Job ID = 1292417 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,136,892 reads read : 12,273,784 reads written : 6,136,892 reads 0-length : 6,136,892 spots read : 6,000,543 reads read : 12,001,086 reads written : 6,000,543 reads 0-length : 6,000,543 spots read : 6,140,704 reads read : 12,281,408 reads written : 6,140,704 reads 0-length : 6,140,704 spots read : 5,933,785 reads read : 11,867,570 reads written : 5,933,785 reads 0-length : 5,933,785 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: 00:09:24 24211924 reads; of these: 24211924 (100.00%) were unpaired; of these: 441348 (1.82%) aligned 0 times 20965273 (86.59%) aligned exactly 1 time 2805303 (11.59%) aligned >1 times 98.18% overall alignment rate Time searching: 00:09:24 Overall time: 00:09:24 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 12 files... [bam_rmdupse_core] 5924229 / 23770576 = 0.2492 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 18:53:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.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 18:53:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:53:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:53:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.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 18:53:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:53:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:53:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.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 18:53:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:53:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:53:34: 1000000 INFO @ Sun, 02 Jun 2019 18:53:38: 1000000 INFO @ Sun, 02 Jun 2019 18:53:38: 1000000 INFO @ Sun, 02 Jun 2019 18:53:43: 2000000 INFO @ Sun, 02 Jun 2019 18:53:50: 2000000 INFO @ Sun, 02 Jun 2019 18:53:51: 2000000 INFO @ Sun, 02 Jun 2019 18:53:51: 3000000 INFO @ Sun, 02 Jun 2019 18:54:00: 4000000 INFO @ Sun, 02 Jun 2019 18:54:01: 3000000 INFO @ Sun, 02 Jun 2019 18:54:03: 3000000 INFO @ Sun, 02 Jun 2019 18:54:08: 5000000 INFO @ Sun, 02 Jun 2019 18:54:12: 4000000 INFO @ Sun, 02 Jun 2019 18:54:16: 4000000 INFO @ Sun, 02 Jun 2019 18:54:17: 6000000 INFO @ Sun, 02 Jun 2019 18:54:22: 5000000 INFO @ Sun, 02 Jun 2019 18:54:25: 7000000 INFO @ Sun, 02 Jun 2019 18:54:28: 5000000 INFO @ Sun, 02 Jun 2019 18:54:33: 6000000 INFO @ Sun, 02 Jun 2019 18:54:34: 8000000 INFO @ Sun, 02 Jun 2019 18:54:41: 6000000 INFO @ Sun, 02 Jun 2019 18:54:44: 9000000 INFO @ Sun, 02 Jun 2019 18:54:44: 7000000 INFO @ Sun, 02 Jun 2019 18:54:52: 10000000 INFO @ Sun, 02 Jun 2019 18:54:53: 7000000 INFO @ Sun, 02 Jun 2019 18:54:55: 8000000 INFO @ Sun, 02 Jun 2019 18:55:02: 11000000 INFO @ Sun, 02 Jun 2019 18:55:06: 8000000 INFO @ Sun, 02 Jun 2019 18:55:07: 9000000 INFO @ Sun, 02 Jun 2019 18:55:12: 12000000 INFO @ Sun, 02 Jun 2019 18:55:17: 10000000 INFO @ Sun, 02 Jun 2019 18:55:18: 9000000 INFO @ Sun, 02 Jun 2019 18:55:20: 13000000 INFO @ Sun, 02 Jun 2019 18:55:28: 11000000 INFO @ Sun, 02 Jun 2019 18:55:28: 14000000 INFO @ Sun, 02 Jun 2019 18:55:31: 10000000 INFO @ Sun, 02 Jun 2019 18:55:37: 15000000 INFO @ Sun, 02 Jun 2019 18:55:39: 12000000 INFO @ Sun, 02 Jun 2019 18:55:43: 11000000 INFO @ Sun, 02 Jun 2019 18:55:47: 16000000 INFO @ Sun, 02 Jun 2019 18:55:50: 13000000 INFO @ Sun, 02 Jun 2019 18:55:55: 12000000 INFO @ Sun, 02 Jun 2019 18:55:57: 17000000 INFO @ Sun, 02 Jun 2019 18:56:01: 14000000 INFO @ Sun, 02 Jun 2019 18:56:04: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 18:56:04: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 18:56:04: #1 total tags in treatment: 17846347 INFO @ Sun, 02 Jun 2019 18:56:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:56:04: #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 18:56:05: #1 tags after filtering in treatment: 17846347 INFO @ Sun, 02 Jun 2019 18:56:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:56:05: #1 finished! INFO @ Sun, 02 Jun 2019 18:56:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:56:06: #2 number of paired peaks: 271 WARNING @ Sun, 02 Jun 2019 18:56:06: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Sun, 02 Jun 2019 18:56:06: start model_add_line... INFO @ Sun, 02 Jun 2019 18:56:06: start X-correlation... INFO @ Sun, 02 Jun 2019 18:56:06: end of X-cor INFO @ Sun, 02 Jun 2019 18:56:06: #2 finished! INFO @ Sun, 02 Jun 2019 18:56:06: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:56:06: #2 alternative fragment length(s) may be 1,25,44,71,556,573 bps INFO @ Sun, 02 Jun 2019 18:56:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.05_model.r WARNING @ Sun, 02 Jun 2019 18:56:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:56:06: #2 You may need to consider one of