Job ID = 2589373 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,013,036 reads read : 27,013,036 reads written : 27,013,036 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: 00:06:40 27013036 reads; of these: 27013036 (100.00%) were unpaired; of these: 285022 (1.06%) aligned 0 times 22371566 (82.82%) aligned exactly 1 time 4356448 (16.13%) aligned >1 times 98.94% overall alignment rate Time searching: 00:06:40 Overall time: 00:06:40 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] 7398433 / 26728014 = 0.2768 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 18:00:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.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 18:00:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:00:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:00:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.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 18:00:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:00:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:00:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.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 18:00:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:00:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:00:32: 1000000 INFO @ Mon, 12 Aug 2019 18:00:33: 1000000 INFO @ Mon, 12 Aug 2019 18:00:34: 1000000 INFO @ Mon, 12 Aug 2019 18:00:40: 2000000 INFO @ Mon, 12 Aug 2019 18:00:40: 2000000 INFO @ Mon, 12 Aug 2019 18:00:42: 2000000 INFO @ Mon, 12 Aug 2019 18:00:46: 3000000 INFO @ Mon, 12 Aug 2019 18:00:47: 3000000 INFO @ Mon, 12 Aug 2019 18:00:49: 3000000 INFO @ Mon, 12 Aug 2019 18:00:53: 4000000 INFO @ Mon, 12 Aug 2019 18:00:54: 4000000 INFO @ Mon, 12 Aug 2019 18:00:56: 4000000 INFO @ Mon, 12 Aug 2019 18:01:00: 5000000 INFO @ Mon, 12 Aug 2019 18:01:02: 5000000 INFO @ Mon, 12 Aug 2019 18:01:03: 5000000 INFO @ Mon, 12 Aug 2019 18:01:06: 6000000 INFO @ Mon, 12 Aug 2019 18:01:09: 6000000 INFO @ Mon, 12 Aug 2019 18:01:11: 6000000 INFO @ Mon, 12 Aug 2019 18:01:13: 7000000 INFO @ Mon, 12 Aug 2019 18:01:16: 7000000 INFO @ Mon, 12 Aug 2019 18:01:18: 7000000 INFO @ Mon, 12 Aug 2019 18:01:20: 8000000 INFO @ Mon, 12 Aug 2019 18:01:24: 8000000 INFO @ Mon, 12 Aug 2019 18:01:25: 8000000 INFO @ Mon, 12 Aug 2019 18:01:26: 9000000 INFO @ Mon, 12 Aug 2019 18:01:31: 9000000 INFO @ Mon, 12 Aug 2019 18:01:32: 9000000 INFO @ Mon, 12 Aug 2019 18:01:33: 10000000 INFO @ Mon, 12 Aug 2019 18:01:40: 10000000 INFO @ Mon, 12 Aug 2019 18:01:40: 11000000 INFO @ Mon, 12 Aug 2019 18:01:41: 10000000 INFO @ Mon, 12 Aug 2019 18:01:46: 12000000 INFO @ Mon, 12 Aug 2019 18:01:47: 11000000 INFO @ Mon, 12 Aug 2019 18:01:50: 11000000 INFO @ Mon, 12 Aug 2019 18:01:53: 13000000 INFO @ Mon, 12 Aug 2019 18:01:54: 12000000 INFO @ Mon, 12 Aug 2019 18:01:57: 12000000 INFO @ Mon, 12 Aug 2019 18:02:00: 14000000 INFO @ Mon, 12 Aug 2019 18:02:01: 13000000 INFO @ Mon, 12 Aug 2019 18:02:04: 13000000 INFO @ Mon, 12 Aug 2019 18:02:06: 15000000 INFO @ Mon, 12 Aug 2019 18:02:09: 14000000 INFO @ Mon, 12 Aug 2019 18:02:11: 14000000 INFO @ Mon, 12 Aug 2019 18:02:13: 16000000 INFO @ Mon, 12 Aug 2019 18:02:16: 15000000 INFO @ Mon, 12 Aug 2019 18:02:19: 15000000 INFO @ Mon, 12 Aug 2019 18:02:20: 17000000 INFO @ Mon, 12 Aug 2019 18:02:23: 16000000 INFO @ Mon, 12 Aug 2019 18:02:26: 16000000 INFO @ Mon, 12 Aug 2019 18:02:26: 18000000 INFO @ Mon, 12 Aug 2019 18:02:30: 17000000 INFO @ Mon, 12 Aug 2019 18:02:33: 17000000 INFO @ Mon, 12 Aug 2019 18:02:33: 19000000 INFO @ Mon, 12 Aug 2019 18:02:35: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:02:35: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:02:35: #1 total tags in treatment: 19329581 INFO @ Mon, 12 Aug 2019 18:02:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:02:35: #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 18:02:36: #1 tags after filtering in treatment: 19329581 INFO @ Mon, 12 Aug 2019 18:02:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:02:36: #1 finished! INFO @ Mon, 12 Aug 2019 18:02:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:02:37: 18000000 INFO @ Mon, 12 Aug 2019 18:02:37: #2 number of paired peaks: 278 WARNING @ Mon, 12 Aug 2019 18:02:37: 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 @ Mon, 12 Aug 2019 18:02:37: start model_add_line... INFO @ Mon, 12 Aug 2019 18:02:38: start X-correlation... INFO @ Mon, 12 Aug 2019 18:02:38: end of X-cor INFO @ Mon, 12 Aug 2019 18:02:38: #2 finished! INFO @ Mon, 12 Aug 2019 18:02:38: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:02:38: #2 alternative fragment length(s) may be 1,42,573,597 bps INFO @ Mon, 12 Aug 2019 18:02:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.10_model.r WARNING @ Mon, 12 Aug 2019 18:02:38: #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 18:02:38: #2 You may need to consider one of the other alternative d(s): 1,42,573,597 WARNING @ Mon, 12 Aug 2019 18:02:38: #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 18:02:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:02:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:02:40: 18000000 INFO @ Mon, 12 Aug 2019 18:02:44: 19000000 INFO @ Mon, 12 Aug 2019 18:02:47: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:02:47: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:02:47: #1 total tags in treatment: 19329581 INFO @ Mon, 12 Aug 2019 18:02:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:02:47: #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 18:02:47: 19000000 INFO @ Mon, 12 Aug 2019 18:02:47: #1 tags after filtering in treatment: 19329581 INFO @ Mon, 12 Aug 2019 18:02:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:02:47: #1 finished! INFO @ Mon, 12 Aug 2019 18:02:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:02:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:02:49: #2 number of paired peaks: 278 WARNING @ Mon, 12 Aug 2019 18:02:49: 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 @ Mon, 12 Aug 2019 18:02:49: start model_add_line... INFO @ Mon, 12 Aug 2019 18:02:49: start X-correlation... INFO @ Mon, 12 Aug 2019 18:02:49: end of X-cor INFO @ Mon, 12 Aug 2019 18:02:49: #2 finished! INFO @ Mon, 12 Aug 2019 18:02:49: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:02:49: #2 alternative fragment length(s) may be 1,42,573,597 bps INFO @ Mon, 12 Aug 2019 18:02:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.20_model.r WARNING @ Mon, 12 Aug 2019 18:02:49: #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 18:02:49: #2 You may need to consider one of the other alternative d(s): 1,42,573,597 WARNING @ Mon, 12 Aug 2019 18:02:49: #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 18:02:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:02:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:02:50: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:02:50: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:02:50: #1 total tags in treatment: 19329581 INFO @ Mon, 12 Aug 2019 18:02:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:02:50: #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 18:02:50: #1 tags after filtering in treatment: 19329581 INFO @ Mon, 12 Aug 2019 18:02:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:02:50: #1 finished! INFO @ Mon, 12 Aug 2019 18:02:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:02:52: #2 number of paired peaks: 278 WARNING @ Mon, 12 Aug 2019 18:02:52: 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 @ Mon, 12 Aug 2019 18:02:52: start model_add_line... INFO @ Mon, 12 Aug 2019 18:02:52: start X-correlation... INFO @ Mon, 12 Aug 2019 18:02:52: end of X-cor INFO @ Mon, 12 Aug 2019 18:02:52: #2 finished! INFO @ Mon, 12 Aug 2019 18:02:52: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:02:52: #2 alternative fragment length(s) may be 1,42,573,597 bps INFO @ Mon, 12 Aug 2019 18:02:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.05_model.r WARNING @ Mon, 12 Aug 2019 18:02:52: #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 18:02:52: #2 You may need to consider one of the other alternative d(s): 1,42,573,597 WARNING @ Mon, 12 Aug 2019 18:02:52: #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 18:02:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:03:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:03:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:03:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.10_summits.bed INFO @ Mon, 12 Aug 2019 18:03:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:03:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:03:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:03:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.20_summits.bed INFO @ Mon, 12 Aug 2019 18:03:51: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:03:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:03:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:03:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078724/SRX1078724.05_summits.bed INFO @ Mon, 12 Aug 2019 18:03:54: 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。