Job ID = 10609013 sra ファイルのダウンロード中... Completed: 284530K bytes transferred in 9 seconds (247684K 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 2923633 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3063100/SRR5901530.sra Written 2923633 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: 00:03:44 2923633 reads; of these: 2923633 (100.00%) were paired; of these: 106755 (3.65%) aligned concordantly 0 times 2546325 (87.09%) aligned concordantly exactly 1 time 270553 (9.25%) aligned concordantly >1 times ---- 106755 pairs aligned concordantly 0 times; of these: 20874 (19.55%) aligned discordantly 1 time ---- 85881 pairs aligned 0 times concordantly or discordantly; of these: 171762 mates make up the pairs; of these: 128594 (74.87%) aligned 0 times 33570 (19.54%) aligned exactly 1 time 9598 (5.59%) aligned >1 times 97.80% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 108999 / 2813641 = 0.0387 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, 03 May 2018 23:11:09: # Command line: callpeak -t SRX3063100.bam -f BAM -g 12100000 -n SRX3063100.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3063100.20 # format = BAM # ChIP-seq file = ['SRX3063100.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, 03 May 2018 23:11:09: # Command line: callpeak -t SRX3063100.bam -f BAM -g 12100000 -n SRX3063100.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3063100.10 # format = BAM # ChIP-seq file = ['SRX3063100.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, 03 May 2018 23:11:09: # Command line: callpeak -t SRX3063100.bam -f BAM -g 12100000 -n SRX3063100.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3063100.05 # format = BAM # ChIP-seq file = ['SRX3063100.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, 03 May 2018 23:11:09: #1 read tag files... INFO @ Thu, 03 May 2018 23:11:09: #1 read tag files... INFO @ Thu, 03 May 2018 23:11:09: #1 read tag files... INFO @ Thu, 03 May 2018 23:11:09: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:11:09: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:11:09: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:11:16: 1000000 INFO @ Thu, 03 May 2018 23:11:16: 1000000 INFO @ Thu, 03 May 2018 23:11:16: 1000000 INFO @ Thu, 03 May 2018 23:11:22: 2000000 INFO @ Thu, 03 May 2018 23:11:23: 2000000 INFO @ Thu, 03 May 2018 23:11:24: 2000000 INFO @ Thu, 03 May 2018 23:11:29: 3000000 INFO @ Thu, 03 May 2018 23:11:31: 3000000 INFO @ Thu, 03 May 2018 23:11:33: 3000000 INFO @ Thu, 03 May 2018 23:11:38: 4000000 INFO @ Thu, 03 May 2018 23:11:41: 4000000 INFO @ Thu, 03 May 2018 23:11:42: 4000000 INFO @ Thu, 03 May 2018 23:11:46: 5000000 INFO @ Thu, 03 May 2018 23:11:50: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:11:50: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:11:50: #1 total tags in treatment: 2708140 INFO @ Thu, 03 May 2018 23:11:50: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:11:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:11:50: #1 tags after filtering in treatment: 2376348 INFO @ Thu, 03 May 2018 23:11:50: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 03 May 2018 23:11:50: #1 finished! INFO @ Thu, 03 May 2018 23:11:50: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:11:50: #2 number of paired peaks: 126 WARNING @ Thu, 03 May 2018 23:11:50: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Thu, 03 May 2018 23:11:50: start model_add_line... INFO @ Thu, 03 May 2018 23:11:50: start X-correlation... INFO @ Thu, 03 May 2018 23:11:50: end of X-cor INFO @ Thu, 03 May 2018 23:11:50: #2 finished! INFO @ Thu, 03 May 2018 23:11:50: #2 predicted fragment length is 109 bps INFO @ Thu, 03 May 2018 23:11:50: #2 alternative fragment length(s) may be 3,76,109,141 bps INFO @ Thu, 03 May 2018 23:11:50: #2.2 Generate R script for model : SRX3063100.05_model.r WARNING @ Thu, 03 May 2018 23:11:50: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:11:50: #2 You may need to consider one of the other alternative d(s): 3,76,109,141 WARNING @ Thu, 03 May 2018 23:11:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 23:11:50: #3 Call peaks... INFO @ Thu, 03 May 2018 23:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:11:51: 5000000 INFO @ Thu, 03 May 2018 23:11:52: 5000000 INFO @ Thu, 03 May 2018 23:11:55: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:11:55: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:11:55: #1 total tags in