Job ID = 1292002 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 18,575,859 reads read : 37,151,718 reads written : 37,151,718 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: 00:31:07 18575859 reads; of these: 18575859 (100.00%) were paired; of these: 2863801 (15.42%) aligned concordantly 0 times 13211567 (71.12%) aligned concordantly exactly 1 time 2500491 (13.46%) aligned concordantly >1 times ---- 2863801 pairs aligned concordantly 0 times; of these: 1726038 (60.27%) aligned discordantly 1 time ---- 1137763 pairs aligned 0 times concordantly or discordantly; of these: 2275526 mates make up the pairs; of these: 1211375 (53.23%) aligned 0 times 608827 (26.76%) aligned exactly 1 time 455324 (20.01%) aligned >1 times 96.74% overall alignment rate Time searching: 00:31:07 Overall time: 00:31:07 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 16 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] 3280380 / 17428873 = 0.1882 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 18:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.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 18:06:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:06:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.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 18:06:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:06:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.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 18:06:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:06:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:06:56: 1000000 INFO @ Sun, 02 Jun 2019 18:06:57: 1000000 INFO @ Sun, 02 Jun 2019 18:06:57: 1000000 INFO @ Sun, 02 Jun 2019 18:07:10: 2000000 INFO @ Sun, 02 Jun 2019 18:07:10: 2000000 INFO @ Sun, 02 Jun 2019 18:07:11: 2000000 INFO @ Sun, 02 Jun 2019 18:07:23: 3000000 INFO @ Sun, 02 Jun 2019 18:07:23: 3000000 INFO @ Sun, 02 Jun 2019 18:07:24: 3000000 INFO @ Sun, 02 Jun 2019 18:07:36: 4000000 INFO @ Sun, 02 Jun 2019 18:07:37: 4000000 INFO @ Sun, 02 Jun 2019 18:07:37: 4000000 INFO @ Sun, 02 Jun 2019 18:07:49: 5000000 INFO @ Sun, 02 Jun 2019 18:07:50: 5000000 INFO @ Sun, 02 Jun 2019 18:07:50: 5000000 INFO @ Sun, 02 Jun 2019 18:08:03: 6000000 INFO @ Sun, 02 Jun 2019 18:08:03: 6000000 INFO @ Sun, 02 Jun 2019 18:08:03: 6000000 INFO @ Sun, 02 Jun 2019 18:08:16: 7000000 INFO @ Sun, 02 Jun 2019 18:08:17: 7000000 INFO @ Sun, 02 Jun 2019 18:08:18: 7000000 INFO @ Sun, 02 Jun 2019 18:08:29: 8000000 INFO @ Sun, 02 Jun 2019 18:08:31: 8000000 INFO @ Sun, 02 Jun 2019 18:08:31: 8000000 INFO @ Sun, 02 Jun 2019 18:08:42: 9000000 INFO @ Sun, 02 Jun 2019 18:08:44: 9000000 INFO @ Sun, 02 Jun 2019 18:08:44: 9000000 INFO @ Sun, 02 Jun 2019 18:08:55: 10000000 INFO @ Sun, 02 Jun 2019 18:08:57: 10000000 INFO @ Sun, 02 Jun 2019 18:08:58: 10000000 INFO @ Sun, 02 Jun 2019 18:09:07: 11000000 INFO @ Sun, 02 Jun 2019 18:09:11: 11000000 INFO @ Sun, 02 Jun 2019 18:09:11: 11000000 INFO @ Sun, 02 Jun 2019 18:09:20: 12000000 INFO @ Sun, 02 Jun 2019 18:09:24: 12000000 INFO @ Sun, 02 Jun 2019 18:09:24: 12000000 INFO @ Sun, 02 Jun 2019 18:09:32: 13000000 INFO @ Sun, 02 Jun 2019 18:09:37: 13000000 INFO @ Sun, 02 Jun 2019 18:09:37: 13000000 INFO @ Sun, 02 Jun 2019 18:09:45: 14000000 INFO @ Sun, 02 Jun 2019 18:09:50: 14000000 INFO @ Sun, 02 Jun 2019 18:09:50: 14000000 INFO @ Sun, 02 Jun 2019 18:09:57: 15000000 INFO @ Sun, 02 Jun 2019 18:10:04: 15000000 INFO @ Sun, 02 Jun 2019 18:10:04: 15000000 INFO @ Sun, 02 Jun 2019 18:10:11: 16000000 INFO @ Sun, 02 Jun 2019 18:10:17: 16000000 INFO @ Sun, 02 Jun 2019 18:10:17: 16000000 INFO @ Sun, 02 Jun 2019 18:10:24: 17000000 INFO @ Sun, 02 Jun 2019 18:10:31: 17000000 INFO @ Sun, 02 Jun 2019 18:10:31: 17000000 INFO @ Sun, 02 Jun 2019 18:10:38: 18000000 INFO @ Sun, 02 Jun 2019 18:10:44: 18000000 INFO @ Sun, 02 Jun 2019 18:10:44: 18000000 INFO @ Sun, 02 Jun 2019 18:10:50: 19000000 INFO @ Sun, 02 Jun 2019 18:10:57: 19000000 INFO @ Sun, 02 Jun 2019 18:10:57: 19000000 INFO @ Sun, 02 Jun 2019 18:11:03: 20000000 INFO @ Sun, 02 Jun 2019 18:11:12: 20000000 INFO @ Sun, 02 Jun 2019 18:11:12: 20000000 INFO @ Sun, 02 Jun 2019 18:11:17: 21000000 INFO @ Sun, 02 Jun 2019 18:11:25: 21000000 INFO @ Sun, 02 Jun 2019 18:11:26: 21000000 INFO @ Sun, 02 Jun 2019 18:11:29: 22000000 INFO @ Sun, 02 Jun 2019 18:11:37: 22000000 INFO @ Sun, 02 Jun 2019 18:11:38: 22000000 INFO @ Sun, 02 Jun 2019 18:11:42: 23000000 INFO @ Sun, 02 Jun 2019 18:11:51: 23000000 INFO @ Sun, 02 Jun 2019 18:11:51: 23000000 INFO @ Sun, 02 Jun 2019 18:11:55: 24000000 INFO @ Sun, 02 Jun 2019 18:12:04: 24000000 INFO @ Sun, 02 Jun 2019 18:12:05: 24000000 INFO @ Sun, 02 Jun 2019 18:12:08: 25000000 INFO @ Sun, 02 Jun 2019 18:12:16: 25000000 INFO @ Sun, 02 Jun 2019 18:12:20: 25000000 INFO @ Sun, 02 Jun 2019 18:12:21: 26000000 INFO @ Sun, 02 Jun 2019 18:12:29: 26000000 INFO @ Sun, 02 Jun 2019 18:12:33: 26000000 INFO @ Sun, 02 Jun 2019 18:12:34: 27000000 INFO @ Sun, 02 Jun 2019 18:12:42: 27000000 INFO @ Sun, 02 Jun 2019 18:12:47: 27000000 INFO @ Sun, 02 Jun 2019 18:12:48: 28000000 INFO @ Sun, 02 Jun 2019 18:12:56: 28000000 INFO @ Sun, 02 Jun 2019 18:13:01: 29000000 INFO @ Sun, 02 Jun 2019 18:13:01: 28000000 INFO @ Sun, 02 Jun 2019 18:13:06: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:13:06: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:13:06: #1 total tags in treatment: 12571784 INFO @ Sun, 02 Jun 2019 18:13:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:13:06: #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 18:13:06: #1 tags after filtering in treatment: 11479778 INFO @ Sun, 02 Jun 2019 18:13:06: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 18:13:06: #1 finished! INFO @ Sun, 02 Jun 2019 18:13:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:13:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:13:07: #2 number of paired peaks: 494 WARNING @ Sun, 02 Jun 2019 18:13:07: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Sun, 02 Jun 2019 18:13:07: start model_add_line... INFO @ Sun, 02 Jun 2019 18:13:08: start X-correlation... INFO @ Sun, 02 Jun 2019 18:13:08: end of X-cor INFO @ Sun, 02 Jun 2019 18:13:08: #2 finished! INFO @ Sun, 02 Jun 2019 18:13:08: #2 predicted fragment length is 144 bps INFO @ Sun, 02 Jun 2019 18:13:08: #2 alternative fragment length(s) may be 4,144 bps INFO @ Sun, 02 Jun 2019 18:13:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.05_model.r INFO @ Sun, 02 Jun 2019 18:13:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:13:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:13:09: 29000000 INFO @ Sun, 02 Jun 2019 18:13:14: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:13:14: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:13:14: #1 total tags in treatment: 12571784 INFO @ Sun, 02 Jun 2019 18:13:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:13:14: #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 18:13:14: 29000000 INFO @ Sun, 02 Jun 2019 18:13:14: #1 tags after filtering in treatment: 11479778 INFO @ Sun, 02 Jun 2019 18:13:14: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 18:13:14: #1 finished! INFO @ Sun, 02 Jun 2019 18:13:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:13:16: #2 number of paired peaks: 494 WARNING @ Sun, 02 Jun 2019 18:13:16: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Sun, 02 Jun 2019 18:13:16: start model_add_line... INFO @ Sun, 02 Jun 2019 18:13:16: start X-correlation... INFO @ Sun, 02 Jun 2019 18:13:16: end of X-cor INFO @ Sun, 02 Jun 2019 18:13:16: #2 finished! INFO @ Sun, 02 Jun 2019 18:13:16: #2 predicted fragment length is 144 bps INFO @ Sun, 02 Jun 2019 18:13:16: #2 alternative fragment length(s) may be 4,144 bps INFO @ Sun, 02 Jun 2019 18:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.10_model.r INFO @ Sun, 02 Jun 2019 18:13:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:13:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:13:19: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:13:19: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:13:19: #1 total tags in treatment: 12571784 INFO @ Sun, 02 Jun 2019 18:13:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:13:19: #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 18:13:19: #1 tags after filtering in treatment: 11479778 INFO @ Sun, 02 Jun 2019 18:13:19: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 18:13:19: #1 finished! INFO @ Sun, 02 Jun 2019 18:13:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:13:21: #2 number of paired peaks: 494 WARNING @ Sun, 02 Jun 2019 18:13:21: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Sun, 02 Jun 2019 18:13:21: start model_add_line... INFO @ Sun, 02 Jun 2019 18:13:21: start X-correlation... INFO @ Sun, 02 Jun 2019 18:13:21: end of X-cor INFO @ Sun, 02 Jun 2019 18:13:21: #2 finished! INFO @ Sun, 02 Jun 2019 18:13:21: #2 predicted fragment length is 144 bps INFO @ Sun, 02 Jun 2019 18:13:21: #2 alternative fragment length(s) may be 4,144 bps INFO @ Sun, 02 Jun 2019 18:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.20_model.r INFO @ Sun, 02 Jun 2019 18:13:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:13:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:13:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:14:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:14:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:14:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:14:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:14:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.05_summits.bed INFO @ Sun, 02 Jun 2019 18:14:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (443 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:14:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:14:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:14:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.10_summits.bed INFO @ Sun, 02 Jun 2019 18:14:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (330 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:14:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:14:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:14:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978698/SRX2978698.20_summits.bed INFO @ Sun, 02 Jun 2019 18:14:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (225 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。