Job ID = 1290582 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,019,307 reads read : 26,038,614 reads written : 26,038,614 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: 00:14:22 13019307 reads; of these: 13019307 (100.00%) were paired; of these: 536307 (4.12%) aligned concordantly 0 times 10586560 (81.31%) aligned concordantly exactly 1 time 1896440 (14.57%) aligned concordantly >1 times ---- 536307 pairs aligned concordantly 0 times; of these: 284287 (53.01%) aligned discordantly 1 time ---- 252020 pairs aligned 0 times concordantly or discordantly; of these: 504040 mates make up the pairs; of these: 234014 (46.43%) aligned 0 times 147922 (29.35%) aligned exactly 1 time 122104 (24.23%) aligned >1 times 99.10% overall alignment rate Time searching: 00:14:22 Overall time: 00:14:22 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] 159218 / 12661221 = 0.0126 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 @ Sat, 01 Jun 2019 22:09:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.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 @ Sat, 01 Jun 2019 22:09:32: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:09:32: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:09:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.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 @ Sat, 01 Jun 2019 22:09:32: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:09:32: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:09:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.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 @ Sat, 01 Jun 2019 22:09:32: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:09:32: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:09:39: 1000000 INFO @ Sat, 01 Jun 2019 22:09:40: 1000000 INFO @ Sat, 01 Jun 2019 22:09:41: 1000000 INFO @ Sat, 01 Jun 2019 22:09:46: 2000000 INFO @ Sat, 01 Jun 2019 22:09:48: 2000000 INFO @ Sat, 01 Jun 2019 22:09:50: 2000000 INFO @ Sat, 01 Jun 2019 22:09:52: 3000000 INFO @ Sat, 01 Jun 2019 22:09:56: 3000000 INFO @ Sat, 01 Jun 2019 22:09:59: 4000000 INFO @ Sat, 01 Jun 2019 22:09:59: 3000000 INFO @ Sat, 01 Jun 2019 22:10:04: 4000000 INFO @ Sat, 01 Jun 2019 22:10:06: 5000000 INFO @ Sat, 01 Jun 2019 22:10:08: 4000000 INFO @ Sat, 01 Jun 2019 22:10:11: 5000000 INFO @ Sat, 01 Jun 2019 22:10:13: 6000000 INFO @ Sat, 01 Jun 2019 22:10:15: 5000000 INFO @ Sat, 01 Jun 2019 22:10:19: 6000000 INFO @ Sat, 01 Jun 2019 22:10:20: 7000000 INFO @ Sat, 01 Jun 2019 22:10:23: 6000000 INFO @ Sat, 01 Jun 2019 22:10:26: 7000000 INFO @ Sat, 01 Jun 2019 22:10:28: 8000000 INFO @ Sat, 01 Jun 2019 22:10:31: 7000000 INFO @ Sat, 01 Jun 2019 22:10:34: 8000000 INFO @ Sat, 01 Jun 2019 22:10:35: 9000000 INFO @ Sat, 01 Jun 2019 22:10:39: 8000000 INFO @ Sat, 01 Jun 2019 22:10:42: 10000000 INFO @ Sat, 01 Jun 2019 22:10:42: 9000000 INFO @ Sat, 01 Jun 2019 22:10:47: 9000000 INFO @ Sat, 01 Jun 2019 22:10:49: 11000000 INFO @ Sat, 01 Jun 2019 22:10:49: 10000000 INFO @ Sat, 01 Jun 2019 22:10:55: 10000000 INFO @ Sat, 01 Jun 2019 22:10:56: 11000000 INFO @ Sat, 01 Jun 2019 22:10:58: 12000000 INFO @ Sat, 01 Jun 2019 22:11:03: 12000000 INFO @ Sat, 01 Jun 2019 22:11:04: 11000000 INFO @ Sat, 01 Jun 2019 22:11:07: 13000000 INFO @ Sat, 01 Jun 2019 22:11:11: 13000000 INFO @ Sat, 01 Jun 2019 22:11:12: 12000000 INFO @ Sat, 01 Jun 2019 22:11:15: 14000000 INFO @ Sat, 01 Jun 2019 22:11:18: 14000000 INFO @ Sat, 01 Jun 2019 22:11:20: 13000000 INFO @ Sat, 01 Jun 2019 22:11:22: 15000000 INFO @ Sat, 01 Jun 2019 22:11:25: 15000000 INFO @ Sat, 01 Jun 2019 22:11:28: 14000000 INFO @ Sat, 01 Jun 2019 22:11:29: 16000000 INFO @ Sat, 01 Jun 2019 22:11:32: 16000000 INFO @ Sat, 01 Jun 2019 22:11:35: 15000000 INFO @ Sat, 01 Jun 2019 22:11:36: 17000000 INFO @ Sat, 01 Jun 2019 22:11:39: 17000000 INFO @ Sat, 01 Jun 2019 22:11:43: 18000000 INFO @ Sat, 01 Jun 2019 22:11:43: 16000000 INFO @ Sat, 01 Jun 2019 22:11:46: 18000000 INFO @ Sat, 01 Jun 2019 22:11:50: 19000000 INFO @ Sat, 01 Jun 2019 22:11:51: 17000000 INFO @ Sat, 01 Jun 2019 22:11:54: 19000000 INFO @ Sat, 01 Jun 2019 22:11:57: 20000000 INFO @ Sat, 01 Jun 2019 22:11:58: 18000000 INFO @ Sat, 01 Jun 2019 22:12:01: 20000000 INFO @ Sat, 01 Jun 2019 22:12:05: 21000000 INFO @ Sat, 01 Jun 2019 22:12:07: 19000000 INFO @ Sat, 01 Jun 2019 22:12:09: 21000000 INFO @ Sat, 01 Jun 2019 22:12:13: 22000000 INFO @ Sat, 01 Jun 2019 22:12:16: 20000000 INFO @ Sat, 01 Jun 2019 22:12:16: 22000000 INFO @ Sat, 01 Jun 2019 22:12:22: 23000000 INFO @ Sat, 01 Jun 2019 22:12:24: 23000000 INFO @ Sat, 01 Jun 2019 22:12:25: 21000000 INFO @ Sat, 01 Jun 2019 22:12:30: 24000000 INFO @ Sat, 01 Jun 2019 22:12:31: 24000000 INFO @ Sat, 01 Jun 2019 22:12:33: 22000000 INFO @ Sat, 01 Jun 2019 22:12:38: 25000000 INFO @ Sat, 01 Jun 2019 22:12:39: 25000000 INFO @ Sat, 01 Jun 2019 22:12:42: 23000000 INFO @ Sat, 01 Jun 2019 22:12:42: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:12:42: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:12:42: #1 total tags in treatment: 12324576 