the other alternative d(s): 1,25,44,71,556,573 WARNING @ Sun, 02 Jun 2019 18:56:06: #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 18:56:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:56:07: 13000000 INFO @ Sun, 02 Jun 2019 18:56:12: 15000000 INFO @ Sun, 02 Jun 2019 18:56:19: 14000000 INFO @ Sun, 02 Jun 2019 18:56:23: 16000000 INFO @ Sun, 02 Jun 2019 18:56:32: 15000000 INFO @ Sun, 02 Jun 2019 18:56:33: 17000000 INFO @ Sun, 02 Jun 2019 18:56:42: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 18:56:42: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 18:56:42: #1 total tags in treatment: 17846347 INFO @ Sun, 02 Jun 2019 18:56:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:56:42: #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 18:56:43: #1 tags after filtering in treatment: 17846347 INFO @ Sun, 02 Jun 2019 18:56:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:56:43: #1 finished! INFO @ Sun, 02 Jun 2019 18:56:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:56:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:56:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:56:44: 16000000 INFO @ Sun, 02 Jun 2019 18:56:44: #2 number of paired peaks: 271 WARNING @ Sun, 02 Jun 2019 18:56:44: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Sun, 02 Jun 2019 18:56:44: start model_add_line... INFO @ Sun, 02 Jun 2019 18:56:44: start X-correlation... INFO @ Sun, 02 Jun 2019 18:56:44: end of X-cor INFO @ Sun, 02 Jun 2019 18:56:44: #2 finished! INFO @ Sun, 02 Jun 2019 18:56:44: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:56:44: #2 alternative fragment length(s) may be 1,25,44,71,556,573 bps INFO @ Sun, 02 Jun 2019 18:56:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.20_model.r WARNING @ Sun, 02 Jun 2019 18:56:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:56:44: #2 You may need to consider one of the other alternative d(s): 1,25,44,71,556,573 WARNING @ Sun, 02 Jun 2019 18:56:44: #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 18:56:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:56:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:56:56: 17000000 INFO @ Sun, 02 Jun 2019 18:57:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:57:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:57:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.05_summits.bed INFO @ Sun, 02 Jun 2019 18:57:01: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:57:06: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 18:57:06: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 18:57:06: #1 total tags in treatment: 17846347 INFO @ Sun, 02 Jun 2019 18:57:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:57:06: #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 18:57:06: #1 tags after filtering in treatment: 17846347 INFO @ Sun, 02 Jun 2019 18:57:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:57:06: #1 finished! INFO @ Sun, 02 Jun 2019 18:57:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:57:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:57:08: #2 number of paired peaks: 271 WARNING @ Sun, 02 Jun 2019 18:57:08: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Sun, 02 Jun 2019 18:57:08: start model_add_line... INFO @ Sun, 02 Jun 2019 18:57:08: start X-correlation... INFO @ Sun, 02 Jun 2019 18:57:08: end of X-cor INFO @ Sun, 02 Jun 2019 18:57:08: #2 finished! INFO @ Sun, 02 Jun 2019 18:57:08: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:57:08: #2 alternative fragment length(s) may be 1,25,44,71,556,573 bps INFO @ Sun, 02 Jun 2019 18:57:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.10_model.r WARNING @ Sun, 02 Jun 2019 18:57:08: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:57:08: #2 You may need to consider one of the other alternative d(s): 1,25,44,71,556,573 WARNING @ Sun, 02 Jun 2019 18:57:08: #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 18:57:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:57:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:57:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:57:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:57:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:57:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.20_summits.bed INFO @ Sun, 02 Jun 2019 18:57:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:57:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:58:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:58:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:58:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194202/SRX4194202.10_summits.bed INFO @ Sun, 02 Jun 2019 18:58:02: 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。