Job ID = 9037702 sra ファイルのダウンロード中... Completed: 145487K bytes transferred in 4 seconds (260810K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 12695 0 12695 0 0 1711 0 --:--:-- 0:00:07 --:--:-- 12594 100 33902 0 33902 0 0 4111 0 --:--:-- 0:00:08 --:--:-- 18435 100 45323 0 45323 0 0 5283 0 --:--:-- 0:00:08 --:--:-- 20876 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 6628918 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977493/SRR1951339.sra Written 6628918 spots total 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: 00:00:46 6628918 reads; of these: 6628918 (100.00%) were unpaired; of these: 2116553 (31.93%) aligned 0 times 3684224 (55.58%) aligned exactly 1 time 828141 (12.49%) aligned >1 times 68.07% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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_rmdupse_core] 4437261 / 4512365 = 0.9834 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 @ Sun, 04 Jun 2017 05:11:57: # Command line: callpeak -t SRX977493.bam -f BAM -g 12100000 -n SRX977493.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977493.05 # format = BAM # ChIP-seq file = ['SRX977493.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 INFO @ Sun, 04 Jun 2017 05:11:57: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:11:57: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:11:57: # Command line: callpeak -t SRX977493.bam -f BAM -g 12100000 -n SRX977493.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977493.20 # format = BAM # ChIP-seq file = ['SRX977493.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 INFO @ Sun, 04 Jun 2017 05:11:57: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:11:57: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:11:57: # Command line: callpeak -t SRX977493.bam -f BAM -g 12100000 -n SRX977493.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977493.10 # format = BAM # ChIP-seq file = ['SRX977493.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 INFO @ Sun, 04 Jun 2017 05:11:57: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:11:57: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:11:57: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:11:57: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:11:57: #1 total tags in treatment: 75104 INFO @ Sun, 04 Jun 2017 05:11:57: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:11:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 05:11:57: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:11:57: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:11:57: #1 total tags in treatment: 75104 INFO @ Sun, 04 Jun 2017 05:11:57: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:11:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 05:11:57: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:11:57: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:11:57: #1 total tags in treatment: 75104 INFO @ Sun, 04 Jun 2017 05:11:57: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:11:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 05:11:57: #1 tags after filtering in treatment: 74936 INFO @ Sun, 04 Jun 2017 05:11:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:11:57: #1 finished! INFO @ Sun, 04 Jun 2017 05:11:57: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:11:57: #1 tags after filtering in treatment: 74936 INFO @ Sun, 04 Jun 2017 05:11:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:11:57: #1 finished! INFO @ Sun, 04 Jun 2017 05:11:57: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:11:57: #1 tags after filtering in treatment: 74936 INFO @ Sun, 04 Jun 2017 05:11:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:11:57: #1 finished! INFO @ Sun, 04 Jun 2017 05:11:57: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:11:57: #2 number of paired peaks: 387 WARNING @ Sun, 04 Jun 2017 05:11:57: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Sun, 04 Jun 2017 05:11:57: start model_add_line... INFO @ Sun, 04 Jun 2017 05:11:57: #2 number of paired peaks: 387 WARNING @ Sun, 04 Jun 2017 05:11:57: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Sun, 04 Jun 2017 05:11:57: start model_add_line... INFO @ Sun, 04 Jun 2017 05:11:57: #2 number of paired peaks: 387 WARNING @ Sun, 04 Jun 2017 05:11:57: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Sun, 04 Jun 2017 05:11:57: start model_add_line... INFO @ Sun, 04 Jun 2017 05:11:58: start X-correlation... INFO @ Sun, 04 Jun 2017 05:11:58: start X-correlation... INFO @ Sun, 04 Jun 2017 05:11:58: end of X-cor INFO @ Sun, 04 Jun 2017 05:11:58: end of X-cor INFO @ Sun, 04 Jun 2017 05:11:58: #2 finished! INFO @ Sun, 04 Jun 2017 05:11:58: #2 finished! INFO @ Sun, 04 Jun 2017 05:11:58: #2 predicted fragment length is 40 bps INFO @ Sun, 04 Jun 2017 05:11:58: #2 predicted fragment length is 40 bps INFO @ Sun, 04 Jun 2017 05:11:58: #2 alternative fragment length(s) may be 21,40,65,105,144,174,213,231,254,279,379,403,434,482,509,534,554 bps INFO @ Sun, 04 Jun 2017 05:11:58: #2 alternative fragment length(s) may be 21,40,65,105,144,174,213,231,254,279,379,403,434,482,509,534,554 bps INFO @ Sun, 04 Jun 2017 05:11:58: #2.2 Generate R script for model : SRX977493.10_model.r INFO @ Sun, 04 Jun 2017 05:11:58: #2.2 Generate R script for model : SRX977493.20_model.r INFO @ Sun, 04 Jun 2017 05:11:58: start X-correlation... INFO @ Sun, 04 Jun 2017 05:11:58: end of X-cor INFO @ Sun, 04 Jun 2017 05:11:58: #2 finished! INFO @ Sun, 04 Jun 2017 05:11:58: #2 predicted fragment length is 40 bps INFO @ Sun, 04 Jun 2017 05:11:58: #2 alternative fragment length(s) may be 21,40,65,105,144,174,213,231,254,279,379,403,434,482,509,534,554 bps INFO @ Sun, 04 Jun 2017 05:11:58: #2.2 Generate R script for model : SRX977493.05_model.r WARNING @ Sun, 04 Jun 2017 05:11:58: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:11:58: #2 You may need to consider one of the other alternative d(s): 21,40,65,105,144,174,213,231,254,279,379,403,434,482,509,534,554 WARNING @ Sun, 04 Jun 2017 05:11:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 05:11:58: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:11:58: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 05:11:58: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:11:58: #2 You may need to consider one of the other alternative d(s): 21,40,65,105,144,174,213,231,254,279,379,403,434,482,509,534,554 WARNING @ Sun, 04 Jun 2017 05:11:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 05:11:58: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:11:58: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 05:11:58: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:11:58: #2 You may need to consider one of the other alternative d(s): 21,40,65,105,144,174,213,231,254,279,379,403,434,482,509,534,554 WARNING @ Sun, 04 Jun 2017 05:11:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 05:11:58: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:11:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:11:58: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:11:58: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:11:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 05:11:59: #4 Write output xls file... SRX977493.05_peaks.xls INFO @ Sun, 04 Jun 2017 05:11:59: #4 Write peak in narrowPeak format file... SRX977493.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:11:59: #4 Write summits bed file... SRX977493.05_summits.bed INFO @ Sun, 04 Jun 2017 05:11:59: Done! BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 05:11:59: #4 Write output xls file... SRX977493.20_peaks.xls INFO @ Sun, 04 Jun 2017 05:11:59: #4 Write peak in narrowPeak format file... SRX977493.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:11:59: #4 Write summits bed file... SRX977493.20_summits.bed INFO @ Sun, 04 Jun 2017 05:11:59: Done! pass1 - making usageList (15 chroms): 0 millis INFO @ Sun, 04 Jun 2017 05:11:59: #4 Write output xls file... SRX977493.10_peaks.xls pass2 - checking and writing primary data (40 records, 4 fields): 2 millis INFO @ Sun, 04 Jun 2017 05:11:59: #4 Write peak in narrowPeak format file... SRX977493.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:11:59: #4 Write summits bed file... SRX977493.10_summits.bed INFO @ Sun, 04 Jun 2017 05:11:59: Done! CompletedMACS2peakCalling pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (25 records, 4 fields): 2 millis CompletedMACS2peakCalling