Job ID = 10536492 sra ファイルのダウンロード中... Completed: 1452034K bytes transferred in 53 seconds (223369K bits/sec), in 1 file. 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 31621395 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671188/SRR6696940.sra Written 31621395 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:13:15 31621395 reads; of these: 31621395 (100.00%) were paired; of these: 16971542 (53.67%) aligned concordantly 0 times 12626072 (39.93%) aligned concordantly exactly 1 time 2023781 (6.40%) aligned concordantly >1 times ---- 16971542 pairs aligned concordantly 0 times; of these: 15591 (0.09%) aligned discordantly 1 time ---- 16955951 pairs aligned 0 times concordantly or discordantly; of these: 33911902 mates make up the pairs; of these: 33650401 (99.23%) aligned 0 times 210109 (0.62%) aligned exactly 1 time 51392 (0.15%) aligned >1 times 46.79% overall alignment rate Time searching: 00:13:15 Overall time: 00:13:15 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 16 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] 11967116 / 14657521 = 0.8164 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 @ Thu, 05 Apr 2018 10:08:22: # Command line: callpeak -t SRX3671188.bam -f BAM -g 12100000 -n SRX3671188.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671188.05 # format = BAM # ChIP-seq file = ['SRX3671188.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 @ Thu, 05 Apr 2018 10:08:22: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:08:22: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:08:22: # Command line: callpeak -t SRX3671188.bam -f BAM -g 12100000 -n SRX3671188.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671188.10 # format = BAM # ChIP-seq file = ['SRX3671188.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 @ Thu, 05 Apr 2018 10:08:22: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:08:22: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:08:22: # Command line: callpeak -t SRX3671188.bam -f BAM -g 12100000 -n SRX3671188.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671188.20 # format = BAM # ChIP-seq file = ['SRX3671188.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 @ Thu, 05 Apr 2018 10:08:22: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:08:22: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:08:27: 1000000 INFO @ Thu, 05 Apr 2018 10:08:27: 1000000 INFO @ Thu, 05 Apr 2018 10:08:27: 1000000 INFO @ Thu, 05 Apr 2018 10:08:33: 2000000 INFO @ Thu, 05 Apr 2018 10:08:33: 2000000 INFO @ Thu, 05 Apr 2018 10:08:33: 2000000 INFO @ Thu, 05 Apr 2018 10:08:39: 3000000 INFO @ Thu, 05 Apr 2018 10:08:39: 3000000 INFO @ Thu, 05 Apr 2018 10:08:39: 3000000 INFO @ Thu, 05 Apr 2018 10:08:45: 4000000 INFO @ Thu, 05 Apr 2018 10:08:45: 4000000 INFO @ Thu, 05 Apr 2018 10:08:46: 4000000 INFO @ Thu, 05 Apr 2018 10:08:51: 5000000 INFO @ Thu, 05 Apr 2018 10:08:51: 5000000 INFO @ Thu, 05 Apr 2018 10:08:52: 5000000 INFO @ Thu, 05 Apr 2018 10:08:55: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:08:55: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:08:55: #1 total tags in treatment: 2692674 INFO @ Thu, 05 Apr 2018 10:08:55: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:08:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:08:55: #1 tags after filtering in treatment: 2212351 INFO @ Thu, 05 Apr 2018 10:08:55: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 05 Apr 2018 10:08:55: #1 finished! INFO @ Thu, 05 Apr 2018 10:08:55: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:08:55: #2 number of paired peaks: 246 WARNING @ Thu, 05 Apr 2018 10:08:55: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Thu, 05 Apr 2018 10:08:55: start model_add_line... INFO @ Thu, 05 Apr 2018 10:08:55: start X-correlation... INFO @ Thu, 05 Apr 2018 10:08:55: end of X-cor INFO @ Thu, 05 Apr 2018 10:08:55: #2 finished! INFO @ Thu, 05 Apr 2018 10:08:55: #2 predicted fragment length is 2 bps INFO @ Thu, 05 Apr 2018 10:08:55: #2 alternative fragment length(s) may be 2,48,73,94,96,114,132,172,522,524 bps INFO @ Thu, 05 Apr 2018 10:08:55: #2.2 Generate R script for model : SRX3671188.20_model.r WARNING @ Thu, 05 Apr 2018 10:08:55: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Apr 2018 10:08:55: #2 You may need to consider one of the other alternative d(s): 2,48,73,94,96,114,132,172,522,524 WARNING @ Thu, 05 Apr 2018 10:08:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Apr 2018 10:08:55: #3 Call peaks... INFO @ Thu, 05 Apr 2018 10:08:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 