Job ID = 2590058 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,695,316 reads read : 15,695,316 reads written : 15,695,316 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:03:50 15695316 reads; of these: 15695316 (100.00%) were unpaired; of these: 1827103 (11.64%) aligned 0 times 11334925 (72.22%) aligned exactly 1 time 2533288 (16.14%) aligned >1 times 88.36% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1281641 / 13868213 = 0.0924 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 @ Mon, 12 Aug 2019 19:30:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 19:30:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:30:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:31:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 19:31:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:31:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:31:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 19:31:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:31:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:31:08: 1000000 INFO @ Mon, 12 Aug 2019 19:31:10: 1000000 INFO @ Mon, 12 Aug 2019 19:31:11: 1000000 INFO @ Mon, 12 Aug 2019 19:31:16: 2000000 INFO @ Mon, 12 Aug 2019 19:31:20: 2000000 INFO @ Mon, 12 Aug 2019 19:31:21: 2000000 INFO @ Mon, 12 Aug 2019 19:31:24: 3000000 INFO @ Mon, 12 Aug 2019 19:31:30: 3000000 INFO @ Mon, 12 Aug 2019 19:31:31: 3000000 INFO @ Mon, 12 Aug 2019 19:31:31: 4000000 INFO @ Mon, 12 Aug 2019 19:31:40: 4000000 INFO @ Mon, 12 Aug 2019 19:31:40: 4000000 INFO @ Mon, 12 Aug 2019 19:31:40: 5000000 INFO @ Mon, 12 Aug 2019 19:31:48: 6000000 INFO @ Mon, 12 Aug 2019 19:31:50: 5000000 INFO @ Mon, 12 Aug 2019 19:31:50: 5000000 INFO @ Mon, 12 Aug 2019 19:31:56: 7000000 INFO @ Mon, 12 Aug 2019 19:32:00: 6000000 INFO @ Mon, 12 Aug 2019 19:32:00: 6000000 INFO @ Mon, 12 Aug 2019 19:32:03: 8000000 INFO @ Mon, 12 Aug 2019 19:32:09: 7000000 INFO @ Mon, 12 Aug 2019 19:32:10: 7000000 INFO @ Mon, 12 Aug 2019 19:32:11: 9000000 INFO @ Mon, 12 Aug 2019 19:32:19: 10000000 INFO @ Mon, 12 Aug 2019 19:32:19: 8000000 INFO @ Mon, 12 Aug 2019 19:32:20: 8000000 INFO @ Mon, 12 Aug 2019 19:32:26: 11000000 INFO @ Mon, 12 Aug 2019 19:32:28: 9000000 INFO @ Mon, 12 Aug 2019 19:32:30: 9000000 INFO @ Mon, 12 Aug 2019 19:32:34: 12000000 INFO @ Mon, 12 Aug 2019 19:32:38: 10000000 INFO @ Mon, 12 Aug 2019 19:32:39: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:32:39: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:32:39: #1 total tags in treatment: 12586572 INFO @ Mon, 12 Aug 2019 19:32:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:32:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:32:39: #1 tags after filtering in treatment: 12586572 INFO @ Mon, 12 Aug 2019 19:32:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:32:39: #1 finished! INFO @ Mon, 12 Aug 2019 19:32:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:32:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:32:40: 10000000 INFO @ Mon, 12 Aug 2019 19:32:40: #2 number of paired peaks: 351 WARNING @ Mon, 12 Aug 2019 19:32:40: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Mon, 12 Aug 2019 19:32:40: start model_add_line... INFO @ Mon, 12 Aug 2019 19:32:40: start X-correlation... INFO @ Mon, 12 Aug 2019 19:32:40: end of X-cor INFO @ Mon, 12 Aug 2019 19:32:40: #2 finished! INFO @ Mon, 12 Aug 2019 19:32:40: #2 predicted fragment length is 44 bps INFO @ Mon, 12 Aug 2019 19:32:40: #2 alternative fragment length(s) may be 2,44 bps INFO @ Mon, 12 Aug 2019 19:32:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.10_model.r WARNING @ Mon, 12 Aug 2019 19:32:40: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:32:40: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Mon, 12 Aug 2019 19:32:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:32:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:32:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:32:47: 11000000 INFO @ Mon, 12 Aug 2019 19:32:50: 11000000 INFO @ Mon, 12 Aug 2019 19:32:57: 12000000 INFO @ Mon, 12 Aug 2019 19:33:00: 12000000 INFO @ Mon, 12 Aug 2019 19:33:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:33:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:33:02: #1 total tags in treatment: 12586572 INFO @ Mon, 12 Aug 2019 19:33:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:33:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:33:03: #1 tags after filtering in treatment: 12586572 INFO @ Mon, 12 Aug 2019 19:33:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:33:03: #1 finished! INFO @ Mon, 12 Aug 2019 19:33:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:33:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:33:04: #2 number of paired peaks: 351 WARNING @ Mon, 12 Aug 2019 19:33:04: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Mon, 12 Aug 2019 19:33:04: start model_add_line... INFO @ Mon, 12 Aug 2019 19:33:04: start X-correlation... INFO @ Mon, 12 Aug 2019 19:33:04: end of X-cor INFO @ Mon, 12 Aug 2019 19:33:04: #2 finished! INFO @ Mon, 12 Aug 2019 19:33:04: #2 predicted fragment length is 44 bps INFO @ Mon, 12 Aug 2019 19:33:04: #2 alternative fragment length(s) may be 2,44 bps INFO @ Mon, 12 Aug 2019 19:33:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.20_model.r WARNING @ Mon, 12 Aug 2019 19:33:04: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:33:04: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Mon, 12 Aug 2019 19:33:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:33:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:33:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:33:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:33:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:33:05: #1 total tags in treatment: 12586572 INFO @ Mon, 12 Aug 2019 19:33:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:33:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:33:05: #1 tags after filtering in treatment: 12586572 INFO @ Mon, 12 Aug 2019 19:33:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:33:05: #1 finished! INFO @ Mon, 12 Aug 2019 19:33:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:33:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:33:07: #2 number of paired peaks: 351 WARNING @ Mon, 12 Aug 2019 19:33:07: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Mon, 12 Aug 2019 19:33:07: start model_add_line... INFO @ Mon, 12 Aug 2019 19:33:07: start X-correlation... INFO @ Mon, 12 Aug 2019 19:33:07: end of X-cor INFO @ Mon, 12 Aug 2019 19:33:07: #2 finished! INFO @ Mon, 12 Aug 2019 19:33:07: #2 predicted fragment length is 44 bps INFO @ Mon, 12 Aug 2019 19:33:07: #2 alternative fragment length(s) may be 2,44 bps INFO @ Mon, 12 Aug 2019 19:33:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.05_model.r WARNING @ Mon, 12 Aug 2019 19:33:07: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:33:07: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Mon, 12 Aug 2019 19:33:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:33:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:33:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:33:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:33:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:33:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:33:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.10_summits.bed INFO @ Mon, 12 Aug 2019 19:33:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (472 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:33:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:33:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.20_summits.bed INFO @ Mon, 12 Aug 2019 19:33:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:33:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:33:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:33:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494902/SRX494902.05_summits.bed INFO @ Mon, 12 Aug 2019 19:33:56: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (668 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。