Job ID = 1291872 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,873,433 reads read : 7,873,433 reads written : 7,873,433 spots read : 10,198,100 reads read : 10,198,100 reads written : 10,198,100 rm: cannot remove ‘fastqDump_tmp*’: 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: 00:04:33 18071533 reads; of these: 18071533 (100.00%) were unpaired; of these: 379834 (2.10%) aligned 0 times 14716338 (81.43%) aligned exactly 1 time 2975361 (16.46%) aligned >1 times 97.90% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 1802533 / 17691699 = 0.1019 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, 02 Jun 2019 17:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.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 @ Sun, 02 Jun 2019 17:08:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:08:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.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 @ Sun, 02 Jun 2019 17:08:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:08:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.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 @ Sun, 02 Jun 2019 17:08:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:08:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:08:08: 1000000 INFO @ Sun, 02 Jun 2019 17:08:08: 1000000 INFO @ Sun, 02 Jun 2019 17:08:09: 1000000 INFO @ Sun, 02 Jun 2019 17:08:15: 2000000 INFO @ Sun, 02 Jun 2019 17:08:15: 2000000 INFO @ Sun, 02 Jun 2019 17:08:17: 2000000 INFO @ Sun, 02 Jun 2019 17:08:23: 3000000 INFO @ Sun, 02 Jun 2019 17:08:23: 3000000 INFO @ Sun, 02 Jun 2019 17:08:25: 3000000 INFO @ Sun, 02 Jun 2019 17:08:30: 4000000 INFO @ Sun, 02 Jun 2019 17:08:30: 4000000 INFO @ Sun, 02 Jun 2019 17:08:33: 4000000 INFO @ Sun, 02 Jun 2019 17:08:37: 5000000 INFO @ Sun, 02 Jun 2019 17:08:37: 5000000 INFO @ Sun, 02 Jun 2019 17:08:42: 5000000 INFO @ Sun, 02 Jun 2019 17:08:45: 6000000 INFO @ Sun, 02 Jun 2019 17:08:45: 6000000 INFO @ Sun, 02 Jun 2019 17:08:50: 6000000 INFO @ Sun, 02 Jun 2019 17:08:52: 7000000 INFO @ Sun, 02 Jun 2019 17:08:52: 7000000 INFO @ Sun, 02 Jun 2019 17:08:58: 7000000 INFO @ Sun, 02 Jun 2019 17:08:59: 8000000 INFO @ Sun, 02 Jun 2019 17:09:00: 8000000 INFO @ Sun, 02 Jun 2019 17:09:06: 8000000 INFO @ Sun, 02 Jun 2019 17:09:07: 9000000 INFO @ Sun, 02 Jun 2019 17:09:07: 9000000 INFO @ Sun, 02 Jun 2019 17:09:14: 10000000 INFO @ Sun, 02 Jun 2019 17:09:14: 10000000 INFO @ Sun, 02 Jun 2019 17:09:15: 9000000 INFO @ Sun, 02 Jun 2019 17:09:21: 11000000 INFO @ Sun, 02 Jun 2019 17:09:22: 11000000 INFO @ Sun, 02 Jun 2019 17:09:23: 10000000 INFO @ Sun, 02 Jun 2019 17:09:28: 12000000 INFO @ Sun, 02 Jun 2019 17:09:29: 12000000 INFO @ Sun, 02 Jun 2019 17:09:31: 11000000 INFO @ Sun, 02 Jun 2019 17:09:36: 13000000 INFO @ Sun, 02 Jun 2019 17:09:36: 13000000 INFO @ Sun, 02 Jun 2019 17:09:40: 12000000 INFO @ Sun, 02 Jun 2019 17:09:43: 14000000 INFO @ Sun, 02 Jun 2019 17:09:43: 14000000 INFO @ Sun, 02 Jun 2019 17:09:48: 13000000 INFO @ Sun, 02 Jun 2019 17:09:50: 15000000 INFO @ Sun, 02 Jun 2019 17:09:50: 15000000 INFO @ Sun, 02 Jun 2019 17:09:56: 14000000 INFO @ Sun, 02 Jun 2019 17:09:56: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:09:56: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:09:56: #1 total tags in treatment: 15889166 INFO @ Sun, 02 Jun 2019 17:09:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:09:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:09:57: #1 tags after filtering in treatment: 15889166 INFO @ Sun, 02 Jun 2019 17:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:09:57: #1 finished! INFO @ Sun, 02 Jun 2019 17:09:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:09:57: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:09:57: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:09:57: #1 total tags in treatment: 15889166 INFO @ Sun, 02 Jun 2019 17:09:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:09:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:09:57: #1 tags after filtering in treatment: 15889166 INFO @ Sun, 02 Jun 2019 17:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:09:57: #1 finished! INFO @ Sun, 02 Jun 2019 17:09:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:09:58: #2 number of paired peaks: 276 WARNING @ Sun, 02 Jun 2019 