28 Jun 2017 00:17:05: end of X-cor INFO @ Wed, 28 Jun 2017 00:17:05: #2 finished! INFO @ Wed, 28 Jun 2017 00:17:05: #2 predicted fragment length is 128 bps INFO @ Wed, 28 Jun 2017 00:17:05: #2 alternative fragment length(s) may be 128 bps INFO @ Wed, 28 Jun 2017 00:17:05: #2.2 Generate R script for model : SRX699108.20_model.r WARNING @ Wed, 28 Jun 2017 00:17:05: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 00:17:05: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Wed, 28 Jun 2017 00:17:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 00:17:05: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:17:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:17:05: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 00:17:05: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 00:17:05: #1 total tags in treatment: 1168973 INFO @ Wed, 28 Jun 2017 00:17:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:17:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:17:05: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 00:17:05: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 00:17:05: #1 total tags in treatment: 1168973 INFO @ Wed, 28 Jun 2017 00:17:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:17:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:17:05: #1 tags after filtering in treatment: 1025053 INFO @ Wed, 28 Jun 2017 00:17:05: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 28 Jun 2017 00:17:05: #1 finished! INFO @ Wed, 28 Jun 2017 00:17:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:17:05: #1 tags after filtering in treatment: 1025053 INFO @ Wed, 28 Jun 2017 00:17:05: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 28 Jun 2017 00:17:05: #1 finished! INFO @ Wed, 28 Jun 2017 00:17:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:17:05: #2 number of paired peaks: 3121 INFO @ Wed, 28 Jun 2017 00:17:05: start model_add_line... INFO @ Wed, 28 Jun 2017 00:17:05: #2 number of paired peaks: 3121 INFO @ Wed, 28 Jun 2017 00:17:05: start model_add_line... INFO @ Wed, 28 Jun 2017 00:17:05: start X-correlation... INFO @ Wed, 28 Jun 2017 00:17:05: end of X-cor INFO @ Wed, 28 Jun 2017 00:17:05: #2 finished! INFO @ Wed, 28 Jun 2017 00:17:05: #2 predicted fragment length is 128 bps INFO @ Wed, 28 Jun 2017 00:17:05: #2 alternative fragment length(s) may be 128 bps INFO @ Wed, 28 Jun 2017 00:17:05: #2.2 Generate R script for model : SRX699108.05_model.r WARNING @ Wed, 28 Jun 2017 00:17:05: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 00:17:05: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Wed, 28 Jun 2017 00:17:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 00:17:05: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:17:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:17:05: start X-correlation... INFO @ Wed, 28 Jun 2017 00:17:05: end of X-cor INFO @ Wed, 28 Jun 2017 00:17:05: #2 finished! INFO @ Wed, 28 Jun 2017 00:17:05: #2 predicted fragment length is 128 bps INFO @ Wed, 28 Jun 2017 00:17:05: #2 alternative fragment length(s) may be 128 bps INFO @ Wed, 28 Jun 2017 00:17:05: #2.2 Generate R script for model : SRX699108.10_model.r WARNING @ Wed, 28 Jun 2017 00:17:05: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 00:17:05: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Wed, 28 Jun 2017 00:17:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 00:17:05: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:17:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:17:08: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:17:08: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:17:08: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:17:09: #4 Write output xls file... SRX699108.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:17:09: #4 Write peak in narrowPeak format file... SRX699108.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:17:09: #4 Write summits bed file... SRX699108.20_summits.bed INFO @ Wed, 28 Jun 2017 00:17:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (501 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:17:10: #4 Write output xls file... SRX699108.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:17:10: #4 Write peak in narrowPeak format file... SRX699108.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:17:10: #4 Write summits bed file... SRX699108.05_summits.bed INFO @ Wed, 28 Jun 2017 00:17:10: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1200 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:17:10: #4 Write output xls file... SRX699108.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:17:10: #4 Write peak in narrowPeak format file... SRX699108.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:17:10: #4 Write summits bed file... SRX699108.10_summits.bed INFO @ Wed, 28 Jun 2017 00:17:10: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (747 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。