Job ID = 2590085 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,175,313 reads read : 25,175,313 reads written : 25,175,313 rm: cannot remove ‘[DSE]RR*’: 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: 00:06:13 25175313 reads; of these: 25175313 (100.00%) were unpaired; of these: 2423845 (9.63%) aligned 0 times 18709515 (74.32%) aligned exactly 1 time 4041953 (16.06%) aligned >1 times 90.37% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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] 3695672 / 22751468 = 0.1624 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, 12 Aug 2019 19:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.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 @ Mon, 12 Aug 2019 19:53:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:53:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.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 @ Mon, 12 Aug 2019 19:53:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:53:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.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 @ Mon, 12 Aug 2019 19:53:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:53:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:53:09: 1000000 INFO @ Mon, 12 Aug 2019 19:53:09: 1000000 INFO @ Mon, 12 Aug 2019 19:53:10: 1000000 INFO @ Mon, 12 Aug 2019 19:53:17: 2000000 INFO @ Mon, 12 Aug 2019 19:53:17: 2000000 INFO @ Mon, 12 Aug 2019 19:53:18: 2000000 INFO @ Mon, 12 Aug 2019 19:53:25: 3000000 INFO @ Mon, 12 Aug 2019 19:53:25: 3000000 INFO @ Mon, 12 Aug 2019 19:53:26: 3000000 INFO @ Mon, 12 Aug 2019 19:53:33: 4000000 INFO @ Mon, 12 Aug 2019 19:53:33: 4000000 INFO @ Mon, 12 Aug 2019 19:53:35: 4000000 INFO @ Mon, 12 Aug 2019 19:53:41: 5000000 INFO @ Mon, 12 Aug 2019 19:53:41: 5000000 INFO @ Mon, 12 Aug 2019 19:53:43: 5000000 INFO @ Mon, 12 Aug 2019 19:53:49: 6000000 INFO @ Mon, 12 Aug 2019 19:53:49: 6000000 INFO @ Mon, 12 Aug 2019 19:53:53: 6000000 INFO @ Mon, 12 Aug 2019 19:53:58: 7000000 INFO @ Mon, 12 Aug 2019 19:53:58: 7000000 INFO @ Mon, 12 Aug 2019 19:54:01: 7000000 INFO @ Mon, 12 Aug 2019 19:54:06: 8000000 INFO @ Mon, 12 Aug 2019 19:54:06: 8000000 INFO @ Mon, 12 Aug 2019 19:54:10: 8000000 INFO @ Mon, 12 Aug 2019 19:54:14: 9000000 INFO @ Mon, 12 Aug 2019 19:54:14: 9000000 INFO @ Mon, 12 Aug 2019 19:54:19: 9000000 INFO @ Mon, 12 Aug 2019 19:54:22: 10000000 INFO @ Mon, 12 Aug 2019 19:54:22: 10000000 INFO @ Mon, 12 Aug 2019 19:54:27: 10000000 INFO @ Mon, 12 Aug 2019 19:54:30: 11000000 INFO @ Mon, 12 Aug 2019 19:54:30: 11000000 INFO @ Mon, 12 Aug 2019 19:54:36: 11000000 INFO @ Mon, 12 Aug 2019 19:54:38: 12000000 INFO @ Mon, 12 Aug 2019 19:54:38: 12000000 INFO @ Mon, 12 Aug 2019 19:54:44: 12000000 INFO @ Mon, 12 Aug 2019 19:54:46: 13000000 INFO @ Mon, 12 Aug 2019 19:54:46: 13000000 INFO @ Mon, 12 Aug 2019 19:54:53: 13000000 INFO @ Mon, 12 Aug 2019 19:54:54: 14000000 INFO @ Mon, 12 Aug 2019 19:54:54: 14000000 INFO @ Mon, 12 Aug 2019 19:55:01: 14000000 INFO @ Mon, 12 Aug 2019 19:55:02: 15000000 INFO @ Mon, 12 Aug 2019 19:55:02: 15000000 INFO @ Mon, 12 Aug 2019 19:55:09: 15000000 INFO @ Mon, 12 Aug 2019 19:55:10: 16000000 INFO @ Mon, 12 Aug 2019 19:55:10: 16000000 INFO @ Mon, 12 Aug 2019 19:55:17: 16000000 INFO @ Mon, 12 Aug 2019 19:55:18: 17000000 INFO @ Mon, 12 Aug 2019 19:55:18: 17000000 INFO @ Mon, 12 Aug 2019 19:55:25: 17000000 INFO @ Mon, 12 Aug 2019 19:55:26: 18000000 INFO @ Mon, 12 Aug 2019 19:55:26: 18000000 INFO @ Mon, 12 Aug 2019 19:55:33: 18000000 INFO @ Mon, 12 Aug 2019 19:55:34: 19000000 INFO @ Mon, 12 Aug 2019 19:55:34: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:55:34: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:55:34: #1 total tags in treatment: 19055796 INFO @ Mon, 12 Aug 2019 19:55:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:55:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:55:35: 19000000 INFO @ Mon, 12 Aug 2019 19:55:35: #1 tags after filtering in treatment: 19055796 INFO @ Mon, 12 Aug 2019 19:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:55:35: #1 finished! INFO @ Mon, 12 Aug 2019 19:55:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:55:35: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:55:35: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:55:35: #1 total tags in treatment: 19055796 INFO @ Mon, 12 Aug 2019 