Job ID = 1295402 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,141,145 reads read : 19,141,145 reads written : 19,141,145 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: 00:04:44 19141145 reads; of these: 19141145 (100.00%) were unpaired; of these: 2467812 (12.89%) aligned 0 times 14881780 (77.75%) aligned exactly 1 time 1791553 (9.36%) aligned >1 times 87.11% overall alignment rate Time searching: 00:04:44 Overall time: 00:04:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2975670 / 16673333 = 0.1785 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, 03 Jun 2019 13:46:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 13:46:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:46:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:46:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 13:46:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:46:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:46:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 13:46:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:46:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:47:04: 1000000 INFO @ Mon, 03 Jun 2019 13:47:04: 1000000 INFO @ Mon, 03 Jun 2019 13:47:04: 1000000 INFO @ Mon, 03 Jun 2019 13:47:12: 2000000 INFO @ Mon, 03 Jun 2019 13:47:12: 2000000 INFO @ Mon, 03 Jun 2019 13:47:12: 2000000 INFO @ Mon, 03 Jun 2019 13:47:19: 3000000 INFO @ Mon, 03 Jun 2019 13:47:20: 3000000 INFO @ Mon, 03 Jun 2019 13:47:21: 3000000 INFO @ Mon, 03 Jun 2019 13:47:27: 4000000 INFO @ Mon, 03 Jun 2019 13:47:28: 4000000 INFO @ Mon, 03 Jun 2019 13:47:28: 4000000 INFO @ Mon, 03 Jun 2019 13:47:35: 5000000 INFO @ Mon, 03 Jun 2019 13:47:36: 5000000 INFO @ Mon, 03 Jun 2019 13:47:36: 5000000 INFO @ Mon, 03 Jun 2019 13:47:43: 6000000 INFO @ Mon, 03 Jun 2019 13:47:44: 6000000 INFO @ Mon, 03 Jun 2019 13:47:44: 6000000 INFO @ Mon, 03 Jun 2019 13:47:50: 7000000 INFO @ Mon, 03 Jun 2019 13:47:51: 7000000 INFO @ Mon, 03 Jun 2019 13:47:52: 7000000 INFO @ Mon, 03 Jun 2019 13:47:58: 8000000 INFO @ Mon, 03 Jun 2019 13:48:00: 8000000 INFO @ Mon, 03 Jun 2019 13:48:00: 8000000 INFO @ Mon, 03 Jun 2019 13:48:06: 9000000 INFO @ Mon, 03 Jun 2019 13:48:08: 9000000 INFO @ Mon, 03 Jun 2019 13:48:08: 9000000 INFO @ Mon, 03 Jun 2019 13:48:14: 10000000 INFO @ Mon, 03 Jun 2019 13:48:16: 10000000 INFO @ Mon, 03 Jun 2019 13:48:16: 10000000 INFO @ Mon, 03 Jun 2019 13:48:22: 11000000 INFO @ Mon, 03 Jun 2019 13:48:24: 11000000 INFO @ Mon, 03 Jun 2019 13:48:24: 11000000 INFO @ Mon, 03 Jun 2019 13:48:30: 12000000 INFO @ Mon, 03 Jun 2019 13:48:32: 12000000 INFO @ Mon, 03 Jun 2019 13:48:32: 12000000 INFO @ Mon, 03 Jun 2019 13:48:37: 13000000 INFO @ Mon, 03 Jun 2019 13:48:40: 13000000 INFO @ Mon, 03 Jun 2019 13:48:40: 13000000 INFO @ Mon, 03 Jun 2019 13:48:43: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 13:48:43: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 13:48:43: #1 total tags in treatment: 13697663 INFO @ Mon, 03 Jun 2019 13:48:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:48:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:48:43: #1 tags after filtering in treatment: 13697663 INFO @ Mon, 03 Jun 2019 13:48:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:48:43: #1 finished! INFO @ Mon, 03 Jun 2019 13:48:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:48:44: #2 number of paired peaks: 104 WARNING @ Mon, 03 Jun 2019 13:48:44: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Mon, 03 Jun 2019 13:48:44: start model_add_line... INFO @ Mon, 03 Jun 2019 13:48:44: start X-correlation... INFO @ Mon, 03 Jun 2019 13:48:44: end of X-cor INFO @ Mon, 03 Jun 2019 13:48:44: #2 finished! INFO @ Mon, 03 Jun 2019 13:48:44: #2 predicted fragment length is 4 bps INFO @ Mon, 03 Jun 2019 13:48:44: #2 alternative fragment length(s) may be 4,7,36,67,541 bps INFO @ Mon, 03 Jun 2019 13:48:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.20_model.r WARNING @ Mon, 03 Jun 2019 13:48:44: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:48:44: #2 You may need to consider one of the other alternative d(s): 4,7,36,67,541 WARNING @ Mon, 03 Jun 2019 13:48:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 