Job ID = 11244873 sra ファイルのダウンロード中... Completed: 585720K bytes transferred in 8 seconds (552956K 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 6013764 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765665/SRR6807388.sra Written 6013764 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765665/SRR6807388.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: 00:08:09 6013764 reads; of these: 6013764 (100.00%) were paired; of these: 206755 (3.44%) aligned concordantly 0 times 5217144 (86.75%) aligned concordantly exactly 1 time 589865 (9.81%) aligned concordantly >1 times ---- 206755 pairs aligned concordantly 0 times; of these: 101306 (49.00%) aligned discordantly 1 time ---- 105449 pairs aligned 0 times concordantly or discordantly; of these: 210898 mates make up the pairs; of these: 103008 (48.84%) aligned 0 times 73605 (34.90%) aligned exactly 1 time 34285 (16.26%) aligned >1 times 99.14% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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] 212114 / 5868623 = 0.0361 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 @ Tue, 09 Oct 2018 22:33:51: # Command line: callpeak -t SRX3765665.bam -f BAM -g 12100000 -n SRX3765665.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3765665.10 # format = BAM # ChIP-seq file = ['SRX3765665.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 @ Tue, 09 Oct 2018 22:33:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:33:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:33:51: # Command line: callpeak -t SRX3765665.bam -f BAM -g 12100000 -n SRX3765665.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3765665.20 # format = BAM # ChIP-seq file = ['SRX3765665.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 @ Tue, 09 Oct 2018 22:33:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:33:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:33:51: # Command line: callpeak -t SRX3765665.bam -f BAM -g 12100000 -n SRX3765665.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3765665.05 # format = BAM # ChIP-seq file = ['SRX3765665.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 @ Tue, 09 Oct 2018 22:33:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:33:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:34:01: 1000000 INFO @ Tue, 09 Oct 2018 22:34:01: 1000000 INFO @ Tue, 09 Oct 2018 22:34:01: 1000000 INFO @ Tue, 09 Oct 2018 22:34:11: 2000000 INFO @ Tue, 09 Oct 2018 22:34:11: 2000000 INFO @ Tue, 09 Oct 2018 22:34:11: 2000000 INFO @ Tue, 09 Oct 2018 22:34:21: 3000000 INFO @ Tue, 09 Oct 2018 22:34:21: 3000000 INFO @ Tue, 09 Oct 2018 22:34:21: 3000000 INFO @ Tue, 09 Oct 2018 22:34:31: 4000000 INFO @ Tue, 09 Oct 2018 22:34:31: 4000000 INFO @ Tue, 09 Oct 2018 22:34:31: 4000000 INFO @ Tue, 09 Oct 2018 22:34:41: 5000000 INFO @ Tue, 09 Oct 2018 22:34:41: 5000000 INFO @ Tue, 09 Oct 2018 22:34:41: 5000000 INFO @ Tue, 09 Oct 2018 22:34:50: 6000000 INFO @ Tue, 09 Oct 2018 22:34:50: 6000000 INFO @ Tue, 09 Oct 2018 22:34:51: 6000000 INFO @ Tue, 09 Oct 2018 22:35:00: 7000000 INFO @ Tue, 09 Oct 2018 22:35:00: 7000000 INFO @ Tue, 09 Oct 2018 22:35:01: 7000000 INFO @ Tue, 09 Oct 2018 22:35:10: 8000000 INFO @ Tue, 09 Oct 2018 22:35:10: 8000000 INFO @ Tue, 09 Oct 2018 22:35:11: 8000000 INFO @ Tue, 09 Oct 2018 22:35:20: 9000000 INFO @ Tue, 09 Oct 2018 22:35:20: 9000000 INFO @ Tue, 09 Oct 2018 22:35:22: 9000000 INFO @ Tue, 09 Oct 2018 22:35:30: 10000000 INFO @ Tue, 09 Oct 2018 22:35:30: 10000000 INFO @ Tue, 09 Oct 2018 22:35:32: 10000000 INFO @ Tue, 09 Oct 2018 22:35:40: 11000000 INFO @ Tue, 09 Oct 2018 22:35:40: 11000000 INFO @ Tue, 09 Oct 2018 22:35:44: 11000000 INFO @ Tue, 09 Oct 2018 22:35:45: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:35:45: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:35:45: #1 total tags in treatment: 5596092 INFO @ Tue, 09 Oct 2018 22:35:45: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:35:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:35:45: #1 tags after filtering in treatment: 4187033 INFO @ Tue, 09 Oct 2018 22:35:45: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 09 Oct 2018 22:35:45: #1 finished! INFO @ Tue, 09 Oct 2018 22:35:45: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:35:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:35:45: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:35:45: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:35:45: #1 total tags in treatment: 5596092 INFO @ Tue, 09 Oct 2018 22:35:45: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:35:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:35:46: #1 tags after filtering in treatment: 4187033 INFO @ Tue, 09 Oct 2018 22:35:46: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 09 Oct 2018 22:35:46: #1 finished! INFO @ Tue, 09 Oct 2018 22:35:46: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:35:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:35:46: #2 number of paired peaks: 137 WARNING @ Tue, 09 Oct 2018 