Job ID = 1291685 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,260,651 reads read : 23,260,651 reads written : 23,260,651 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: 00:05:29 23260651 reads; of these: 23260651 (100.00%) were unpaired; of these: 1390828 (5.98%) aligned 0 times 18612354 (80.02%) aligned exactly 1 time 3257469 (14.00%) aligned >1 times 94.02% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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] 2367644 / 21869823 = 0.1083 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 16:28:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.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 16:28:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:28:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:28:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.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 16:28:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:28:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:28:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.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 16:28:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:28:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:28:18: 1000000 INFO @ Sun, 02 Jun 2019 16:28:18: 1000000 INFO @ Sun, 02 Jun 2019 16:28:18: 1000000 INFO @ Sun, 02 Jun 2019 16:28:27: 2000000 INFO @ Sun, 02 Jun 2019 16:28:27: 2000000 INFO @ Sun, 02 Jun 2019 16:28:27: 2000000 INFO @ Sun, 02 Jun 2019 16:28:36: 3000000 INFO @ Sun, 02 Jun 2019 16:28:37: 3000000 INFO @ Sun, 02 Jun 2019 16:28:37: 3000000 INFO @ Sun, 02 Jun 2019 16:28:44: 4000000 INFO @ Sun, 02 Jun 2019 16:28:46: 4000000 INFO @ Sun, 02 Jun 2019 16:28:46: 4000000 INFO @ Sun, 02 Jun 2019 16:28:53: 5000000 INFO @ Sun, 02 Jun 2019 16:28:55: 5000000 INFO @ Sun, 02 Jun 2019 16:28:56: 5000000 INFO @ Sun, 02 Jun 2019 16:29:01: 6000000 INFO @ Sun, 02 Jun 2019 16:29:04: 6000000 INFO @ Sun, 02 Jun 2019 16:29:05: 6000000 INFO @ Sun, 02 Jun 2019 16:29:10: 7000000 INFO @ Sun, 02 Jun 2019 16:29:13: 7000000 INFO @ Sun, 02 Jun 2019 16:29:14: 7000000 INFO @ Sun, 02 Jun 2019 16:29:18: 8000000 INFO @ Sun, 02 Jun 2019 16:29:22: 8000000 INFO @ Sun, 02 Jun 2019 16:29:22: 8000000 INFO @ Sun, 02 Jun 2019 16:29:26: 9000000 INFO @ Sun, 02 Jun 2019 16:29:31: 9000000 INFO @ Sun, 02 Jun 2019 16:29:31: 9000000 INFO @ Sun, 02 Jun 2019 16:29:35: 10000000 INFO @ Sun, 02 Jun 2019 16:29:40: 10000000 INFO @ Sun, 02 Jun 2019 16:29:40: 10000000 INFO @ Sun, 02 Jun 2019 16:29:43: 11000000 INFO @ Sun, 02 Jun 2019 16:29:49: 11000000 INFO @ Sun, 02 Jun 2019 16:29:49: 11000000 INFO @ Sun, 02 Jun 2019 16:29:51: 12000000 INFO @ Sun, 02 Jun 2019 16:29:57: 12000000 INFO @ Sun, 02 Jun 2019 16:29:57: 12000000 INFO @ Sun, 02 Jun 2019 16:29:59: 13000000 INFO @ Sun, 02 Jun 2019 16:30:06: 13000000 INFO @ Sun, 02 Jun 2019 16:30:06: 13000000 INFO @ Sun, 02 Jun 2019 16:30:07: 14000000 INFO @ Sun, 02 Jun 2019 16:30:14: 14000000 INFO @ Sun, 02 Jun 2019 16:30:15: 14000000 INFO @ Sun, 02 Jun 2019 16:30:15: 15000000 INFO @ Sun, 02 Jun 2019 16:30:23: 15000000 INFO @ Sun, 02 Jun 2019 16:30:23: 16000000 INFO @ Sun, 02 Jun 2019 16:30:23: 15000000 INFO @ Sun, 02 Jun 2019 16:30:31: 17000000 INFO @ Sun, 02 Jun 2019 16:30:31: 16000000 INFO @ Sun, 02 Jun 2019 16:30:32: 16000000 INFO @ Sun, 02 Jun 2019 16:30:39: 18000000 INFO @ Sun, 02 Jun 2019 16:30:40: 17000000 INFO @ Sun, 02 Jun 2019 16:30:41: 17000000 INFO @ Sun, 02 Jun 2019 16:30:47: 19000000 INFO @ Sun, 02 Jun 2019 16:30:49: 18000000 INFO @ Sun, 02 Jun 2019 16:30:49: 18000000 INFO @ Sun, 02 Jun 2019 16:30:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:30:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:30:51: #1 total tags in treatment: 19502179 INFO @ Sun, 02 Jun 2019 16:30:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:30:51: #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 16:30:51: #1 tags after filtering in treatment: 19502179 INFO @ Sun, 02 Jun 2019 16:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:30:51: #1 finished! INFO @ Sun, 02 Jun 2019 16:30:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:30:53: #2 number of paired peaks: 202 WARNING @ Sun, 02 Jun 2019 16:30:53: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sun, 02 Jun 2019 16:30:53: start model_add_line... INFO @ Sun, 02 Jun 2019 16:30:53: start X-correlation... INFO @ Sun, 02 Jun 2019 16:30:53: end of X-cor INFO @ Sun, 02 Jun 2019 16:30:53: #2 finished! INFO @ Sun, 02 Jun 2019 16:30:53: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:30:53: #2 alternative fragment length(s) may be 1,48,592 bps INFO @ Sun, 02 Jun 2019 16:30:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.10_model.r