treatment: 2708140 INFO @ Thu, 03 May 2018 23:11:55: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:11:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:11:56: #1 tags after filtering in treatment: 2376348 INFO @ Thu, 03 May 2018 23:11:56: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 03 May 2018 23:11:56: #1 finished! INFO @ Thu, 03 May 2018 23:11:56: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:11:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:11:56: #2 number of paired peaks: 126 WARNING @ Thu, 03 May 2018 23:11:56: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Thu, 03 May 2018 23:11:56: start model_add_line... INFO @ Thu, 03 May 2018 23:11:56: start X-correlation... INFO @ Thu, 03 May 2018 23:11:56: end of X-cor INFO @ Thu, 03 May 2018 23:11:56: #2 finished! INFO @ Thu, 03 May 2018 23:11:56: #2 predicted fragment length is 109 bps INFO @ Thu, 03 May 2018 23:11:56: #2 alternative fragment length(s) may be 3,76,109,141 bps INFO @ Thu, 03 May 2018 23:11:56: #2.2 Generate R script for model : SRX3063100.10_model.r WARNING @ Thu, 03 May 2018 23:11:56: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:11:56: #2 You may need to consider one of the other alternative d(s): 3,76,109,141 WARNING @ Thu, 03 May 2018 23:11:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 23:11:56: #3 Call peaks... INFO @ Thu, 03 May 2018 23:11:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:11:57: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:11:57: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:11:57: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:11:57: #1 total tags in treatment: 2708140 INFO @ Thu, 03 May 2018 23:11:57: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:11:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:11:57: #1 tags after filtering in treatment: 2376348 INFO @ Thu, 03 May 2018 23:11:57: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 03 May 2018 23:11:57: #1 finished! INFO @ Thu, 03 May 2018 23:11:57: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:11:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:11:57: #2 number of paired peaks: 126 WARNING @ Thu, 03 May 2018 23:11:57: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Thu, 03 May 2018 23:11:57: start model_add_line... INFO @ Thu, 03 May 2018 23:11:57: start X-correlation... INFO @ Thu, 03 May 2018 23:11:57: end of X-cor INFO @ Thu, 03 May 2018 23:11:57: #2 finished! INFO @ Thu, 03 May 2018 23:11:57: #2 predicted fragment length is 109 bps INFO @ Thu, 03 May 2018 23:11:57: #2 alternative fragment length(s) may be 3,76,109,141 bps INFO @ Thu, 03 May 2018 23:11:57: #2.2 Generate R script for model : SRX3063100.20_model.r WARNING @ Thu, 03 May 2018 23:11:57: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:11:57: #2 You may need to consider one of the other alternative d(s): 3,76,109,141 WARNING @ Thu, 03 May 2018 23:11:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 23:11:57: #3 Call peaks... INFO @ Thu, 03 May 2018 23:11:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:11:59: #4 Write output xls file... SRX3063100.05_peaks.xls INFO @ Thu, 03 May 2018 23:11:59: #4 Write peak in narrowPeak format file... SRX3063100.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:11:59: #4 Write summits bed file... SRX3063100.05_summits.bed INFO @ Thu, 03 May 2018 23:11:59: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (993 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 23:12:02: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:12:04: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:12:05: #4 Write output xls file... SRX3063100.10_peaks.xls INFO @ Thu, 03 May 2018 23:12:05: #4 Write peak in narrowPeak format file... SRX3063100.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:12:05: #4 Write summits bed file... SRX3063100.10_summits.bed INFO @ Thu, 03 May 2018 23:12:05: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (496 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 23:12:06: #4 Write output xls file... SRX3063100.20_peaks.xls INFO @ Thu, 03 May 2018 23:12:06: #4 Write peak in narrowPeak format file... SRX3063100.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:12:06: #4 Write summits bed file... SRX3063100.20_summits.bed INFO @ Thu, 03 May 2018 23:12:06: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (206 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。