22:35:46: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 09 Oct 2018 22:35:46: start model_add_line... INFO @ Tue, 09 Oct 2018 22:35:46: start X-correlation... INFO @ Tue, 09 Oct 2018 22:35:46: end of X-cor INFO @ Tue, 09 Oct 2018 22:35:46: #2 finished! INFO @ Tue, 09 Oct 2018 22:35:46: #2 predicted fragment length is 187 bps INFO @ Tue, 09 Oct 2018 22:35:46: #2 alternative fragment length(s) may be 81,113,147,187,207,237,280,348,383,386,432,456,496,558,564,587 bps INFO @ Tue, 09 Oct 2018 22:35:46: #2.2 Generate R script for model : SRX3765665.20_model.r WARNING @ Tue, 09 Oct 2018 22:35:46: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:35:46: #2 You may need to consider one of the other alternative d(s): 81,113,147,187,207,237,280,348,383,386,432,456,496,558,564,587 WARNING @ Tue, 09 Oct 2018 22:35:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:35:46: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:35:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:35:46: #2 number of paired peaks: 137 WARNING @ Tue, 09 Oct 2018 22:35:46: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 09 Oct 2018 22:35:46: start model_add_line... INFO @ Tue, 09 Oct 2018 22:35:46: start X-correlation... INFO @ Tue, 09 Oct 2018 22:35:46: end of X-cor INFO @ Tue, 09 Oct 2018 22:35:46: #2 finished! INFO @ Tue, 09 Oct 2018 22:35:46: #2 predicted fragment length is 187 bps INFO @ Tue, 09 Oct 2018 22:35:46: #2 alternative fragment length(s) may be 81,113,147,187,207,237,280,348,383,386,432,456,496,558,564,587 bps INFO @ Tue, 09 Oct 2018 22:35:46: #2.2 Generate R script for model : SRX3765665.10_model.r WARNING @ Tue, 09 Oct 2018 22:35:46: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:35:46: #2 You may need to consider one of the other alternative d(s): 81,113,147,187,207,237,280,348,383,386,432,456,496,558,564,587 WARNING @ Tue, 09 Oct 2018 22:35:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:35:46: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:35:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:35:49: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:35:49: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:35:49: #1 total tags in treatment: 5596092 INFO @ Tue, 09 Oct 2018 22:35:49: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:35:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:35:49: #1 tags after filtering in treatment: 4187033 INFO @ Tue, 09 Oct 2018 22:35:49: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 09 Oct 2018 22:35:49: #1 finished! INFO @ Tue, 09 Oct 2018 22:35:49: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:35:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:35:50: #2 number of paired peaks: 137 WARNING @ Tue, 09 Oct 2018 22:35:50: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 09 Oct 2018 22:35:50: start model_add_line... INFO @ Tue, 09 Oct 2018 22:35:50: start X-correlation... INFO @ Tue, 09 Oct 2018 22:35:50: end of X-cor INFO @ Tue, 09 Oct 2018 22:35:50: #2 finished! INFO @ Tue, 09 Oct 2018 22:35:50: #2 predicted fragment length is 187 bps INFO @ Tue, 09 Oct 2018 22:35:50: #2 alternative fragment length(s) may be 81,113,147,187,207,237,280,348,383,386,432,456,496,558,564,587 bps INFO @ Tue, 09 Oct 2018 22:35:50: #2.2 Generate R script for model : SRX3765665.05_model.r WARNING @ Tue, 09 Oct 2018 22:35:50: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:35:50: #2 You may need to consider one of the other alternative d(s): 81,113,147,187,207,237,280,348,383,386,432,456,496,558,564,587 WARNING @ Tue, 09 Oct 2018 22:35:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:35:50: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:35:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:35:54: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:35:54: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:35:57: #4 Write output xls file... SRX3765665.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:35:57: #4 Write peak in narrowPeak format file... SRX3765665.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:35:57: #4 Write summits bed file... SRX3765665.20_summits.bed INFO @ Tue, 09 Oct 2018 22:35:57: Done! INFO @ Tue, 09 Oct 2018 22:35:57: #4 Write output xls file... SRX3765665.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:35:57: #4 Write peak in narrowPeak format file... SRX3765665.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:35:57: #4 Write summits bed file... SRX3765665.10_summits.bed INFO @ Tue, 09 Oct 2018 22:35:57: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:35:57: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:36:01: #4 Write output xls file... SRX3765665.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:36:01: #4 Write peak in narrowPeak format file... SRX3765665.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:36:01: #4 Write summits bed file... SRX3765665.05_summits.bed INFO @ Tue, 09 Oct 2018 22:36:01: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (22 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。