Job ID = 9162305 sra ファイルのダウンロード中... Completed: 560143K bytes transferred in 11 seconds (392192K bits/sec), in 1 file, 2 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 4582651 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1872746/SRR3713219.sra Written 4582651 spots total 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: 00:05:38 4582651 reads; of these: 4582651 (100.00%) were paired; of these: 1018474 (22.22%) aligned concordantly 0 times 2577881 (56.25%) aligned concordantly exactly 1 time 986296 (21.52%) aligned concordantly >1 times ---- 1018474 pairs aligned concordantly 0 times; of these: 319133 (31.33%) aligned discordantly 1 time ---- 699341 pairs aligned 0 times concordantly or discordantly; of these: 1398682 mates make up the pairs; of these: 1028368 (73.52%) aligned 0 times 74634 (5.34%) aligned exactly 1 time 295680 (21.14%) aligned >1 times 88.78% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 163948 / 3851682 = 0.0426 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 07:24:23: # Command line: callpeak -t SRX1872746.bam -f BAM -g 12100000 -n SRX1872746.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872746.20 # format = BAM # ChIP-seq file = ['SRX1872746.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 28 Jun 2017 07:24:23: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:24:23: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:24:23: # Command line: callpeak -t SRX1872746.bam -f BAM -g 12100000 -n SRX1872746.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872746.10 # format = BAM # ChIP-seq file = ['SRX1872746.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 28 Jun 2017 07:24:23: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:24:23: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:24:23: # Command line: callpeak -t SRX1872746.bam -f BAM -g 12100000 -n SRX1872746.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872746.05 # format = BAM # ChIP-seq file = ['SRX1872746.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 28 Jun 2017 07:24:23: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:24:23: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:24:30: 1000000 INFO @ Wed, 28 Jun 2017 07:24:30: 1000000 INFO @ Wed, 28 Jun 2017 07:24:30: 1000000 INFO @ Wed, 28 Jun 2017 07:24:37: 2000000 INFO @ Wed, 28 Jun 2017 07:24:37: 2000000 INFO @ Wed, 28 Jun 2017 07:24:37: 2000000 INFO @ Wed, 28 Jun 2017 07:24:44: 3000000 INFO @ Wed, 28 Jun 2017 07:24:44: 3000000 INFO @ Wed, 28 Jun 2017 07:24:45: 3000000 INFO @ Wed, 28 Jun 2017 07:24:52: 4000000 INFO @ Wed, 28 Jun 2017 07:24:52: 4000000 INFO @ Wed, 28 Jun 2017 07:24:53: 4000000 INFO @ Wed, 28 Jun 2017 07:24:59: 5000000 INFO @ Wed, 28 Jun 2017 07:24:59: 5000000 INFO @ Wed, 28 Jun 2017 07:25:01: 5000000 INFO @ Wed, 28 Jun 2017 07:25:07: 6000000 INFO @ Wed, 28 Jun 2017 07:25:07: 6000000 INFO @ Wed, 28 Jun 2017 07:25:09: 6000000 INFO @ Wed, 28 Jun 2017 07:25:15: 7000000 INFO @ Wed, 28 Jun 2017 07:25:15: 7000000 INFO @ Wed, 28 Jun 2017 07:25:17: 7000000 INFO @ Wed, 28 Jun 2017 07:25:21: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:25:21: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:25:21: #1 total tags in treatment: 3408158 INFO @ Wed, 28 Jun 2017 07:25:21: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:25:21: #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 07:25:21: #1 tags after filtering in treatment: 2315385 INFO @ Wed, 28 Jun 2017 07:25:21: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 07:25:21: #1 finished! INFO @ Wed, 28 Jun 2017 07:25:21: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:25:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:25:22: #2 number of paired peaks: 178 WARNING @ Wed, 28 Jun 2017 07:25:22: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Wed, 28 Jun 2017 07:25:22: start model_add_line... INFO @ Wed, 28 Jun 2017 07:25:22: start X-correlation... INFO @ Wed, 28 Jun 2017 07:25:22: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:25:22: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:25:22: #1 total tags in treatment: 3408158 INFO @ Wed, 28 Jun 2017 07:25:22: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:25:22: #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 07:25:22: end of X-cor INFO @ Wed, 28 Jun 2017 07:25:22: #2 finished! INFO @ Wed, 28 Jun 2017 07:25:22: #2 predicted fragment length is 103 bps INFO @ Wed, 28 Jun 2017 07:25:22: #2 alternative fragment length(s) may be 11,26,84,103,130,156,165,169,211,232,261,307,364,386,415,461,479,503,519,538,561,590 bps INFO @ Wed, 28 Jun 2017 07:25:22: #2.2 Generate R script for model : SRX1872746.10_model.r WARNING @ Wed, 28 Jun 2017 07:25:22: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:25:22: #2 You may need to consider one of the other alternative d(s): 11,26,84,103,130,156,165,169,211,232,261,307,364,386,415,461,479,503,519,538,561,590 WARNING @ Wed, 28 Jun 2017 07:25:22: #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 07:25:22: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:25:22: #1 tags after filtering in treatment: 2315385 INFO @ Wed, 28 Jun 2017 07:25:22: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 07:25:22: #1 finished! INFO @ Wed, 28 Jun 2017 07:25:22: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:25:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:25:22: #2 number of paired peaks: 178 WARNING @ Wed, 28 Jun 2017 07:25:22: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Wed, 28 Jun 2017 07:25:22: start model_add_line... INFO @ Wed, 28 Jun 2017 07:25:22: start X-correlation... INFO @ Wed, 28 Jun 2017 07:25:22: end of X-cor INFO @ Wed, 28 Jun 2017 07:25:22: #2 finished! INFO @ Wed, 28 Jun 2017 07:25:22: #2 predicted fragment length is 103 bps INFO @ Wed, 28 Jun 2017 07:25:22: #2 alternative fragment length(s) may be 11,26,84,103,130,156,165,169,211,232,261,307,364,386,415,461,479,503,519,538,561,590 bps INFO @ Wed, 28 Jun 2017 07:25:22: #2.2 Generate R script for model : SRX1872746.20_model.r WARNING @ Wed, 28 Jun 2017 07:25:22: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:25:22: #2 You may need to consider one of the other alternative d(s): 11,26,84,103,130,156,165,169,211,232,261,307,364,386,415,461,479,503,519,538,561,590 WARNING @ Wed, 28 Jun 2017 07:25:22: #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 07:25:22: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:25:24: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:25:24: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:25:24: #1 total tags in treatment: 3408158 INFO @ Wed, 28 Jun 2017 07:25:24: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:25:24: #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 07:25:24: #1 tags after filtering in treatment: 2315385 INFO @ Wed, 28 Jun 2017 07:25:24: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 07:25:24: #1 finished! INFO @ Wed, 28 Jun 2017 07:25:24: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:25:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:25:24: #2 number of paired peaks: 178 WARNING @ Wed, 28 Jun 2017 07:25:24: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Wed, 28 Jun 2017 07:25:24: start model_add_line... INFO @ Wed, 28 Jun 2017 07:25:24: start X-correlation... INFO @ Wed, 28 Jun 2017 07:25:24: end of X-cor INFO @ Wed, 28 Jun 2017 07:25:24: #2 finished! INFO @ Wed, 28 Jun 2017 07:25:24: #2 predicted fragment length is 103 bps INFO @ Wed, 28 Jun 2017 07:25:24: #2 alternative fragment length(s) may be 11,26,84,103,130,156,165,169,211,232,261,307,364,386,415,461,479,503,519,538,561,590 bps INFO @ Wed, 28 Jun 2017 07:25:24: #2.2 Generate R script for model : SRX1872746.05_model.r WARNING @ Wed, 28 Jun 2017 07:25:24: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:25:24: #2 You may need to consider one of the other alternative d(s): 11,26,84,103,130,156,165,169,211,232,261,307,364,386,415,461,479,503,519,538,561,590 WARNING @ Wed, 28 Jun 2017 07:25:24: #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 07:25:24: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:25:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:25:26: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:25:27: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:25:28: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:25:29: #4 Write output xls file... SRX1872746.20_peaks.xls INFO @ Wed, 28 Jun 2017 07:25:29: #4 Write peak in narrowPeak format file... SRX1872746.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:25:29: #4 Write summits bed file... SRX1872746.20_summits.bed INFO @ Wed, 28 Jun 2017 07:25:29: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 07:25:29: #4 Write output xls file... SRX1872746.10_peaks.xls INFO @ Wed, 28 Jun 2017 07:25:29: #4 Write peak in narrowPeak format file... SRX1872746.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:25:29: #4 Write summits bed file... SRX1872746.10_summits.bed INFO @ Wed, 28 Jun 2017 07:25:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 07:25:30: #4 Write output xls file... SRX1872746.05_peaks.xls INFO @ Wed, 28 Jun 2017 07:25:30: #4 Write peak in narrowPeak format file... SRX1872746.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:25:30: #4 Write summits bed file... SRX1872746.05_summits.bed INFO @ Wed, 28 Jun 2017 07:25:30: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (27 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。