Job ID = 1292874 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,986,985 reads read : 27,973,970 reads written : 27,973,970 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:17:20 13986985 reads; of these: 13986985 (100.00%) were paired; of these: 2051064 (14.66%) aligned concordantly 0 times 9693496 (69.30%) aligned concordantly exactly 1 time 2242425 (16.03%) aligned concordantly >1 times ---- 2051064 pairs aligned concordantly 0 times; of these: 1027456 (50.09%) aligned discordantly 1 time ---- 1023608 pairs aligned 0 times concordantly or discordantly; of these: 2047216 mates make up the pairs; of these: 1399454 (68.36%) aligned 0 times 309985 (15.14%) aligned exactly 1 time 337777 (16.50%) aligned >1 times 95.00% overall alignment rate Time searching: 00:17:20 Overall time: 00:17:20 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 5266035 / 12955395 = 0.4065 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 21:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.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 21:25:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:25:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.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 21:25:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:25:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.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 21:25:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:25:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:25:58: 1000000 INFO @ Sun, 02 Jun 2019 21:25:58: 1000000 INFO @ Sun, 02 Jun 2019 21:25:58: 1000000 INFO @ Sun, 02 Jun 2019 21:26:04: 2000000 INFO @ Sun, 02 Jun 2019 21:26:06: 2000000 INFO @ Sun, 02 Jun 2019 21:26:06: 2000000 INFO @ Sun, 02 Jun 2019 21:26:11: 3000000 INFO @ Sun, 02 Jun 2019 21:26:13: 3000000 INFO @ Sun, 02 Jun 2019 21:26:14: 3000000 INFO @ Sun, 02 Jun 2019 21:26:18: 4000000 INFO @ Sun, 02 Jun 2019 21:26:21: 4000000 INFO @ Sun, 02 Jun 2019 21:26:21: 4000000 INFO @ Sun, 02 Jun 2019 21:26:24: 5000000 INFO @ Sun, 02 Jun 2019 21:26:29: 5000000 INFO @ Sun, 02 Jun 2019 21:26:29: 5000000 INFO @ Sun, 02 Jun 2019 21:26:31: 6000000 INFO @ Sun, 02 Jun 2019 21:26:36: 6000000 INFO @ Sun, 02 Jun 2019 21:26:37: 6000000 INFO @ Sun, 02 Jun 2019 21:26:38: 7000000 INFO @ Sun, 02 Jun 2019 21:26:44: 7000000 INFO @ Sun, 02 Jun 2019 21:26:45: 7000000 INFO @ Sun, 02 Jun 2019 21:26:45: 8000000 INFO @ Sun, 02 Jun 2019 21:26:51: 9000000 INFO @ Sun, 02 Jun 2019 21:26:52: 8000000 INFO @ Sun, 02 Jun 2019 21:26:53: 8000000 INFO @ Sun, 02 Jun 2019 21:26:58: 10000000 INFO @ Sun, 02 Jun 2019 21:27:01: 9000000 INFO @ Sun, 02 Jun 2019 21:27:01: 9000000 INFO @ Sun, 02 Jun 2019 21:27:05: 11000000 INFO @ Sun, 02 Jun 2019 21:27:08: 10000000 INFO @ Sun, 02 Jun 2019 21:27:09: 10000000 INFO @ Sun, 02 Jun 2019 21:27:12: 12000000 INFO @ Sun, 02 Jun 2019 21:27:17: 11000000 INFO @ Sun, 02 Jun 2019 21:27:17: 11000000 INFO @ Sun, 02 Jun 2019 21:27:19: 13000000 INFO @ Sun, 02 Jun 2019 21:27:25: 12000000 INFO @ Sun, 02 Jun 2019 21:27:25: 12000000 INFO @ Sun, 02 Jun 2019 21:27:26: 14000000 INFO @ Sun, 02 Jun 2019 21:27:33: 15000000 INFO @ Sun, 02 Jun 2019 21:27:33: 13000000 INFO @ Sun, 02 Jun 2019 21:27:33: 13000000 INFO @ Sun, 02 Jun 2019 21:27:40: 16000000 INFO @ Sun, 02 Jun 2019 21:27:40: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:27:40: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:27:40: #1 total tags in treatment: 6896796 INFO @ Sun, 02 Jun 2019 21:27:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:27:40: #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 21:27:40: #1 tags after filtering in treatment: 6242999 INFO @ Sun, 02 Jun 2019 21:27:40: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:27:40: #1 finished! INFO @ Sun, 02 Jun 2019 21:27:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:27:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:27:41: #2 number of paired peaks: 709 WARNING @ Sun, 02 Jun 2019 21:27:41: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Sun, 02 Jun 2019 21:27:41: start model_add_line... INFO @ Sun, 02 Jun 2019 21:27:41: start X-correlation... INFO @ Sun, 02 Jun 2019 