Job ID = 2589184 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,518,129 reads read : 2,518,129 reads written : 2,518,129 spots read : 2,487,991 reads read : 2,487,991 reads written : 2,487,991 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107566.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107567.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: 00:00:58 5006120 reads; of these: 5006120 (100.00%) were unpaired; of these: 233199 (4.66%) aligned 0 times 4011916 (80.14%) aligned exactly 1 time 761005 (15.20%) aligned >1 times 95.34% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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] 416128 / 4772921 = 0.0872 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 17:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.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 17:08:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:08:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:08:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.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 17:08:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:08:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:08:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.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 17:08:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:08:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:08:11: 1000000 INFO @ Mon, 12 Aug 2019 17:08:13: 1000000 INFO @ Mon, 12 Aug 2019 17:08:13: 1000000 INFO @ Mon, 12 Aug 2019 17:08:19: 2000000 INFO @ Mon, 12 Aug 2019 17:08:21: 2000000 INFO @ Mon, 12 Aug 2019 17:08:21: 2000000 INFO @ Mon, 12 Aug 2019 17:08:26: 3000000 INFO @ Mon, 12 Aug 2019 17:08:29: 3000000 INFO @ Mon, 12 Aug 2019 17:08:29: 3000000 INFO @ Mon, 12 Aug 2019 17:08:34: 4000000 INFO @ Mon, 12 Aug 2019 17:08:36: 4000000 INFO @ Mon, 12 Aug 2019 17:08:36: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:08:36: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:08:36: #1 total tags in treatment: 4356793 INFO @ Mon, 12 Aug 2019 17:08:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:08:36: #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 17:08:36: #1 tags after filtering in treatment: 4356793 INFO @ Mon, 12 Aug 2019 17:08:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:08:36: #1 finished! INFO @ Mon, 12 Aug 2019 17:08:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:08:37: #2 number of paired peaks: 406 WARNING @ Mon, 12 Aug 2019 17:08:37: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Mon, 12 Aug 2019 17:08:37: start model_add_line... INFO @ Mon, 12 Aug 2019 17:08:37: start X-correlation... INFO @ Mon, 12 Aug 2019 17:08:37: end of X-cor INFO @ Mon, 12 Aug 2019 17:08:37: #2 finished! INFO @ Mon, 12 Aug 2019 17:08:37: #2 predicted fragment length is 107 bps INFO @ Mon, 12 Aug 2019 17:08:37: #2 alternative fragment length(s) may be 107,575,590 bps INFO @ Mon, 12 Aug 2019 17:08:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.05_model.r INFO @ Mon, 12 Aug 2019 17:08:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:08:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:08:37: 4000000 INFO @ Mon, 12 Aug 2019 17:08:39: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:08:39: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:08:39: #1 total tags in treatment: 4356793 INFO @ Mon, 12 Aug 2019 17:08:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:08:39: #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 17:08:39: #1 tags after filtering in treatment: 4356793 INFO @ Mon, 12 Aug 2019 17:08:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:08:39: #1 finished! INFO @ Mon, 12 Aug 2019 17:08:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:08:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:08:39: #2 number of paired peaks: 406 WARNING @ Mon, 12 Aug 2019 17:08:39: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Mon, 12 Aug 2019 17:08:39: start model_add_line... INFO @ Mon, 12 Aug 2019 17:08:39: start X-correlation... INFO @ Mon, 12 Aug 2019 17:08:39: end of X-cor INFO @ Mon, 12 Aug 2019 17:08:39: #2 finished! INFO @ Mon, 12 Aug 2019 17:08:39: #2 predicted fragment length is 107 bps INFO @ Mon, 12 Aug 2019 17:08:39: #2 alternative fragment length(s) may be 107,575,590 bps INFO @ Mon, 12 Aug 2019 17:08:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.20_model.r INFO @ Mon, 12 Aug 2019 17:08:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:08:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:08:40: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:08:40: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:08:40: #1 total tags in treatment: 4356793 INFO @ Mon, 12 Aug 2019 17:08:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:08:40: #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 17:08:40: #1 tags after filtering in treatment: 4356793 INFO @ Mon, 12 Aug 2019 17:08:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:08:40: #1 finished! INFO @ Mon, 12 Aug 2019 17:08:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:08:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:08:41: #2 number of paired peaks: 406 WARNING @ Mon, 12 Aug 2019 17:08:41: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Mon, 12 Aug 2019 17:08:41: start model_add_line... INFO @ Mon, 12 Aug 2019 17:08:41: start X-correlation... INFO @ Mon, 12 Aug 2019 17:08:41: end of X-cor INFO @ Mon, 12 Aug 2019 17:08:41: #2 finished! INFO @ Mon, 12 Aug 2019 17:08:41: #2 predicted fragment length is 107 bps INFO @ Mon, 12 Aug 2019 17:08:41: #2 alternative fragment length(s) may be 107,575,590 bps INFO @ Mon, 12 Aug 2019 17:08:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.10_model.r INFO @ Mon, 12 Aug 2019 17:08:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:08:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:08:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:08:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:08:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:08:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:08:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:08:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.05_summits.bed INFO @ Mon, 12 Aug 2019 17:08:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1843 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:08:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:08:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.20_summits.bed INFO @ Mon, 12 Aug 2019 17:08:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (175 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:09:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:09:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:09:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043991/SRX043991.10_summits.bed INFO @ Mon, 12 Aug 2019 17:09:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (687 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。