Job ID = 2590116 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,634,552 reads read : 22,634,552 reads written : 22,634,552 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: 00:04:51 22634552 reads; of these: 22634552 (100.00%) were unpaired; of these: 3509005 (15.50%) aligned 0 times 16087783 (71.08%) aligned exactly 1 time 3037764 (13.42%) aligned >1 times 84.50% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 3758329 / 19125547 = 0.1965 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 20:07:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.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 20:07:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:07:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:07:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.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 20:07:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:07:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:07:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.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 20:07:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:07:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:07:54: 1000000 INFO @ Mon, 12 Aug 2019 20:07:55: 1000000 INFO @ Mon, 12 Aug 2019 20:07:56: 1000000 INFO @ Mon, 12 Aug 2019 20:08:01: 2000000 INFO @ Mon, 12 Aug 2019 20:08:03: 2000000 INFO @ Mon, 12 Aug 2019 20:08:03: 2000000 INFO @ Mon, 12 Aug 2019 20:08:09: 3000000 INFO @ Mon, 12 Aug 2019 20:08:10: 3000000 INFO @ Mon, 12 Aug 2019 20:08:10: 3000000 INFO @ Mon, 12 Aug 2019 20:08:16: 4000000 INFO @ Mon, 12 Aug 2019 20:08:17: 4000000 INFO @ Mon, 12 Aug 2019 20:08:18: 4000000 INFO @ Mon, 12 Aug 2019 20:08:23: 5000000 INFO @ Mon, 12 Aug 2019 20:08:25: 5000000 INFO @ Mon, 12 Aug 2019 20:08:25: 5000000 INFO @ Mon, 12 Aug 2019 20:08:30: 6000000 INFO @ Mon, 12 Aug 2019 20:08:32: 6000000 INFO @ Mon, 12 Aug 2019 20:08:32: 6000000 INFO @ Mon, 12 Aug 2019 20:08:37: 7000000 INFO @ Mon, 12 Aug 2019 20:08:39: 7000000 INFO @ Mon, 12 Aug 2019 20:08:39: 7000000 INFO @ Mon, 12 Aug 2019 20:08:44: 8000000 INFO @ Mon, 12 Aug 2019 20:08:46: 8000000 INFO @ Mon, 12 Aug 2019 20:08:47: 8000000 INFO @ Mon, 12 Aug 2019 20:08:51: 9000000 INFO @ Mon, 12 Aug 2019 20:08:54: 9000000 INFO @ Mon, 12 Aug 2019 20:08:54: 9000000 INFO @ Mon, 12 Aug 2019 20:08:58: 10000000 INFO @ Mon, 12 Aug 2019 20:09:01: 10000000 INFO @ Mon, 12 Aug 2019 20:09:01: 10000000 INFO @ Mon, 12 Aug 2019 20:09:06: 11000000 INFO @ Mon, 12 Aug 2019 20:09:09: 11000000 INFO @ Mon, 12 Aug 2019 20:09:09: 11000000 INFO @ Mon, 12 Aug 2019 20:09:13: 12000000 INFO @ Mon, 12 Aug 2019 20:09:16: 12000000 INFO @ Mon, 12 Aug 2019 20:09:17: 12000000 INFO @ Mon, 12 Aug 2019 20:09:20: 13000000 INFO @ Mon, 12 Aug 2019 20:09:23: 13000000 INFO @ Mon, 12 Aug 2019 20:09:25: 13000000 INFO @ Mon, 12 Aug 2019 20:09:27: 14000000 INFO @ Mon, 12 Aug 2019 20:09:30: 14000000 INFO @ Mon, 12 Aug 2019 20:09:33: 14000000 INFO @ Mon, 12 Aug 2019 20:09:34: 15000000 INFO @ Mon, 12 Aug 2019 20:09:37: 15000000 INFO @ Mon, 12 Aug 2019 20:09:37: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:09:37: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:09:37: #1 total tags in treatment: 15367218 INFO @ Mon, 12 Aug 2019 20:09:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:09:37: #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 20:09:37: #1 tags after filtering in treatment: 15367218 INFO @ Mon, 12 Aug 2019 20:09:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:09:37: #1 finished! INFO @ Mon, 12 Aug 2019 20:09:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:09:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:09:38: #2 number of paired peaks: 260 WARNING @ Mon, 12 Aug 2019 20:09:38: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Mon, 12 Aug 2019 20:09:38: start model_add_line... INFO @ Mon, 12 Aug 2019 20:09:39: start X-correlation... INFO @ Mon, 12 Aug 2019 20:09:39: end of X-cor INFO @ Mon, 12 Aug 2019 20:09:39: #2 finished! INFO @ Mon, 12 Aug 2019 20:09:39: #2 predicted fragment length is 55 bps INFO @ Mon, 12 Aug 2019 20:09:39: #2 alternative fragment length(s) may be 1,55,575 bps INFO @ Mon, 12 Aug 2019 20:09:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.05_model.r WARNING @ Mon, 12 Aug 2019 20:09:39: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:09:39: #2 You may need to consider one of the other alternative d(s): 1,55,575 WARNING @ Mon, 