21:27:41: end of X-cor INFO @ Sun, 02 Jun 2019 21:27:41: #2 finished! INFO @ Sun, 02 Jun 2019 21:27:41: #2 predicted fragment length is 163 bps INFO @ Sun, 02 Jun 2019 21:27:41: #2 alternative fragment length(s) may be 4,163 bps INFO @ Sun, 02 Jun 2019 21:27:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.05_model.r INFO @ Sun, 02 Jun 2019 21:27:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:27:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:27:41: 14000000 INFO @ Sun, 02 Jun 2019 21:27:42: 14000000 INFO @ Sun, 02 Jun 2019 21:27:50: 15000000 INFO @ Sun, 02 Jun 2019 21:27:50: 15000000 INFO @ Sun, 02 Jun 2019 21:27:58: 16000000 INFO @ Sun, 02 Jun 2019 21:27:58: 16000000 INFO @ Sun, 02 Jun 2019 21:27:58: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:27:58: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:27:58: #1 total tags in treatment: 6896796 INFO @ Sun, 02 Jun 2019 21:27:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:27:58: #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 21:27:58: #1 tags after filtering in treatment: 6242999 INFO @ Sun, 02 Jun 2019 21:27:58: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:27:58: #1 finished! INFO @ Sun, 02 Jun 2019 21:27:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:27:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:27:58: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:27:58: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:27:58: #1 total tags in treatment: 6896796 INFO @ Sun, 02 Jun 2019 21:27:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:27:58: #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 21:27:59: #1 tags after filtering in treatment: 6242999 INFO @ Sun, 02 Jun 2019 21:27:59: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:27:59: #1 finished! INFO @ Sun, 02 Jun 2019 21:27:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:27:59: #2 number of paired peaks: 709 WARNING @ Sun, 02 Jun 2019 21:27:59: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Sun, 02 Jun 2019 21:27:59: start model_add_line... INFO @ Sun, 02 Jun 2019 21:27:59: start X-correlation... INFO @ Sun, 02 Jun 2019 21:27:59: end of X-cor INFO @ Sun, 02 Jun 2019 21:27:59: #2 finished! INFO @ Sun, 02 Jun 2019 21:27:59: #2 predicted fragment length is 163 bps INFO @ Sun, 02 Jun 2019 21:27:59: #2 alternative fragment length(s) may be 4,163 bps INFO @ Sun, 02 Jun 2019 21:27:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.10_model.r INFO @ Sun, 02 Jun 2019 21:27:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:27:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:27:59: #2 number of paired peaks: 709 WARNING @ Sun, 02 Jun 2019 21:27:59: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Sun, 02 Jun 2019 21:27:59: start model_add_line... INFO @ Sun, 02 Jun 2019 21:27:59: start X-correlation... INFO @ Sun, 02 Jun 2019 21:27:59: end of X-cor INFO @ Sun, 02 Jun 2019 21:27:59: #2 finished! INFO @ Sun, 02 Jun 2019 21:27:59: #2 predicted fragment length is 163 bps INFO @ Sun, 02 Jun 2019 21:27:59: #2 alternative fragment length(s) may be 4,163 bps INFO @ Sun, 02 Jun 2019 21:27:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.20_model.r INFO @ Sun, 02 Jun 2019 21:27:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:27:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:28:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:28:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:28:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:28:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.05_summits.bed INFO @ Sun, 02 Jun 2019 21:28:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (442 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:28:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:28:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.20_summits.bed INFO @ Sun, 02 Jun 2019 21:28:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (211 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996805/SRX4996805.10_summits.bed INFO @ Sun, 02 Jun 2019 21:28:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (316 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。