Job ID = 1290580 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 14,134,670 reads read : 28,269,340 reads written : 28,269,340 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: 00:16:27 14134670 reads; of these: 14134670 (100.00%) were paired; of these: 590490 (4.18%) aligned concordantly 0 times 11499535 (81.36%) aligned concordantly exactly 1 time 2044645 (14.47%) aligned concordantly >1 times ---- 590490 pairs aligned concordantly 0 times; of these: 316134 (53.54%) aligned discordantly 1 time ---- 274356 pairs aligned 0 times concordantly or discordantly; of these: 548712 mates make up the pairs; of these: 240397 (43.81%) aligned 0 times 167833 (30.59%) aligned exactly 1 time 140482 (25.60%) aligned >1 times 99.15% overall alignment rate Time searching: 00:16:27 Overall time: 00:16:27 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] 175199 / 13719600 = 0.0128 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 22:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.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 22:12:58: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:12:58: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.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 22:12:58: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:12:58: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.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 22:12:58: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:12:58: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:13:05: 1000000 INFO @ Sat, 01 Jun 2019 22:13:06: 1000000 INFO @ Sat, 01 Jun 2019 22:13:07: 1000000 INFO @ Sat, 01 Jun 2019 22:13:12: 2000000 INFO @ Sat, 01 Jun 2019 22:13:14: 2000000 INFO @ Sat, 01 Jun 2019 22:13:15: 2000000 INFO @ Sat, 01 Jun 2019 22:13:19: 3000000 INFO @ Sat, 01 Jun 2019 22:13:21: 3000000 INFO @ Sat, 01 Jun 2019 22:13:23: 3000000 INFO @ Sat, 01 Jun 2019 22:13:26: 4000000 INFO @ Sat, 01 Jun 2019 22:13:29: 4000000 INFO @ Sat, 01 Jun 2019 22:13:31: 4000000 INFO @ Sat, 01 Jun 2019 22:13:32: 5000000 INFO @ Sat, 01 Jun 2019 22:13:36: 5000000 INFO @ Sat, 01 Jun 2019 22:13:39: 5000000 INFO @ Sat, 01 Jun 2019 22:13:39: 6000000 INFO @ Sat, 01 Jun 2019 22:13:43: 6000000 INFO @ Sat, 01 Jun 2019 22:13:46: 7000000 INFO @ Sat, 01 Jun 2019 22:13:46: 6000000 INFO @ Sat, 01 Jun 2019 22:13:50: 7000000 INFO @ Sat, 01 Jun 2019 22:13:52: 8000000 INFO @ Sat, 01 Jun 2019 22:13:54: 7000000 INFO @ Sat, 01 Jun 2019 22:13:57: 8000000 INFO @ Sat, 01 Jun 2019 22:13:59: 9000000 INFO @ Sat, 01 Jun 2019 22:14:02: 8000000 INFO @ Sat, 01 Jun 2019 22:14:05: 9000000 INFO @ Sat, 01 Jun 2019 22:14:06: 10000000 INFO @ Sat, 01 Jun 2019 22:14:09: 9000000 INFO @ Sat, 01 Jun 2019 22:14:12: 10000000 INFO @ Sat, 01 Jun 2019 22:14:12: 11000000 INFO @ Sat, 01 Jun 2019 22:14:16: 10000000 INFO @ Sat, 01 Jun 2019 22:14:18: 11000000 INFO @ Sat, 01 Jun 2019 22:14:18: 12000000 INFO @ Sat, 01 Jun 2019 22:14:24: 11000000 INFO @ Sat, 01 Jun 2019 22:14:25: 13000000 INFO @ Sat, 01 Jun 2019 22:14:25: 12000000 INFO @ Sat, 01 Jun 2019 22:14:31: 12000000 INFO @ Sat, 01 Jun 2019 22:14:31: 14000000 INFO @ Sat, 01 Jun 2019 22:14:32: 13000000 INFO @ Sat, 01 Jun 2019 22:14:38: 15000000 INFO @ Sat, 01 Jun 2019 22:14:38: 13000000 INFO @ Sat, 01 Jun 2019 22:14:39: 14000000 INFO @ Sat, 01 Jun 2019 22:14:44: 16000000 INFO @ Sat, 01 Jun 2019 22:14:45: 14000000 INFO @ Sat, 01 Jun 2019 22:14:46: 15000000 INFO @ Sat, 01 Jun 2019 22:14:51: 17000000 INFO @ Sat, 01 Jun 2019 22:14:53: 15000000 INFO @ Sat, 01 Jun 2019 22:14:53: 16000000 INFO @ Sat, 01 Jun 2019 22:14:57: 18000000 INFO @ Sat, 01 Jun 2019 22:15:00: 16000000 INFO @ Sat, 01 Jun 2019 22:15:00: 17000000 INFO @ Sat, 01 Jun 2019 22:15:04: 19000000 INFO @ Sat, 01 Jun 2019 22:15:07: 18000000 INFO @ Sat, 01 Jun 2019 22:15:07: 17000000 INFO @ Sat, 01 Jun 2019 22:15:11: 20000000 INFO @ Sat, 01 Jun 2019 22:15:14: 19000000 INFO @ Sat, 01 Jun 2019 22:15:14: 18000000 INFO @ Sat, 01 Jun 2019 22:15:17: 21000000 INFO @ Sat, 01 Jun 2019 22:15:21: 20000000 INFO @ Sat, 01 Jun 2019 22:15:21: 19000000 INFO @ Sat, 01 Jun 2019 22:15:24: 22000000 INFO @ Sat, 01 Jun 2019 22:15:28: 21000000 INFO @ Sat, 01 Jun 2019 22:15:29: 20000000 INFO @ Sat, 01 Jun 2019 22:15:31: 23000000 INFO @ Sat, 01 Jun 2019 22:15:34: 22000000 INFO @ Sat, 01 Jun 2019 22:15:36: 21000000 INFO @ Sat, 01 Jun 2019 22:15:38: 24000000 INFO @ Sat, 01 Jun 2019 22:15:41: 23000000 INFO @ Sat, 01 Jun 2019 22:15:43: 22000000 INFO @ Sat, 01 Jun 2019 22:15:44: 25000000 INFO @ Sat, 01 Jun 2019 22:15:48: 24000000 INFO @ Sat, 01 Jun 2019 22:15:50: 23000000 INFO @ Sat, 01 Jun 2019 22:15:51: 26000000 INFO @ Sat, 01 Jun 2019 22:15:55: 25000000 INFO @ Sat, 01 Jun 2019 22:15:57: 24000000 INFO @ Sat, 01 Jun 2019 22:15:58: 27000000 INFO @ Sat, 01 Jun 2019 22:16:02: 26000000 INFO @ Sat, 01 Jun 2019 22:16:02: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:16:02: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:16:02: #1 total tags in treatment: 13369747 INFO @ Sat, 01 Jun 2019 22:16:02: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:16:02: #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 22:16:03: #1 tags after filtering in treatment: 12272758 INFO @ Sat, 01 Jun 2019 22:16:03: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 01 Jun 2019 22:16:03: #1 finished! INFO @ Sat, 01 Jun 2019 22:16:03: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:16:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:16:04: #2 number of paired peaks: 338 WARNING @ Sat, 01 Jun 2019 22:16:04: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Sat, 01 Jun 2019 22:16:04: start model_add_line... INFO @ Sat, 01 Jun 2019 22:16:04: start X-correlation... INFO @ Sat, 01 Jun 2019 22:16:04: end of X-cor INFO @ Sat, 01 Jun 2019 22:16:04: #2 finished! INFO @ Sat, 01 Jun 2019 22:16:04: #2 predicted fragment length is 119 bps INFO @ Sat, 01 Jun 2019 22:16:04: #2 alternative fragment length(s) may be 4,119 bps INFO @ Sat, 01 Jun 2019 22:16:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.05_model.r INFO @ Sat, 01 Jun 2019 22:16:04: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:16:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:16:04: 25000000 INFO @ Sat, 01 Jun 2019 22:16:09: 27000000 INFO @ Sat, 01 Jun 2019 22:16:12: 26000000 INFO @ Sat, 01 Jun 2019 22:16:13: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:16:13: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:16:13: #1 total tags in treatment: 13369747 INFO @ Sat, 01 Jun 2019 22:16:13: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:16:13: #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 22:16:14: #1 tags after filtering in treatment: 12272758 INFO @ Sat, 01 Jun 2019 22:16:14: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 01 Jun 2019 22:16:14: #1 finished! INFO @ Sat, 01 Jun 2019 22:16:14: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:16:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:16:15: #2 number of paired peaks: 338 WARNING @ Sat, 01 Jun 2019 22:16:15: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Sat, 01 Jun 2019 22:16:15: start model_add_line... INFO @ Sat, 01 Jun 2019 22:16:15: start X-correlation... INFO @ Sat, 01 Jun 2019 22:16:15: end of X-cor INFO @ Sat, 01 Jun 2019 22:16:15: #2 finished! INFO @ Sat, 01 Jun 2019 22:16:15: #2 predicted fragment length is 119 bps INFO @ Sat, 01 Jun 2019 22:16:15: #2 alternative fragment length(s) may be 4,119 bps INFO @ Sat, 01 Jun 2019 22:16:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.20_model.r INFO @ Sat, 01 Jun 2019 22:16:15: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:16:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:16:19: 27000000 INFO @ Sat, 01 Jun 2019 22:16:24: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:16:24: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:16:24: #1 total tags in treatment: 13369747 INFO @ Sat, 01 Jun 2019 22:16:24: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:16:24: #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 22:16:24: #1 tags after filtering in treatment: 12272758 INFO @ Sat, 01 Jun 2019 22:16:24: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 01 Jun 2019 22:16:24: #1 finished! INFO @ Sat, 01 Jun 2019 22:16:24: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:16:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:16:25: #2 number of paired peaks: 338 WARNING @ Sat, 01 Jun 2019 22:16:25: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Sat, 01 Jun 2019 22:16:25: start model_add_line... INFO @ Sat, 01 Jun 2019 22:16:25: start X-correlation... INFO @ Sat, 01 Jun 2019 22:16:25: end of X-cor INFO @ Sat, 01 Jun 2019 22:16:25: #2 finished! INFO @ Sat, 01 Jun 2019 22:16:25: #2 predicted fragment length is 119 bps INFO @ Sat, 01 Jun 2019 22:16:25: #2 alternative fragment length(s) may be 4,119 bps INFO @ Sat, 01 Jun 2019 22:16:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.10_model.r INFO @ Sat, 01 Jun 2019 22:16:25: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:16:38: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:16:48: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.05_peaks.xls INFO @ Sat, 01 Jun 2019 22:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:16:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.05_summits.bed INFO @ Sat, 01 Jun 2019 22:16:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (621 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:16:58: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.20_peaks.xls INFO @ Sat, 01 Jun 2019 22:17:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:17:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.20_summits.bed INFO @ Sat, 01 Jun 2019 22:17:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (197 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:17:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.10_peaks.xls INFO @ Sat, 01 Jun 2019 22:17:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:17:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353659/SRX1353659.10_summits.bed INFO @ Sat, 01 Jun 2019 22:17:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (317 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。