19:55:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:55:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:55:36: #1 tags after filtering in treatment: 19055796 INFO @ Mon, 12 Aug 2019 19:55:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:55:36: #1 finished! INFO @ Mon, 12 Aug 2019 19:55:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:55:37: #2 number of paired peaks: 242 WARNING @ Mon, 12 Aug 2019 19:55:37: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Mon, 12 Aug 2019 19:55:37: start model_add_line... INFO @ Mon, 12 Aug 2019 19:55:37: start X-correlation... INFO @ Mon, 12 Aug 2019 19:55:37: end of X-cor INFO @ Mon, 12 Aug 2019 19:55:37: #2 finished! INFO @ Mon, 12 Aug 2019 19:55:37: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:55:37: #2 alternative fragment length(s) may be 1,45 bps INFO @ Mon, 12 Aug 2019 19:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.05_model.r WARNING @ Mon, 12 Aug 2019 19:55:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:55:37: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Mon, 12 Aug 2019 19:55:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:55:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:55:37: #2 number of paired peaks: 242 WARNING @ Mon, 12 Aug 2019 19:55:37: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Mon, 12 Aug 2019 19:55:37: start model_add_line... INFO @ Mon, 12 Aug 2019 19:55:37: start X-correlation... INFO @ Mon, 12 Aug 2019 19:55:37: end of X-cor INFO @ Mon, 12 Aug 2019 19:55:37: #2 finished! INFO @ Mon, 12 Aug 2019 19:55:37: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:55:37: #2 alternative fragment length(s) may be 1,45 bps INFO @ Mon, 12 Aug 2019 19:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.10_model.r WARNING @ Mon, 12 Aug 2019 19:55:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:55:37: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Mon, 12 Aug 2019 19:55:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:55:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:55:41: 19000000 INFO @ Mon, 12 Aug 2019 19:55:42: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:55:42: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:55:42: #1 total tags in treatment: 19055796 INFO @ Mon, 12 Aug 2019 19:55:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:55:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:55:42: #1 tags after filtering in treatment: 19055796 INFO @ Mon, 12 Aug 2019 19:55:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:55:42: #1 finished! INFO @ Mon, 12 Aug 2019 19:55:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:55:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:55:44: #2 number of paired peaks: 242 WARNING @ Mon, 12 Aug 2019 19:55:44: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Mon, 12 Aug 2019 19:55:44: start model_add_line... INFO @ Mon, 12 Aug 2019 19:55:44: start X-correlation... INFO @ Mon, 12 Aug 2019 19:55:44: end of X-cor INFO @ Mon, 12 Aug 2019 19:55:44: #2 finished! INFO @ Mon, 12 Aug 2019 19:55:44: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:55:44: #2 alternative fragment length(s) may be 1,45 bps INFO @ Mon, 12 Aug 2019 19:55:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.20_model.r WARNING @ Mon, 12 Aug 2019 19:55:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:55:44: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Mon, 12 Aug 2019 19:55:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:55:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:55:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:56:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:56:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:56:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.05_summits.bed INFO @ Mon, 12 Aug 2019 19:56:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:56:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:56:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:56:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.10_summits.bed INFO @ Mon, 12 Aug 2019 19:56:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:56:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:56:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:56:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494927/SRX494927.20_summits.bed INFO @ Mon, 12 Aug 2019 19:56:44: 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。