INFO @ Sat, 01 Jun 2019 22:12:42: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:12:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:12:42: #1 tags after filtering in treatment: 11402465 INFO @ Sat, 01 Jun 2019 22:12:42: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 01 Jun 2019 22:12:42: #1 finished! INFO @ Sat, 01 Jun 2019 22:12:42: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:12:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:12:43: #2 number of paired peaks: 328 WARNING @ Sat, 01 Jun 2019 22:12:43: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sat, 01 Jun 2019 22:12:43: start model_add_line... INFO @ Sat, 01 Jun 2019 22:12:43: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:12:43: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:12:43: #1 total tags in treatment: 12324576 INFO @ Sat, 01 Jun 2019 22:12:43: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:12:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:12:43: start X-correlation... INFO @ Sat, 01 Jun 2019 22:12:44: end of X-cor INFO @ Sat, 01 Jun 2019 22:12:44: #2 finished! INFO @ Sat, 01 Jun 2019 22:12:44: #2 predicted fragment length is 169 bps INFO @ Sat, 01 Jun 2019 22:12:44: #2 alternative fragment length(s) may be 4,169 bps INFO @ Sat, 01 Jun 2019 22:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.10_model.r INFO @ Sat, 01 Jun 2019 22:12:44: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:12:44: #1 tags after filtering in treatment: 11402465 INFO @ Sat, 01 Jun 2019 22:12:44: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 01 Jun 2019 22:12:44: #1 finished! INFO @ Sat, 01 Jun 2019 22:12:44: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:12:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:12:45: #2 number of paired peaks: 328 WARNING @ Sat, 01 Jun 2019 22:12:45: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sat, 01 Jun 2019 22:12:45: start model_add_line... INFO @ Sat, 01 Jun 2019 22:12:45: start X-correlation... INFO @ Sat, 01 Jun 2019 22:12:45: end of X-cor INFO @ Sat, 01 Jun 2019 22:12:45: #2 finished! INFO @ Sat, 01 Jun 2019 22:12:45: #2 predicted fragment length is 169 bps INFO @ Sat, 01 Jun 2019 22:12:45: #2 alternative fragment length(s) may be 4,169 bps INFO @ Sat, 01 Jun 2019 22:12:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.20_model.r INFO @ Sat, 01 Jun 2019 22:12:45: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:12:50: 24000000 INFO @ Sat, 01 Jun 2019 22:12:58: 25000000 INFO @ Sat, 01 Jun 2019 22:13:02: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:13:02: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:13:02: #1 total tags in treatment: 12324576 INFO @ Sat, 01 Jun 2019 22:13:02: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:13:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:13:02: #1 tags after filtering in treatment: 11402465 INFO @ Sat, 01 Jun 2019 22:13:02: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 01 Jun 2019 22:13:02: #1 finished! INFO @ Sat, 01 Jun 2019 22:13:02: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:13:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:13:04: #2 number of paired peaks: 328 WARNING @ Sat, 01 Jun 2019 22:13:04: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sat, 01 Jun 2019 22:13:04: start model_add_line... INFO @ Sat, 01 Jun 2019 22:13:04: start X-correlation... INFO @ Sat, 01 Jun 2019 22:13:04: end of X-cor INFO @ Sat, 01 Jun 2019 22:13:04: #2 finished! INFO @ Sat, 01 Jun 2019 22:13:04: #2 predicted fragment length is 169 bps INFO @ Sat, 01 Jun 2019 22:13:04: #2 alternative fragment length(s) may be 4,169 bps INFO @ Sat, 01 Jun 2019 22:13:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.05_model.r INFO @ Sat, 01 Jun 2019 22:13:04: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:13:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:13:16: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:13:17: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.10_peaks.xls INFO @ Sat, 01 Jun 2019 22:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.10_summits.bed INFO @ Sat, 01 Jun 2019 22:13:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (294 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:13:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.20_peaks.xls INFO @ Sat, 01 Jun 2019 22:13:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:13:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.20_summits.bed INFO @ Sat, 01 Jun 2019 22:13:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:13:36: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:13:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.05_peaks.xls INFO @ Sat, 01 Jun 2019 22:13:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:13:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353657/SRX1353657.05_summits.bed INFO @ Sat, 01 Jun 2019 22:13:51: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (751 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。