Job ID = 1292337 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,854,814 reads read : 18,854,814 reads written : 18,854,814 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:03:54 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 289130 (1.53%) aligned 0 times 14953773 (79.31%) aligned exactly 1 time 3611911 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 3522239 / 18565684 = 0.1897 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 18:01:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.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 18:01:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.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 18:01:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.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 18:01:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:02:05: 1000000 INFO @ Sun, 02 Jun 2019 18:02:06: 1000000 INFO @ Sun, 02 Jun 2019 18:02:06: 1000000 INFO @ Sun, 02 Jun 2019 18:02:13: 2000000 INFO @ Sun, 02 Jun 2019 18:02:13: 2000000 INFO @ Sun, 02 Jun 2019 18:02:13: 2000000 INFO @ Sun, 02 Jun 2019 18:02:20: 3000000 INFO @ Sun, 02 Jun 2019 18:02:20: 3000000 INFO @ Sun, 02 Jun 2019 18:02:21: 3000000 INFO @ Sun, 02 Jun 2019 18:02:27: 4000000 INFO @ Sun, 02 Jun 2019 18:02:28: 4000000 INFO @ Sun, 02 Jun 2019 18:02:28: 4000000 INFO @ Sun, 02 Jun 2019 18:02:33: 5000000 INFO @ Sun, 02 Jun 2019 18:02:34: 5000000 INFO @ Sun, 02 Jun 2019 18:02:35: 5000000 INFO @ Sun, 02 Jun 2019 18:02:40: 6000000 INFO @ Sun, 02 Jun 2019 18:02:41: 6000000 INFO @ Sun, 02 Jun 2019 18:02:42: 6000000 INFO @ Sun, 02 Jun 2019 18:02:47: 7000000 INFO @ Sun, 02 Jun 2019 18:02:48: 7000000 INFO @ Sun, 02 Jun 2019 18:02:49: 7000000 INFO @ Sun, 02 Jun 2019 18:02:54: 8000000 INFO @ Sun, 02 Jun 2019 18:02:55: 8000000 INFO @ Sun, 02 Jun 2019 18:02:56: 8000000 INFO @ Sun, 02 Jun 2019 18:03:00: 9000000 INFO @ Sun, 02 Jun 2019 18:03:02: 9000000 INFO @ Sun, 02 Jun 2019 18:03:03: 9000000 INFO @ Sun, 02 Jun 2019 18:03:07: 10000000 INFO @ Sun, 02 Jun 2019 18:03:09: 10000000 INFO @ Sun, 02 Jun 2019 18:03:10: 10000000 INFO @ Sun, 02 Jun 2019 18:03:14: 11000000 INFO @ Sun, 02 Jun 2019 18:03:15: 11000000 INFO @ Sun, 02 Jun 2019 18:03:16: 11000000 INFO @ Sun, 02 Jun 2019 18:03:20: 12000000 INFO @ Sun, 02 Jun 2019 18:03:22: 12000000 INFO @ Sun, 02 Jun 2019 18:03:23: 12000000 INFO @ Sun, 02 Jun 2019 18:03:27: 13000000 INFO @ Sun, 02 Jun 2019 18:03:29: 13000000 INFO @ Sun, 02 Jun 2019 18:03:30: 13000000 INFO @ Sun, 02 Jun 2019 18:03:34: 14000000 INFO @ Sun, 02 Jun 2019 18:03:36: 14000000 INFO @ Sun, 02 Jun 2019 18:03:37: 14000000 INFO @ Sun, 02 Jun 2019 18:03:40: 15000000 INFO @ Sun, 02 Jun 2019 18:03:41: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:03:41: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:03:41: #1 total tags in treatment: 15043445 INFO @ Sun, 02 Jun 2019 18:03:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:03:41: #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 18:03:41: #1 tags after filtering in treatment: 15043445 INFO @ Sun, 02 Jun 2019 18:03:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:03:41: #1 finished! INFO @ Sun, 02 Jun 2019 18:03:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:03:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:03:42: 15000000 INFO @ Sun, 02 Jun 2019 18:03:42: #2 number of paired peaks: 438 WARNING @ Sun, 02 Jun 2019 18:03:42: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sun, 02 Jun 2019 18:03:42: start model_add_line... INFO @ Sun, 02 Jun 2019 18:03:43: start X-correlation... INFO @ Sun, 02 Jun 2019 18:03:43: end of X-cor INFO @ Sun, 02 Jun 2019 18:03:43: #2 finished! INFO @ Sun, 02 Jun 2019 18:03:43: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 18:03:43: #2 alternative fragment length(s) may be 2,45 bps INFO @ Sun, 02 Jun 2019 18:03:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.20_model.r WARNING @ Sun, 02 Jun 2019 18:03:43: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:03:43: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Sun, 02 Jun 2019 18:03:43: #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 18:03:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:03:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:03:43: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:03:43: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:03:43: #1 total tags in treatment: 15043445 INFO @ Sun, 02 Jun 2019 18:03:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:03:43: #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 18:03:43: #1 tags after filtering in treatment: 15043445 INFO @ Sun, 02 Jun 2019 18:03:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:03:43: #1 finished! INFO @ Sun, 02 Jun 2019 18:03:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:03:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:03:44: 15000000 INFO @ Sun, 02 Jun 2019 18:03:44: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:03:44: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:03:44: #1 total tags in treatment: 15043445 INFO @ Sun, 02 Jun 2019 18:03:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:03:44: #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 18:03:44: #1 tags after filtering in treatment: 15043445 INFO @ Sun, 02 Jun 2019 18:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:03:44: #1 finished! INFO @ Sun, 02 Jun 2019 18:03:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:03:44: #2 number of paired peaks: 438 WARNING @ Sun, 02 Jun 2019 18:03:44: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sun, 02 Jun 2019 18:03:44: start model_add_line... INFO @ Sun, 02 Jun 2019 18:03:45: start X-correlation... INFO @ Sun, 02 Jun 2019 18:03:45: end of X-cor INFO @ Sun, 02 Jun 2019 18:03:45: #2 finished! INFO @ Sun, 02 Jun 2019 18:03:45: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 18:03:45: #2 alternative fragment length(s) may be 2,45 bps INFO @ Sun, 02 Jun 2019 18:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.05_model.r WARNING @ Sun, 02 Jun 2019 18:03:45: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:03:45: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Sun, 02 Jun 2019 18:03:45: #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 18:03:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:03:46: #2 number of paired peaks: 438 WARNING @ Sun, 02 Jun 2019 18:03:46: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sun, 02 Jun 2019 18:03:46: start model_add_line... INFO @ Sun, 02 Jun 2019 18:03:46: start X-correlation... INFO @ Sun, 02 Jun 2019 18:03:46: end of X-cor INFO @ Sun, 02 Jun 2019 18:03:46: #2 finished! INFO @ Sun, 02 Jun 2019 18:03:46: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 18:03:46: #2 alternative fragment length(s) may be 2,45 bps INFO @ Sun, 02 Jun 2019 18:03:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.10_model.r WARNING @ Sun, 02 Jun 2019 18:03:46: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:03:46: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Sun, 02 Jun 2019 18:03:46: #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 18:03:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:03:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:04:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:04:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:04:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:04:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:04:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:04:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.20_summits.bed INFO @ Sun, 02 Jun 2019 18:04:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (274 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:04:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:04:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:04:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.05_summits.bed INFO @ Sun, 02 Jun 2019 18:04:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3840 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331361/SRX331361.10_summits.bed INFO @ Sun, 02 Jun 2019 18:04:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (921 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。