17:09:58: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 02 Jun 2019 17:09:58: start model_add_line... INFO @ Sun, 02 Jun 2019 17:09:58: start X-correlation... INFO @ Sun, 02 Jun 2019 17:09:58: end of X-cor INFO @ Sun, 02 Jun 2019 17:09:58: #2 finished! INFO @ Sun, 02 Jun 2019 17:09:58: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 17:09:58: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sun, 02 Jun 2019 17:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.05_model.r WARNING @ Sun, 02 Jun 2019 17:09:58: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:09:58: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sun, 02 Jun 2019 17:09:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:09:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:09:59: #2 number of paired peaks: 276 WARNING @ Sun, 02 Jun 2019 17:09:59: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 02 Jun 2019 17:09:59: start model_add_line... INFO @ Sun, 02 Jun 2019 17:09:59: start X-correlation... INFO @ Sun, 02 Jun 2019 17:09:59: end of X-cor INFO @ Sun, 02 Jun 2019 17:09:59: #2 finished! INFO @ Sun, 02 Jun 2019 17:09:59: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 17:09:59: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sun, 02 Jun 2019 17:09:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.10_model.r WARNING @ Sun, 02 Jun 2019 17:09:59: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:09:59: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sun, 02 Jun 2019 17:09:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:09:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:10:04: 15000000 INFO @ Sun, 02 Jun 2019 17:10:11: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:10:11: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:10:11: #1 total tags in treatment: 15889166 INFO @ Sun, 02 Jun 2019 17:10:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:10:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:10:11: #1 tags after filtering in treatment: 15889166 INFO @ Sun, 02 Jun 2019 17:10:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:10:11: #1 finished! INFO @ Sun, 02 Jun 2019 17:10:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:10:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:10:13: #2 number of paired peaks: 276 WARNING @ Sun, 02 Jun 2019 17:10:13: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 02 Jun 2019 17:10:13: start model_add_line... INFO @ Sun, 02 Jun 2019 17:10:13: start X-correlation... INFO @ Sun, 02 Jun 2019 17:10:13: end of X-cor INFO @ Sun, 02 Jun 2019 17:10:13: #2 finished! INFO @ Sun, 02 Jun 2019 17:10:13: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 17:10:13: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sun, 02 Jun 2019 17:10:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.20_model.r WARNING @ Sun, 02 Jun 2019 17:10:13: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:10:13: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sun, 02 Jun 2019 17:10:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:10:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:10:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:10:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:10:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:10:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:10:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:10:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.05_summits.bed INFO @ Sun, 02 Jun 2019 17:10:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (710 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:10:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:10:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:10:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.10_summits.bed INFO @ Sun, 02 Jun 2019 17:10:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (466 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:11:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:11:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:11:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257707/SRX257707.20_summits.bed INFO @ Sun, 02 Jun 2019 17:11:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (191 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。