Job ID = 2589190 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,977,962 reads read : 2,977,962 reads written : 2,977,962 spots read : 3,364,196 reads read : 3,364,196 reads written : 3,364,196 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107576.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107577.sra.cache’: 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: 00:01:13 6342158 reads; of these: 6342158 (100.00%) were unpaired; of these: 133046 (2.10%) aligned 0 times 5235360 (82.55%) aligned exactly 1 time 973752 (15.35%) aligned >1 times 97.90% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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_rmdupse_core] 367657 / 6209112 = 0.0592 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 17:09:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.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 17:09:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:09:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.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 17:09:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:09:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:09:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.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 17:09:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:09:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:09:49: 1000000 INFO @ Mon, 12 Aug 2019 17:09:49: 1000000 INFO @ Mon, 12 Aug 2019 17:09:51: 1000000 INFO @ Mon, 12 Aug 2019 17:09:56: 2000000 INFO @ Mon, 12 Aug 2019 17:09:57: 2000000 INFO @ Mon, 12 Aug 2019 17:09:58: 2000000 INFO @ Mon, 12 Aug 2019 17:10:02: 3000000 INFO @ Mon, 12 Aug 2019 17:10:04: 3000000 INFO @ Mon, 12 Aug 2019 17:10:06: 3000000 INFO @ Mon, 12 Aug 2019 17:10:09: 4000000 INFO @ Mon, 12 Aug 2019 17:10:11: 4000000 INFO @ Mon, 12 Aug 2019 17:10:13: 4000000 INFO @ Mon, 12 Aug 2019 17:10:16: 5000000 INFO @ Mon, 12 Aug 2019 17:10:17: 5000000 INFO @ Mon, 12 Aug 2019 17:10:20: 5000000 INFO @ Mon, 12 Aug 2019 17:10:22: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:10:22: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:10:22: #1 total tags in treatment: 5841455 INFO @ Mon, 12 Aug 2019 17:10:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:10:22: #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 17:10:22: #1 tags after filtering in treatment: 5841455 INFO @ Mon, 12 Aug 2019 17:10:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:10:22: #1 finished! INFO @ Mon, 12 Aug 2019 17:10:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:10:22: #2 number of paired peaks: 331 WARNING @ Mon, 12 Aug 2019 17:10:22: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Mon, 12 Aug 2019 17:10:22: start model_add_line... INFO @ Mon, 12 Aug 2019 17:10:22: start X-correlation... INFO @ Mon, 12 Aug 2019 17:10:22: end of X-cor INFO @ Mon, 12 Aug 2019 17:10:22: #2 finished! INFO @ Mon, 12 Aug 2019 17:10:22: #2 predicted fragment length is 35 bps INFO @ Mon, 12 Aug 2019 17:10:22: #2 alternative fragment length(s) may be 3,35,76,97,109,458,561 bps INFO @ Mon, 12 Aug 2019 17:10:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.10_model.r WARNING @ Mon, 12 Aug 2019 17:10:23: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:10:23: #2 You may need to consider one of the other alternative d(s): 3,35,76,97,109,458,561 WARNING @ Mon, 12 Aug 2019 17:10:23: #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 17:10:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:10:23: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:10:23: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:10:23: #1 total tags in treatment: 5841455 INFO @ Mon, 12 Aug 2019 17:10:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:10:23: #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 17:10:23: #1 tags after filtering in treatment: 5841455 INFO @ Mon, 12 Aug 2019 17:10:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:10:23: #1 finished! INFO @ Mon, 12 Aug 2019 17:10:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:10:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:10:24: #2 number of paired peaks: 331 WARNING @ Mon, 12 Aug 2019 17:10:24: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Mon, 12 Aug 2019 17:10:24: start model_add_line... INFO @ Mon, 12 Aug 2019 17:10:24: start X-correlation... INFO @ Mon, 12 Aug 2019 17:10:24: end of X-cor INFO @ Mon, 12 Aug 2019 17:10:24: #2 finished! INFO @ Mon, 12 Aug 2019 17:10:24: #2 predicted fragment length is 35 bps INFO @ Mon, 12 Aug 2019 17:10:24: #2 alternative fragment length(s) may be 3,35,76,97,109,458,561 bps INFO @ Mon, 12 Aug 2019 17:10:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.05_model.r WARNING @ Mon, 12 Aug 2019 17:10:24: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:10:24: #2 You may need to consider one of the other alternative d(s): 3,35,76,97,109,458,561 WARNING @ Mon, 12 Aug 2019 17:10:24: #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 17:10:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:10:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:10:26: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:10:26: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:10:26: #1 total tags in treatment: 5841455 INFO @ Mon, 12 Aug 2019 17:10:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:10:26: #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 17:10:26: #1 tags after filtering in treatment: 5841455 INFO @ Mon, 12 Aug 2019 17:10:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:10:26: #1 finished! INFO @ Mon, 12 Aug 2019 17:10:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:10:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:10:27: #2 number of paired peaks: 331 WARNING @ Mon, 12 Aug 2019 17:10:27: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Mon, 12 Aug 2019 17:10:27: start model_add_line... INFO @ Mon, 12 Aug 2019 17:10:27: start X-correlation... INFO @ Mon, 12 Aug 2019 17:10:27: end of X-cor INFO @ Mon, 12 Aug 2019 17:10:27: #2 finished! INFO @ Mon, 12 Aug 2019 17:10:27: #2 predicted fragment length is 35 bps INFO @ Mon, 12 Aug 2019 17:10:27: #2 alternative fragment length(s) may be 3,35,76,97,109,458,561 bps INFO @ Mon, 12 Aug 2019 17:10:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.20_model.r WARNING @ Mon, 12 Aug 2019 17:10:27: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:10:27: #2 You may need to consider one of the other alternative d(s): 3,35,76,97,109,458,561 WARNING @ Mon, 12 Aug 2019 17:10:27: #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 17:10:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:10:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:10:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:10:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:10:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:10:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:10:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.10_summits.bed INFO @ Mon, 12 Aug 2019 17:10:47: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (156 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:10:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.05_summits.bed INFO @ Mon, 12 Aug 2019 17:10:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:10:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:10:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:10:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043997/SRX043997.20_summits.bed INFO @ Mon, 12 Aug 2019 17:10:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (40 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。