Job ID = 9161789 sra ファイルのダウンロード中... Completed: 733586K bytes transferred in 9 seconds (609980K 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 11908597 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1044176/SRR2045657.sra Written 11908597 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: 00:07:39 11908597 reads; of these: 11908597 (100.00%) were paired; of these: 3376424 (28.35%) aligned concordantly 0 times 7675322 (64.45%) aligned concordantly exactly 1 time 856851 (7.20%) aligned concordantly >1 times ---- 3376424 pairs aligned concordantly 0 times; of these: 178070 (5.27%) aligned discordantly 1 time ---- 3198354 pairs aligned 0 times concordantly or discordantly; of these: 6396708 mates make up the pairs; of these: 6170530 (96.46%) aligned 0 times 158220 (2.47%) aligned exactly 1 time 67958 (1.06%) aligned >1 times 74.09% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 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_sort_core] merging from 8 files... [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] 7111734 / 8672161 = 0.8201 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 04:45:39: # Command line: callpeak -t SRX1044176.bam -f BAM -g 12100000 -n SRX1044176.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1044176.05 # format = BAM # ChIP-seq file = ['SRX1044176.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 04:45:39: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:45:39: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:45:39: # Command line: callpeak -t SRX1044176.bam -f BAM -g 12100000 -n SRX1044176.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1044176.20 # format = BAM # ChIP-seq file = ['SRX1044176.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 04:45:39: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:45:39: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:45:39: # Command line: callpeak -t SRX1044176.bam -f BAM -g 12100000 -n SRX1044176.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1044176.10 # format = BAM # ChIP-seq file = ['SRX1044176.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 04:45:39: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:45:39: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:45:45: 1000000 INFO @ Wed, 28 Jun 2017 04:45:45: 1000000 INFO @ Wed, 28 Jun 2017 04:45:45: 1000000 INFO @ Wed, 28 Jun 2017 04:45:50: 2000000 INFO @ Wed, 28 Jun 2017 04:45:51: 2000000 INFO @ Wed, 28 Jun 2017 04:45:51: 2000000 INFO @ Wed, 28 Jun 2017 04:45:56: 3000000 INFO @ Wed, 28 Jun 2017 04:45:56: 3000000 INFO @ Wed, 28 Jun 2017 04:45:57: 3000000 INFO @ Wed, 28 Jun 2017 04:45:59: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:45:59: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:45:59: #1 total tags in treatment: 1537739 INFO @ Wed, 28 Jun 2017 04:45:59: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:45:59: #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 04:45:59: #1 tags after filtering in treatment: 1287985 INFO @ Wed, 28 Jun 2017 04:45:59: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 28 Jun 2017 04:45:59: #1 finished! INFO @ Wed, 28 Jun 2017 04:45:59: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:45:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:45:59: #2 number of paired peaks: 222 WARNING @ Wed, 28 Jun 2017 04:45:59: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Wed, 28 Jun 2017 04:45:59: start model_add_line... INFO @ Wed, 28 Jun 2017 04:45:59: start X-correlation... INFO @ Wed, 28 Jun 2017 04:45:59: end of X-cor INFO @ Wed, 28 Jun 2017 04:45:59: #2 finished! INFO @ Wed, 28 Jun 2017 04:45:59: #2 predicted fragment length is 3 bps INFO @ Wed, 28 Jun 2017 04:45:59: #2 alternative fragment length(s) may be 3,16,37,69 bps INFO @ Wed, 28 Jun 2017 04:45:59: #2.2 Generate R script for model : SRX1044176.20_model.r WARNING @ Wed, 28 Jun 2017 04:45:59: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 04:45:59: #2 You may need to consider one of the other alternative d(s): 3,16,37,69 WARNING @ Wed, 28 Jun 2017 04:45:59: #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 04:45:59: #3 Call peaks... INFO @ Wed, 28 Jun 2017 04:45:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 04:45:59: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:45:59: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:45:59: #1 total tags in treatment: 1537739 INFO @ Wed, 28 Jun 2017 04:45:59: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:45:59: #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 04:45:59: #1 tags after filtering in treatment: 1287985 INFO @ Wed, 28 Jun 2017 04:45:59: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 28 Jun 2017 04:45:59: #1 finished! INFO @ Wed, 28 Jun 2017 04:45:59: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:45:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:45:59: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:45:59: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:45:59: #1 total tags in treatment: 1537739 INFO @ Wed, 28 Jun 2017 04:45:59: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:45:59: #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 04:45:59: #2 number of paired peaks: 222 WARNING @ Wed, 28 Jun 2017 04:45:59: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Wed, 28 Jun 2017 04:45:59: start model_add_line... INFO @ Wed, 28 Jun 2017 04:45:59: start X-correlation... INFO @ Wed, 28 Jun 2017 04:45:59: end of X-cor INFO @ Wed, 28 Jun 2017 04:45:59: #2 finished! INFO @ Wed, 28 Jun 2017 04:45:59: #2 predicted fragment length is 3 bps INFO @ Wed, 28 Jun 2017 04:45:59: #2 alternative fragment length(s) may be 3,16,37,69 bps INFO @ Wed, 28 Jun 2017 04:45:59: #2.2 Generate R script for model : SRX1044176.10_model.r INFO @ Wed, 28 Jun 2017 04:45:59: #1 tags after filtering in treatment: 1287985 INFO @ Wed, 28 Jun 2017 04:45:59: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 28 Jun 2017 04:45:59: #1 finished! INFO @ Wed, 28 Jun 2017 04:45:59: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:45:59: #2 looking for paired plus/minus strand peaks... WARNING @ Wed, 28 Jun 2017 04:45:59: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 04:45:59: #2 You may need to consider one of the other alternative d(s): 3,16,37,69 WARNING @ Wed, 28 Jun 2017 04:45:59: #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 04:45:59: #3 Call peaks... INFO @ Wed, 28 Jun 2017 04:45:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 04:45:59: #2 number of paired peaks: 222 WARNING @ Wed, 28 Jun 2017 04:45:59: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Wed, 28 Jun 2017 04:45:59: start model_add_line... INFO @ Wed, 28 Jun 2017 04:45:59: start X-correlation... INFO @ Wed, 28 Jun 2017 04:45:59: end of X-cor INFO @ Wed, 28 Jun 2017 04:45:59: #2 finished! INFO @ Wed, 28 Jun 2017 04:45:59: #2 predicted fragment length is 3 bps INFO @ Wed, 28 Jun 2017 04:45:59: #2 alternative fragment length(s) may be 3,16,37,69 bps INFO @ Wed, 28 Jun 2017 04:45:59: #2.2 Generate R script for model : SRX1044176.05_model.r WARNING @ Wed, 28 Jun 2017 04:45:59: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 04:45:59: #2 You may need to consider one of the other alternative d(s): 3,16,37,69 WARNING @ Wed, 28 Jun 2017 04:45:59: #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 04:45:59: #3 Call peaks... INFO @ Wed, 28 Jun 2017 04:45:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 04:46:01: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 04:46:01: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 04:46:02: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 04:46:02: #4 Write output xls file... SRX1044176.20_peaks.xls INFO @ Wed, 28 Jun 2017 04:46:02: #4 Write peak in narrowPeak format file... SRX1044176.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 04:46:02: #4 Write summits bed file... SRX1044176.20_summits.bed INFO @ Wed, 28 Jun 2017 04:46:02: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 04:46:03: #4 Write output xls file... SRX1044176.10_peaks.xls INFO @ Wed, 28 Jun 2017 04:46:03: #4 Write peak in narrowPeak format file... SRX1044176.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 04:46:03: #4 Write summits bed file... SRX1044176.10_summits.bed INFO @ Wed, 28 Jun 2017 04:46:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 04:46:03: #4 Write output xls file... SRX1044176.05_peaks.xls INFO @ Wed, 28 Jun 2017 04:46:03: #4 Write peak in narrowPeak format file... SRX1044176.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 04:46:03: #4 Write summits bed file... SRX1044176.05_summits.bed INFO @ Wed, 28 Jun 2017 04:46:03: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。