12 Aug 2019 20:09:39: #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 20:09:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:09:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:09:40: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:09:40: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:09:40: #1 total tags in treatment: 15367218 INFO @ Mon, 12 Aug 2019 20:09:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:09:40: #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 20:09:40: #1 tags after filtering in treatment: 15367218 INFO @ Mon, 12 Aug 2019 20:09:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:09:40: #1 finished! INFO @ Mon, 12 Aug 2019 20:09:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:09:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:09:41: 15000000 INFO @ Mon, 12 Aug 2019 20:09:41: #2 number of paired peaks: 260 WARNING @ Mon, 12 Aug 2019 20:09:41: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Mon, 12 Aug 2019 20:09:41: start model_add_line... INFO @ Mon, 12 Aug 2019 20:09:41: start X-correlation... INFO @ Mon, 12 Aug 2019 20:09:41: end of X-cor INFO @ Mon, 12 Aug 2019 20:09:41: #2 finished! INFO @ Mon, 12 Aug 2019 20:09:41: #2 predicted fragment length is 55 bps INFO @ Mon, 12 Aug 2019 20:09:41: #2 alternative fragment length(s) may be 1,55,575 bps INFO @ Mon, 12 Aug 2019 20:09:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.20_model.r WARNING @ Mon, 12 Aug 2019 20:09:41: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:09:41: #2 You may need to consider one of the other alternative d(s): 1,55,575 WARNING @ Mon, 12 Aug 2019 20:09:41: #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 20:09:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:09:44: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:09:44: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:09:44: #1 total tags in treatment: 15367218 INFO @ Mon, 12 Aug 2019 20:09:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:09:44: #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 20:09:44: #1 tags after filtering in treatment: 15367218 INFO @ Mon, 12 Aug 2019 20:09:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:09:44: #1 finished! INFO @ Mon, 12 Aug 2019 20:09:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:09:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:09:45: #2 number of paired peaks: 260 WARNING @ Mon, 12 Aug 2019 20:09:45: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Mon, 12 Aug 2019 20:09:45: start model_add_line... INFO @ Mon, 12 Aug 2019 20:09:45: start X-correlation... INFO @ Mon, 12 Aug 2019 20:09:45: end of X-cor INFO @ Mon, 12 Aug 2019 20:09:45: #2 finished! INFO @ Mon, 12 Aug 2019 20:09:45: #2 predicted fragment length is 55 bps INFO @ Mon, 12 Aug 2019 20:09:45: #2 alternative fragment length(s) may be 1,55,575 bps INFO @ Mon, 12 Aug 2019 20:09:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.10_model.r WARNING @ Mon, 12 Aug 2019 20:09:45: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:09:45: #2 You may need to consider one of the other alternative d(s): 1,55,575 WARNING @ Mon, 12 Aug 2019 20:09:45: #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 20:09:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:09:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:10:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:10:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:10:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:10:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:10:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:10:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.05_summits.bed INFO @ Mon, 12 Aug 2019 20:10:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (696 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:10:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:10:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:10:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.20_summits.bed INFO @ Mon, 12 Aug 2019 20:10:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:10:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:10:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:10:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494998/SRX494998.10_summits.bed INFO @ Mon, 12 Aug 2019 20:10:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (378 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。