Job ID = 10536357 sra ファイルのダウンロード中... Completed: 1035211K bytes transferred in 71 seconds (118107K 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 26252956 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433220/SRR6333861.sra Written 26252956 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: 00:13:18 26252956 reads; of these: 26252956 (100.00%) were paired; of these: 10700252 (40.76%) aligned concordantly 0 times 14136066 (53.85%) aligned concordantly exactly 1 time 1416638 (5.40%) aligned concordantly >1 times ---- 10700252 pairs aligned concordantly 0 times; of these: 163880 (1.53%) aligned discordantly 1 time ---- 10536372 pairs aligned 0 times concordantly or discordantly; of these: 21072744 mates make up the pairs; of these: 20711370 (98.29%) aligned 0 times 291490 (1.38%) aligned exactly 1 time 69884 (0.33%) aligned >1 times 60.55% overall alignment rate Time searching: 00:13:18 Overall time: 00:13:18 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] 12192701 / 15569561 = 0.7831 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 09:14:03: # Command line: callpeak -t SRX3433220.bam -f BAM -g 12100000 -n SRX3433220.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433220.20 # format = BAM # ChIP-seq file = ['SRX3433220.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 09:14:03: # Command line: callpeak -t SRX3433220.bam -f BAM -g 12100000 -n SRX3433220.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433220.10 # format = BAM # ChIP-seq file = ['SRX3433220.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 09:14:03: # Command line: callpeak -t SRX3433220.bam -f BAM -g 12100000 -n SRX3433220.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433220.05 # format = BAM # ChIP-seq file = ['SRX3433220.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 09:14:03: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:14:03: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:14:03: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:14:03: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:14:03: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:14:03: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:14:09: 1000000 INFO @ Thu, 05 Apr 2018 09:14:09: 1000000 INFO @ Thu, 05 Apr 2018 09:14:09: 1000000 INFO @ Thu, 05 Apr 2018 09:14:15: 2000000 INFO @ Thu, 05 Apr 2018 09:14:15: 2000000 INFO @ Thu, 05 Apr 2018 09:14:15: 2000000 INFO @ Thu, 05 Apr 2018 09:14:21: 3000000 INFO @ Thu, 05 Apr 2018 09:14:21: 3000000 INFO @ Thu, 05 Apr 2018 09:14:21: 3000000 INFO @ Thu, 05 Apr 2018 09:14:27: 4000000 INFO @ Thu, 05 Apr 2018 09:14:27: 4000000 INFO @ Thu, 05 Apr 2018 09:14:28: 4000000 INFO @ Thu, 05 Apr 2018 09:14:33: 5000000 INFO @ Thu, 05 Apr 2018 09:14:33: 5000000 INFO @ Thu, 05 Apr 2018 09:14:34: 5000000 INFO @ Thu, 05 Apr 2018 09:14:40: 6000000 INFO @ Thu, 05 Apr 2018 09:14:40: 6000000 INFO @ Thu, 05 Apr 2018 09:14:40: 6000000 INFO @ Thu, 05 Apr 2018 09:14:46: 7000000 INFO @ Thu, 05 Apr 2018 09:14:46: 7000000 INFO @ Thu, 05 Apr 2018 09:14:46: 7000000 INFO @ Thu, 05 Apr 2018 09:14:48: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:14:48: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:14:48: #1 total tags in treatment: 3373185 INFO @ Thu, 05 Apr 2018 09:14:48: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:14:48: #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 09:14:48: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:14:48: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:14:48: #1 total tags in treatment: 3373185 INFO @ Thu, 05 Apr 2018 09:14:48: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:14:48: #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 09:14:48: #1 tags after filtering in treatment: 2851432 INFO @ Thu, 05 Apr 2018 09:14:48: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 05 Apr 2018 09:14:48: #1 finished! INFO @ Thu, 05 Apr 2018 09:14:48: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:14:48: #1 tags after filtering in treatment: 2851432 INFO @ Thu, 05 Apr 2018 09:14:48: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 05 Apr 2018 09:14:48: #1 finished! INFO @ Thu, 05 Apr 2018 09:14:48: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:14:48: #2 number of paired peaks: 126 WARNING @ Thu, 05 Apr 2018 09:14:48: 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, 05 Apr 2018 09:14:48: start model_add_line... INFO @ Thu, 05 Apr 2018 09:14:48: #2 number of paired peaks: 126 WARNING @ Thu, 05 Apr 2018 09:14:48: 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, 05 Apr 2018 09:14:48: start model_add_line... INFO @ Thu, 05 Apr 2018 09:14:48: start X-correlation... INFO @ Thu, 05 Apr 2018 09:14:48: start X-correlation... INFO @ Thu, 05 Apr 2018 09:14:48: end of X-cor INFO @ Thu, 05 Apr 2018 09:14:48: #2 finished! INFO @ Thu, 05 Apr 2018 09:14:48: #2 predicted fragment length is 86 bps INFO @ Thu, 05 Apr 2018 09:14:48: #2 alternative fragment length(s) may be 3,34,60,86,111 bps INFO @ Thu, 05 Apr 2018 09:14:48: #2.2 Generate R script for model : SRX3433220.05_model.r INFO @ Thu, 05 Apr 2018 09:14:48: end of X-cor INFO @ Thu, 05 Apr 2018 09:14:48: #2 finished! INFO @ Thu, 05 Apr 2018 09:14:48: #2 predicted fragment length is 86 bps INFO @ Thu, 05 Apr 2018 09:14:48: #2 alternative fragment length(s) may be 3,34,60,86,111 bps INFO @ Thu, 05 Apr 2018 09:14:48: #2.2 Generate R script for model : SRX3433220.10_model.r WARNING @ Thu, 05 Apr 2018 09:14:48: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Apr 2018 09:14:48: #2 You may need to consider one of the other alternative d(s): 3,34,60,86,111 WARNING @ Thu, 05 Apr 2018 09:14:48: #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 09:14:48: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:14:48: #3 Pre-compute pvalue-qvalue table... WARNING @ Thu, 05 Apr 2018 09:14:48: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Apr 2018 09:14:48: #2 You may need to consider one of the other alternative d(s): 3,34,60,86,111 WARNING @ Thu, 05 Apr 2018 09:14:48: #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 09:14:48: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:14:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:14:49: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:14:49: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:14:49: #1 total tags in treatment: 3373185 INFO @ Thu, 05 Apr 2018 09:14:49: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:14:49: #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 09:14:49: #1 tags after filtering in treatment: 2851432 INFO @ Thu, 05 Apr 2018 09:14:49: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 05 Apr 2018 09:14:49: #1 finished! INFO @ Thu, 05 Apr 2018 09:14:49: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:14:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:14:49: #2 number of paired peaks: 126 WARNING @ Thu, 05 Apr 2018 09:14:49: 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, 05 Apr 2018 09:14:49: start model_add_line... INFO @ Thu, 05 Apr 2018 09:14:49: start X-correlation... INFO @ Thu, 05 Apr 2018 09:14:49: end of X-cor INFO @ Thu, 05 Apr 2018 09:14:49: #2 finished! INFO @ Thu, 05 Apr 2018 09:14:49: #2 predicted fragment length is 86 bps INFO @ Thu, 05 Apr 2018 09:14:49: #2 alternative fragment length(s) may be 3,34,60,86,111 bps INFO @ Thu, 05 Apr 2018 09:14:49: #2.2 Generate R script for model : SRX3433220.20_model.r WARNING @ Thu, 05 Apr 2018 09:14:49: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Apr 2018 09:14:49: #2 You may need to consider one of the other alternative d(s): 3,34,60,86,111 WARNING @ Thu, 05 Apr 2018 09:14:49: #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 09:14:49: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:14:56: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:14:56: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:14:56: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:14:58: #4 Write output xls file... SRX3433220.10_peaks.xls INFO @ Thu, 05 Apr 2018 09:14:58: #4 Write peak in narrowPeak format file... SRX3433220.10_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:14:58: #4 Write summits bed file... SRX3433220.10_summits.bed INFO @ Thu, 05 Apr 2018 09:14:58: Done! INFO @ Thu, 05 Apr 2018 09:14:58: #4 Write output xls file... SRX3433220.05_peaks.xls pass1 - making usageList (16 chroms): 1 millis INFO @ Thu, 05 Apr 2018 09:14:58: #4 Write peak in narrowPeak format file... SRX3433220.05_peaks.narrowPeak pass2 - checking and writing primary data (554 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 09:14:58: #4 Write summits bed file... SRX3433220.05_summits.bed INFO @ Thu, 05 Apr 2018 09:14:58: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (1052 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 09:14:59: #4 Write output xls file... SRX3433220.20_peaks.xls INFO @ Thu, 05 Apr 2018 09:14:59: #4 Write peak in narrowPeak format file... SRX3433220.20_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:14:59: #4 Write summits bed file... SRX3433220.20_summits.bed INFO @ Thu, 05 Apr 2018 09:14:59: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (204 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。