10:08:55: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:08:55: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:08:55: #1 total tags in treatment: 2692674 INFO @ Thu, 05 Apr 2018 10:08:55: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:08:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:08:55: #1 tags after filtering in treatment: 2212351 INFO @ Thu, 05 Apr 2018 10:08:55: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 05 Apr 2018 10:08:55: #1 finished! INFO @ Thu, 05 Apr 2018 10:08:55: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:08:55: #2 number of paired peaks: 246 WARNING @ Thu, 05 Apr 2018 10:08:55: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Thu, 05 Apr 2018 10:08:55: start model_add_line... INFO @ Thu, 05 Apr 2018 10:08:56: start X-correlation... INFO @ Thu, 05 Apr 2018 10:08:56: end of X-cor INFO @ Thu, 05 Apr 2018 10:08:56: #2 finished! INFO @ Thu, 05 Apr 2018 10:08:56: #2 predicted fragment length is 2 bps INFO @ Thu, 05 Apr 2018 10:08:56: #2 alternative fragment length(s) may be 2,48,73,94,96,114,132,172,522,524 bps INFO @ Thu, 05 Apr 2018 10:08:56: #2.2 Generate R script for model : SRX3671188.10_model.r WARNING @ Thu, 05 Apr 2018 10:08:56: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Apr 2018 10:08:56: #2 You may need to consider one of the other alternative d(s): 2,48,73,94,96,114,132,172,522,524 WARNING @ Thu, 05 Apr 2018 10:08:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Apr 2018 10:08:56: #3 Call peaks... INFO @ Thu, 05 Apr 2018 10:08:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 10:08:56: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:08:56: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:08:56: #1 total tags in treatment: 2692674 INFO @ Thu, 05 Apr 2018 10:08:56: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:08:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:08:56: #1 tags after filtering in treatment: 2212351 INFO @ Thu, 05 Apr 2018 10:08:56: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 05 Apr 2018 10:08:56: #1 finished! INFO @ Thu, 05 Apr 2018 10:08:56: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:08:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:08:56: #2 number of paired peaks: 246 WARNING @ Thu, 05 Apr 2018 10:08:56: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Thu, 05 Apr 2018 10:08:56: start model_add_line... INFO @ Thu, 05 Apr 2018 10:08:56: start X-correlation... INFO @ Thu, 05 Apr 2018 10:08:56: end of X-cor INFO @ Thu, 05 Apr 2018 10:08:56: #2 finished! INFO @ Thu, 05 Apr 2018 10:08:56: #2 predicted fragment length is 2 bps INFO @ Thu, 05 Apr 2018 10:08:56: #2 alternative fragment length(s) may be 2,48,73,94,96,114,132,172,522,524 bps INFO @ Thu, 05 Apr 2018 10:08:56: #2.2 Generate R script for model : SRX3671188.05_model.r WARNING @ Thu, 05 Apr 2018 10:08:56: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Apr 2018 10:08:56: #2 You may need to consider one of the other alternative d(s): 2,48,73,94,96,114,132,172,522,524 WARNING @ Thu, 05 Apr 2018 10:08:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Apr 2018 10:08:56: #3 Call peaks... INFO @ Thu, 05 Apr 2018 10:08:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 10:08:59: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 10:09:00: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 10:09:00: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 10:09:01: #4 Write output xls file... SRX3671188.20_peaks.xls INFO @ Thu, 05 Apr 2018 10:09:01: #4 Write peak in narrowPeak format file... SRX3671188.20_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 10:09:01: #4 Write summits bed file... SRX3671188.20_summits.bed INFO @ Thu, 05 Apr 2018 10:09:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 10:09:01: #4 Write output xls file... SRX3671188.10_peaks.xls INFO @ Thu, 05 Apr 2018 10:09:01: #4 Write peak in narrowPeak format file... SRX3671188.10_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 10:09:01: #4 Write summits bed file... SRX3671188.10_summits.bed INFO @ Thu, 05 Apr 2018 10:09:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 10:09:02: #4 Write output xls file... SRX3671188.05_peaks.xls INFO @ Thu, 05 Apr 2018 10:09:02: #4 Write peak in narrowPeak format file... SRX3671188.05_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 10:09:02: #4 Write summits bed file... SRX3671188.05_summits.bed INFO @ Thu, 05 Apr 2018 10:09:02: 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。