WARNING @ Sun, 02 Jun 2019 16:30:53: #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 16:30:53: #2 You may need to consider one of the other alternative d(s): 1,48,592 WARNING @ Sun, 02 Jun 2019 16:30:53: #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 16:30:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:30:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:30:58: 19000000 INFO @ Sun, 02 Jun 2019 16:30:58: 19000000 INFO @ Sun, 02 Jun 2019 16:31:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:31:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:31:02: #1 total tags in treatment: 19502179 INFO @ Sun, 02 Jun 2019 16:31:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:31:02: #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 16:31:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:31:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:31:02: #1 total tags in treatment: 19502179 INFO @ Sun, 02 Jun 2019 16:31:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:31:02: #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 16:31:02: #1 tags after filtering in treatment: 19502179 INFO @ Sun, 02 Jun 2019 16:31:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:31:02: #1 finished! INFO @ Sun, 02 Jun 2019 16:31:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:31:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:31:03: #1 tags after filtering in treatment: 19502179 INFO @ Sun, 02 Jun 2019 16:31:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:31:03: #1 finished! INFO @ Sun, 02 Jun 2019 16:31:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:31:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:31:04: #2 number of paired peaks: 202 WARNING @ Sun, 02 Jun 2019 16:31:04: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sun, 02 Jun 2019 16:31:04: start model_add_line... INFO @ Sun, 02 Jun 2019 16:31:04: start X-correlation... INFO @ Sun, 02 Jun 2019 16:31:04: end of X-cor INFO @ Sun, 02 Jun 2019 16:31:04: #2 finished! INFO @ Sun, 02 Jun 2019 16:31:04: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:31:04: #2 alternative fragment length(s) may be 1,48,592 bps INFO @ Sun, 02 Jun 2019 16:31:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.20_model.r WARNING @ Sun, 02 Jun 2019 16:31:04: #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 16:31:04: #2 You may need to consider one of the other alternative d(s): 1,48,592 WARNING @ Sun, 02 Jun 2019 16:31:04: #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 16:31:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:31:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:31:04: #2 number of paired peaks: 202 WARNING @ Sun, 02 Jun 2019 16:31:04: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sun, 02 Jun 2019 16:31:04: start model_add_line... INFO @ Sun, 02 Jun 2019 16:31:05: start X-correlation... INFO @ Sun, 02 Jun 2019 16:31:05: end of X-cor INFO @ Sun, 02 Jun 2019 16:31:05: #2 finished! INFO @ Sun, 02 Jun 2019 16:31:05: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:31:05: #2 alternative fragment length(s) may be 1,48,592 bps INFO @ Sun, 02 Jun 2019 16:31:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.05_model.r WARNING @ Sun, 02 Jun 2019 16:31:05: #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 16:31:05: #2 You may need to consider one of the other alternative d(s): 1,48,592 WARNING @ Sun, 02 Jun 2019 16:31:05: #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 16:31:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:31:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:31:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:31:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:31:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:31:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:31:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:31:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.10_summits.bed INFO @ Sun, 02 Jun 2019 16:31:56: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:32:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:32:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:32:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.20_summits.bed INFO @ Sun, 02 Jun 2019 16:32:06: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:32:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:32:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:32:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216754/SRX216754.05_summits.bed INFO @ Sun, 02 Jun 2019 16:32:07: Done! pass1 - making usageList (0 chroms): 2 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。