13:48:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:48:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:48:45: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 13:48:45: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 13:48:45: #1 total tags in treatment: 13697663 INFO @ Mon, 03 Jun 2019 13:48:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:48:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:48:46: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 13:48:46: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 13:48:46: #1 total tags in treatment: 13697663 INFO @ Mon, 03 Jun 2019 13:48:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:48:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:48:46: #1 tags after filtering in treatment: 13697663 INFO @ Mon, 03 Jun 2019 13:48:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:48:46: #1 finished! INFO @ Mon, 03 Jun 2019 13:48:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:48:46: #1 tags after filtering in treatment: 13697663 INFO @ Mon, 03 Jun 2019 13:48:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:48:46: #1 finished! INFO @ Mon, 03 Jun 2019 13:48:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:48:47: #2 number of paired peaks: 104 WARNING @ Mon, 03 Jun 2019 13:48:47: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Mon, 03 Jun 2019 13:48:47: start model_add_line... INFO @ Mon, 03 Jun 2019 13:48:47: start X-correlation... INFO @ Mon, 03 Jun 2019 13:48:47: end of X-cor INFO @ Mon, 03 Jun 2019 13:48:47: #2 finished! INFO @ Mon, 03 Jun 2019 13:48:47: #2 predicted fragment length is 4 bps INFO @ Mon, 03 Jun 2019 13:48:47: #2 alternative fragment length(s) may be 4,7,36,67,541 bps INFO @ Mon, 03 Jun 2019 13:48:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.05_model.r WARNING @ Mon, 03 Jun 2019 13:48:47: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:48:47: #2 You may need to consider one of the other alternative d(s): 4,7,36,67,541 WARNING @ Mon, 03 Jun 2019 13:48:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 13:48:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:48:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:48:47: #2 number of paired peaks: 104 WARNING @ Mon, 03 Jun 2019 13:48:47: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Mon, 03 Jun 2019 13:48:47: start model_add_line... INFO @ Mon, 03 Jun 2019 13:48:47: start X-correlation... INFO @ Mon, 03 Jun 2019 13:48:47: end of X-cor INFO @ Mon, 03 Jun 2019 13:48:47: #2 finished! INFO @ Mon, 03 Jun 2019 13:48:47: #2 predicted fragment length is 4 bps INFO @ Mon, 03 Jun 2019 13:48:47: #2 alternative fragment length(s) may be 4,7,36,67,541 bps INFO @ Mon, 03 Jun 2019 13:48:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.10_model.r WARNING @ Mon, 03 Jun 2019 13:48:47: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:48:47: #2 You may need to consider one of the other alternative d(s): 4,7,36,67,541 WARNING @ Mon, 03 Jun 2019 13:48:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 13:48:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:48:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:49:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:49:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:49:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:49:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:49:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:49:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.20_summits.bed INFO @ Mon, 03 Jun 2019 13:49:37: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:49:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:49:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:49:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.05_summits.bed INFO @ Mon, 03 Jun 2019 13:49:40: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:49:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:49:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:49:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX336279/SRX336279.10_summits.bed INFO @ Mon, 03 Jun 2019 13:49:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。