Job ID = 9159820 sra ファイルのダウンロード中... Completed: 768098K bytes transferred in 8 seconds (727981K 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 3325072 spots for /home/okishinya/chipatlas/results/dm3/SRX699116/SRR1573163.sra Written 3325072 spots total Written 3376548 spots for /home/okishinya/chipatlas/results/dm3/SRX699116/SRR1573164.sra Written 3376548 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: 00:15:46 6701620 reads; of these: 6701620 (100.00%) were paired; of these: 203105 (3.03%) aligned concordantly 0 times 5660822 (84.47%) aligned concordantly exactly 1 time 837693 (12.50%) aligned concordantly >1 times ---- 203105 pairs aligned concordantly 0 times; of these: 11435 (5.63%) aligned discordantly 1 time ---- 191670 pairs aligned 0 times concordantly or discordantly; of these: 383340 mates make up the pairs; of these: 218702 (57.05%) aligned 0 times 111050 (28.97%) aligned exactly 1 time 53588 (13.98%) aligned >1 times 98.37% overall alignment rate Time searching: 00:15:46 Overall time: 00:15:46 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] 743873 / 6505406 = 0.1143 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 00:12:46: # Command line: callpeak -t SRX699116.bam -f BAM -g dm -n SRX699116.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX699116.20 # format = BAM # ChIP-seq file = ['SRX699116.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 00:12:46: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:12:46: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:12:46: # Command line: callpeak -t SRX699116.bam -f BAM -g dm -n SRX699116.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX699116.10 # format = BAM # ChIP-seq file = ['SRX699116.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 00:12:46: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:12:46: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:12:46: # Command line: callpeak -t SRX699116.bam -f BAM -g dm -n SRX699116.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX699116.05 # format = BAM # ChIP-seq file = ['SRX699116.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 00:12:46: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:12:46: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:12:54: 1000000 INFO @ Wed, 28 Jun 2017 00:12:54: 1000000 INFO @ Wed, 28 Jun 2017 00:12:54: 1000000 INFO @ Wed, 28 Jun 2017 00:13:02: 2000000 INFO @ Wed, 28 Jun 2017 00:13:03: 2000000 INFO @ Wed, 28 Jun 2017 00:13:03: 2000000 INFO @ Wed, 28 Jun 2017 00:13:11: 3000000 INFO @ Wed, 28 Jun 2017 00:13:11: 3000000 INFO @ Wed, 28 Jun 2017 00:13:12: 3000000 INFO @ Wed, 28 Jun 2017 00:13:21: 4000000 INFO @ Wed, 28 Jun 2017 00:13:21: 4000000 INFO @ Wed, 28 Jun 2017 00:13:22: 4000000 INFO @ Wed, 28 Jun 2017 00:13:29: 5000000 INFO @ Wed, 28 Jun 2017 00:13:30: 5000000 INFO @ Wed, 28 Jun 2017 00:13:31: 5000000 INFO @ Wed, 28 Jun 2017 00:13:38: 6000000 INFO @ Wed, 28 Jun 2017 00:13:38: 6000000 INFO @ Wed, 28 Jun 2017 00:13:40: 6000000 INFO @ Wed, 28 Jun 2017 00:13:46: 7000000 INFO @ Wed, 28 Jun 2017 00:13:47: 7000000 INFO @ Wed, 28 Jun 2017 00:13:49: 7000000 INFO @ Wed, 28 Jun 2017 00:13:55: 8000000 INFO @ Wed, 28 Jun 2017 00:13:56: 8000000 INFO @ Wed, 28 Jun 2017 00:13:58: 8000000 INFO @ Wed, 28 Jun 2017 00:14:04: 9000000 INFO @ Wed, 28 Jun 2017 00:14:05: 9000000 INFO @ Wed, 28 Jun 2017 00:14:07: 9000000 INFO @ Wed, 28 Jun 2017 00:14:12: 10000000 INFO @ Wed, 28 Jun 2017 00:14:13: 10000000 INFO @ Wed, 28 Jun 2017 00:14:15: 10000000 INFO @ Wed, 28 Jun 2017 00:14:21: 11000000 INFO @ Wed, 28 Jun 2017 00:14:22: 11000000 INFO @ Wed, 28 Jun 2017 00:14:24: 11000000 INFO @ Wed, 28 Jun 2017 00:14:27: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 00:14:27: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 00:14:27: #1 total tags in treatment: 5755620 INFO @ Wed, 28 Jun 2017 00:14:27: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:14:27: #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 00:14:27: #1 tags after filtering in treatment: 5467387 INFO @ Wed, 28 Jun 2017 00:14:27: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:14:27: #1 finished! INFO @ Wed, 28 Jun 2017 00:14:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:14:28: #2 number of paired peaks: 1803 INFO @ Wed, 28 Jun 2017 00:14:28: start model_add_line... INFO @ Wed, 28 Jun 2017 00:14:28: start X-correlation... INFO @ Wed, 28 Jun 2017 00:14:28: end of X-cor INFO @ Wed, 28 Jun 2017 00:14:28: #2 finished! INFO @ Wed, 28 Jun 2017 00:14:28: #2 predicted fragment length is 195 bps INFO @ Wed, 28 Jun 2017 00:14:28: #2 alternative fragment length(s) may be 195 bps INFO @ Wed, 28 Jun 2017 00:14:28: #2.2 Generate R script for model : SRX699116.20_model.r WARNING @ Wed, 28 Jun 2017 00:14:28: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 00:14:28: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Wed, 28 Jun 2017 00:14:28: #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 00:14:28: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:14:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:14:28: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 00:14:28: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 00:14:28: #1 total tags in treatment: 5755620 INFO @ Wed, 28 Jun 2017 00:14:28: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:14:28: #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 00:14:28: #1 tags after filtering in treatment: 5467387 INFO @ Wed, 28 Jun 2017 00:14:28: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:14:28: #1 finished! INFO @ Wed, 28 Jun 2017 00:14:28: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:14:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:14:29: #2 number of paired peaks: 1803 INFO @ Wed, 28 Jun 2017 00:14:29: start model_add_line... INFO @ Wed, 28 Jun 2017 00:14:29: start X-correlation... INFO @ Wed, 28 Jun 2017 00:14:29: end of X-cor INFO @ Wed, 28 Jun 2017 00:14:29: #2 finished! INFO @ Wed, 28 Jun 2017 00:14:29: #2 predicted fragment length is 195 bps INFO @ Wed, 28 Jun 2017 00:14:29: #2 alternative fragment length(s) may be 195 bps INFO @ Wed, 28 Jun 2017 00:14:29: #2.2 Generate R script for model : SRX699116.05_model.r WARNING @ Wed, 28 Jun 2017 00:14:29: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 00:14:29: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Wed, 28 Jun 2017 00:14:29: #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 00:14:29: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:14:30: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 00:14:30: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 00:14:30: #1 total tags in treatment: 5755620 INFO @ Wed, 28 Jun 2017 00:14:30: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:14:30: #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 00:14:30: #1 tags after filtering in treatment: 5467387 INFO @ Wed, 28 Jun 2017 00:14:30: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:14:30: #1 finished! INFO @ Wed, 28 Jun 2017 00:14:30: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:14:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:14:31: #2 number of paired peaks: 1803 INFO @ Wed, 28 Jun 2017 00:14:31: start model_add_line... INFO @ Wed, 28 Jun 2017 00:14:31: start X-correlation... INFO @ Wed, 28 Jun 2017 00:14:31: end of X-cor INFO @ Wed, 28 Jun 2017 00:14:31: #2 finished! INFO @ Wed, 28 Jun 2017 00:14:31: #2 predicted fragment length is 195 bps INFO @ Wed, 28 Jun 2017 00:14:31: #2 alternative fragment length(s) may be 195 bps INFO @ Wed, 28 Jun 2017 00:14:31: #2.2 Generate R script for model : SRX699116.10_model.r WARNING @ Wed, 28 Jun 2017 00:14:31: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 00:14:31: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Wed, 28 Jun 2017 00:14:31: #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 00:14:31: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:14:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:14:44: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:14:44: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:14:46: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:14:51: #4 Write output xls file... SRX699116.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:14:51: #4 Write peak in narrowPeak format file... SRX699116.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:14:51: #4 Write summits bed file... SRX699116.20_summits.bed INFO @ Wed, 28 Jun 2017 00:14:51: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (231 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:14:51: #4 Write output xls file... SRX699116.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:14:51: #4 Write peak in narrowPeak format file... SRX699116.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:14:51: #4 Write summits bed file... SRX699116.05_summits.bed INFO @ Wed, 28 Jun 2017 00:14:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2142 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:14:54: #4 Write output xls file... SRX699116.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:14:54: #4 Write peak in narrowPeak format file... SRX699116.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:14:54: #4 Write summits bed file... SRX699116.10_summits.bed INFO @ Wed, 28 Jun 2017 00:14:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (660 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。