Job ID = 10845216 sra ファイルのダウンロード中... Completed: 219510K bytes transferred in 26 seconds (67154K 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... Read 3802707 spots for /home/okishinya/chipatlas/results/dm3/SRX3632912/SRR6655558.sra Written 3802707 spots for /home/okishinya/chipatlas/results/dm3/SRX3632912/SRR6655558.sra 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: 00:09:47 3802707 reads; of these: 3802707 (100.00%) were paired; of these: 464816 (12.22%) aligned concordantly 0 times 2693824 (70.84%) aligned concordantly exactly 1 time 644067 (16.94%) aligned concordantly >1 times ---- 464816 pairs aligned concordantly 0 times; of these: 96399 (20.74%) aligned discordantly 1 time ---- 368417 pairs aligned 0 times concordantly or discordantly; of these: 736834 mates make up the pairs; of these: 541148 (73.44%) aligned 0 times 120093 (16.30%) aligned exactly 1 time 75593 (10.26%) aligned >1 times 92.88% overall alignment rate Time searching: 00:09:47 Overall time: 00:09:47 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_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] 184790 / 3398160 = 0.0544 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, 04 Jul 2018 09:40:07: # Command line: callpeak -t SRX3632912.bam -f BAM -g dm -n SRX3632912.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3632912.05 # format = BAM # ChIP-seq file = ['SRX3632912.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, 04 Jul 2018 09:40:07: # Command line: callpeak -t SRX3632912.bam -f BAM -g dm -n SRX3632912.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3632912.20 # format = BAM # ChIP-seq file = ['SRX3632912.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, 04 Jul 2018 09:40:07: # Command line: callpeak -t SRX3632912.bam -f BAM -g dm -n SRX3632912.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3632912.10 # format = BAM # ChIP-seq file = ['SRX3632912.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, 04 Jul 2018 09:40:07: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:40:07: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:40:07: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:40:07: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:40:07: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:40:07: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:40:15: 1000000 INFO @ Wed, 04 Jul 2018 09:40:15: 1000000 INFO @ Wed, 04 Jul 2018 09:40:15: 1000000 INFO @ Wed, 04 Jul 2018 09:40:24: 2000000 INFO @ Wed, 04 Jul 2018 09:40:24: 2000000 INFO @ Wed, 04 Jul 2018 09:40:24: 2000000 INFO @ Wed, 04 Jul 2018 09:40:32: 3000000 INFO @ Wed, 04 Jul 2018 09:40:32: 3000000 INFO @ Wed, 04 Jul 2018 09:40:32: 3000000 INFO @ Wed, 04 Jul 2018 09:40:41: 4000000 INFO @ Wed, 04 Jul 2018 09:40:41: 4000000 INFO @ Wed, 04 Jul 2018 09:40:41: 4000000 INFO @ Wed, 04 Jul 2018 09:40:49: 5000000 INFO @ Wed, 04 Jul 2018 09:40:49: 5000000 INFO @ Wed, 04 Jul 2018 09:40:49: 5000000 INFO @ Wed, 04 Jul 2018 09:40:58: 6000000 INFO @ Wed, 04 Jul 2018 09:40:58: 6000000 INFO @ Wed, 04 Jul 2018 09:40:58: 6000000 INFO @ Wed, 04 Jul 2018 09:41:03: #1 tag size is determined as 74 bps INFO @ Wed, 04 Jul 2018 09:41:03: #1 tag size = 74 INFO @ Wed, 04 Jul 2018 09:41:03: #1 total tags in treatment: 3160845 INFO @ Wed, 04 Jul 2018 09:41:03: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:41:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:41:03: #1 tags after filtering in treatment: 3048158 INFO @ Wed, 04 Jul 2018 09:41:03: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 04 Jul 2018 09:41:03: #1 finished! INFO @ Wed, 04 Jul 2018 09:41:03: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:41:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:41:04: #2 number of paired peaks: 164 WARNING @ Wed, 04 Jul 2018 09:41:04: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Wed, 04 Jul 2018 09:41:04: start model_add_line... INFO @ Wed, 04 Jul 2018 09:41:04: start X-correlation... INFO @ Wed, 04 Jul 2018 09:41:04: #1 tag size is determined as 74 bps INFO @ Wed, 04 Jul 2018 09:41:04: #1 tag size is determined as 74 bps INFO @ Wed, 04 Jul 2018 09:41:04: #1 tag size = 74 INFO @ Wed, 04 Jul 2018 09:41:04: #1 tag size = 74 INFO @ Wed, 04 Jul 2018 09:41:04: #1 total tags in treatment: 3160845 INFO @ Wed, 04 Jul 2018 09:41:04: #1 total tags in treatment: 3160845 INFO @ Wed, 04 Jul 2018 09:41:04: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:41:04: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:41:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:41:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:41:04: #1 tags after filtering in treatment: 3048158 INFO @ Wed, 04 Jul 2018 09:41:04: #1 tags after filtering in treatment: 3048158 INFO @ Wed, 04 Jul 2018 09:41:04: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 04 Jul 2018 09:41:04: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 04 Jul 2018 09:41:04: #1 finished! INFO @ Wed, 04 Jul 2018 09:41:04: #1 finished! INFO @ Wed, 04 Jul 2018 09:41:04: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:41:04: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:41:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:41:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:41:04: end of X-cor INFO @ Wed, 04 Jul 2018 09:41:04: #2 finished! INFO @ Wed, 04 Jul 2018 09:41:04: #2 predicted fragment length is 125 bps INFO @ Wed, 04 Jul 2018 09:41:04: #2 alternative fragment length(s) may be 125 bps INFO @ Wed, 04 Jul 2018 09:41:04: #2.2 Generate R script for model : SRX3632912.10_model.r WARNING @ Wed, 04 Jul 2018 09:41:04: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:41:04: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Wed, 04 Jul 2018 09:41:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:41:04: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:41:04: #2 number of paired peaks: 164 WARNING @ Wed, 04 Jul 2018 09:41:04: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Wed, 04 Jul 2018 09:41:04: start model_add_line... INFO @ Wed, 04 Jul 2018 09:41:04: start X-correlation... INFO @ Wed, 04 Jul 2018 09:41:04: end of X-cor INFO @ Wed, 04 Jul 2018 09:41:04: #2 finished! INFO @ Wed, 04 Jul 2018 09:41:04: #2 predicted fragment length is 125 bps INFO @ Wed, 04 Jul 2018 09:41:04: #2 alternative fragment length(s) may be 125 bps INFO @ Wed, 04 Jul 2018 09:41:04: #2.2 Generate R script for model : SRX3632912.05_model.r INFO @ Wed, 04 Jul 2018 09:41:04: #2 number of paired peaks: 164 WARNING @ Wed, 04 Jul 2018 09:41:04: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Wed, 04 Jul 2018 09:41:04: start model_add_line... WARNING @ Wed, 04 Jul 2018 09:41:04: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:41:04: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Wed, 04 Jul 2018 09:41:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:41:04: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:41:04: start X-correlation... INFO @ Wed, 04 Jul 2018 09:41:04: end of X-cor INFO @ Wed, 04 Jul 2018 09:41:04: #2 finished! INFO @ Wed, 04 Jul 2018 09:41:04: #2 predicted fragment length is 125 bps INFO @ Wed, 04 Jul 2018 09:41:04: #2 alternative fragment length(s) may be 125 bps INFO @ Wed, 04 Jul 2018 09:41:04: #2.2 Generate R script for model : SRX3632912.20_model.r WARNING @ Wed, 04 Jul 2018 09:41:04: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:41:04: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Wed, 04 Jul 2018 09:41:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:41:04: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:41:11: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:41:11: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:41:11: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:41:15: #4 Write output xls file... SRX3632912.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:41:15: #4 Write peak in narrowPeak format file... SRX3632912.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:41:15: #4 Write summits bed file... SRX3632912.10_summits.bed INFO @ Wed, 04 Jul 2018 09:41:15: Done! INFO @ Wed, 04 Jul 2018 09:41:15: #4 Write output xls file... SRX3632912.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:41:15: #4 Write peak in narrowPeak format file... SRX3632912.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:41:15: #4 Write output xls file... SRX3632912.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:41:15: #4 Write peak in narrowPeak format file... SRX3632912.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:41:15: #4 Write summits bed file... SRX3632912.20_summits.bed INFO @ Wed, 04 Jul 2018 09:41:15: Done! INFO @ Wed, 04 Jul 2018 09:41:15: #4 Write summits bed file... SRX3632912.05_summits.bed INFO @ Wed, 04 Jul 2018 09:41:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 3 millis pass1 - making usageList (4 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (116 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (385 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。