Job ID = 1292395 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,590,563 reads read : 7,590,563 reads written : 7,590,563 spots read : 6,200,523 reads read : 6,200,523 reads written : 6,200,523 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: 00:02:15 13791086 reads; of these: 13791086 (100.00%) were unpaired; of these: 869259 (6.30%) aligned 0 times 10869374 (78.81%) aligned exactly 1 time 2052453 (14.88%) aligned >1 times 93.70% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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_rmdupse_core] 1615145 / 12921827 = 0.1250 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 18:24:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.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 18:24:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:24:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:24:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.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 18:24:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:24:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:24:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.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 18:24:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:24:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:24:28: 1000000 INFO @ Sun, 02 Jun 2019 18:24:28: 1000000 INFO @ Sun, 02 Jun 2019 18:24:28: 1000000 INFO @ Sun, 02 Jun 2019 18:24:35: 2000000 INFO @ Sun, 02 Jun 2019 18:24:35: 2000000 INFO @ Sun, 02 Jun 2019 18:24:36: 2000000 INFO @ Sun, 02 Jun 2019 18:24:41: 3000000 INFO @ Sun, 02 Jun 2019 18:24:41: 3000000 INFO @ Sun, 02 Jun 2019 18:24:43: 3000000 INFO @ Sun, 02 Jun 2019 18:24:48: 4000000 INFO @ Sun, 02 Jun 2019 18:24:48: 4000000 INFO @ Sun, 02 Jun 2019 18:24:50: 4000000 INFO @ Sun, 02 Jun 2019 18:24:54: 5000000 INFO @ Sun, 02 Jun 2019 18:24:54: 5000000 INFO @ Sun, 02 Jun 2019 18:24:57: 5000000 INFO @ Sun, 02 Jun 2019 18:25:01: 6000000 INFO @ Sun, 02 Jun 2019 18:25:01: 6000000 INFO @ Sun, 02 Jun 2019 18:25:04: 6000000 INFO @ Sun, 02 Jun 2019 18:25:08: 7000000 INFO @ Sun, 02 Jun 2019 18:25:08: 7000000 INFO @ Sun, 02 Jun 2019 18:25:11: 7000000 INFO @ Sun, 02 Jun 2019 18:25:14: 8000000 INFO @ Sun, 02 Jun 2019 18:25:14: 8000000 INFO @ Sun, 02 Jun 2019 18:25:18: 8000000 INFO @ Sun, 02 Jun 2019 18:25:21: 9000000 INFO @ Sun, 02 Jun 2019 18:25:21: 9000000 INFO @ Sun, 02 Jun 2019 18:25:25: 9000000 INFO @ Sun, 02 Jun 2019 18:25:27: 10000000 INFO @ Sun, 02 Jun 2019 18:25:27: 10000000 INFO @ Sun, 02 Jun 2019 18:25:32: 10000000 INFO @ Sun, 02 Jun 2019 18:25:34: 11000000 INFO @ Sun, 02 Jun 2019 18:25:34: 11000000 INFO @ Sun, 02 Jun 2019 18:25:36: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 18:25:36: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 18:25:36: #1 total tags in treatment: 11306682 INFO @ Sun, 02 Jun 2019 18:25:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:25:36: #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 18:25:36: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 18:25:36: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 18:25:36: #1 total tags in treatment: 11306682 INFO @ Sun, 02 Jun 2019 18:25:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:25:36: #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 18:25:36: #1 tags after filtering in treatment: 11306682 INFO @ Sun, 02 Jun 2019 18:25:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:25:36: #1 finished! INFO @ Sun, 02 Jun 2019 18:25:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:25:36: #1 tags after filtering in treatment: 11306682 INFO @ Sun, 02 Jun 2019 18:25:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:25:36: #1 finished! INFO @ Sun, 02 Jun 2019 18:25:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:25:37: #2 number of paired peaks: 278 WARNING @ Sun, 02 Jun 2019 18:25:37: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Sun, 02 Jun 2019 18:25:37: start model_add_line... INFO @ Sun, 02 Jun 2019 18:25:37: #2 number of paired peaks: 278 WARNING @ Sun, 02 Jun 2019 18:25:37: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Sun, 02 Jun 2019 18:25:37: start model_add_line... INFO @ Sun, 02 Jun 2019 18:25:37: start X-correlation... INFO @ Sun, 02 Jun 2019 18:25:37: end of X-cor INFO @ Sun, 02 Jun 2019 18:25:37: #2 finished! INFO @ Sun, 02 Jun 2019 18:25:37: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:25:37: #2 alternative fragment length(s) may be 1,32,505,585 bps INFO @ Sun, 02 Jun 2019 18:25:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.05_model.r WARNING @ Sun, 02 Jun 2019 18:25:37: #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 18:25:37: #2 You may need to consider one of the other alternative d(s): 1,32,505,585 WARNING @ Sun, 02 Jun 2019 18:25:37: #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 18:25:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:25:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:25:37: start X-correlation... INFO @ Sun, 02 Jun 2019 18:25:37: end of X-cor INFO @ Sun, 02 Jun 2019 18:25:37: #2 finished! INFO @ Sun, 02 Jun 2019 18:25:37: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:25:37: #2 alternative fragment length(s) may be 1,32,505,585 bps INFO @ Sun, 02 Jun 2019 18:25:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.20_model.r WARNING @ Sun, 02 Jun 2019 18:25:37: #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 18:25:37: #2 You may need to consider one of the other alternative d(s): 1,32,505,585 WARNING @ Sun, 02 Jun 2019 18:25:37: #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 18:25:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:25:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:25:39: 11000000 INFO @ Sun, 02 Jun 2019 18:25:41: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 18:25:41: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 18:25:41: #1 total tags in treatment: 11306682 INFO @ Sun, 02 Jun 2019 18:25:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:25:41: #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 18:25:41: #1 tags after filtering in treatment: 11306682 INFO @ Sun, 02 Jun 2019 18:25:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:25:41: #1 finished! INFO @ Sun, 02 Jun 2019 18:25:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:25:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:25:42: #2 number of paired peaks: 278 WARNING @ Sun, 02 Jun 2019 18:25:42: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Sun, 02 Jun 2019 18:25:42: start model_add_line... INFO @ Sun, 02 Jun 2019 18:25:42: start X-correlation... INFO @ Sun, 02 Jun 2019 18:25:42: end of X-cor INFO @ Sun, 02 Jun 2019 18:25:42: #2 finished! INFO @ Sun, 02 Jun 2019 18:25:42: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:25:42: #2 alternative fragment length(s) may be 1,32,505,585 bps INFO @ Sun, 02 Jun 2019 18:25:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.10_model.r WARNING @ Sun, 02 Jun 2019 18:25:42: #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 18:25:42: #2 You may need to consider one of the other alternative d(s): 1,32,505,585 WARNING @ Sun, 02 Jun 2019 18:25:42: #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 18:25:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:25:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:26:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:26:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:26:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:26:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:26:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:26:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.20_summits.bed INFO @ Sun, 02 Jun 2019 18:26:18: Done! INFO @ Sun, 02 Jun 2019 18:26:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:26:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:26:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.05_summits.bed INFO @ Sun, 02 Jun 2019 18:26:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis CompletedMACS2peakCalling needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:26:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:26:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:26:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX395528/SRX395528.10_summits.bed INFO @ Sun, 02 Jun 2019 18:26:23: 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。