Job ID = 1292871 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,341,230 reads read : 42,682,460 reads written : 42,682,460 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: 00:27:01 21341230 reads; of these: 21341230 (100.00%) were paired; of these: 1594394 (7.47%) aligned concordantly 0 times 15978471 (74.87%) aligned concordantly exactly 1 time 3768365 (17.66%) aligned concordantly >1 times ---- 1594394 pairs aligned concordantly 0 times; of these: 814165 (51.06%) aligned discordantly 1 time ---- 780229 pairs aligned 0 times concordantly or discordantly; of these: 1560458 mates make up the pairs; of these: 785177 (50.32%) aligned 0 times 424888 (27.23%) aligned exactly 1 time 350393 (22.45%) aligned >1 times 98.16% overall alignment rate Time searching: 00:27:01 Overall time: 00:27:01 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 20 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] 1963625 / 20530991 = 0.0956 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 21:45:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.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 21:45:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:45:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:45:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.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 21:45:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:45:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:45:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.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 21:45:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:45:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:45:55: 1000000 INFO @ Sun, 02 Jun 2019 21:45:57: 1000000 INFO @ Sun, 02 Jun 2019 21:45:58: 1000000 INFO @ Sun, 02 Jun 2019 21:46:03: 2000000 INFO @ Sun, 02 Jun 2019 21:46:06: 2000000 INFO @ Sun, 02 Jun 2019 21:46:07: 2000000 INFO @ Sun, 02 Jun 2019 21:46:11: 3000000 INFO @ Sun, 02 Jun 2019 21:46:13: 3000000 INFO @ Sun, 02 Jun 2019 21:46:16: 3000000 INFO @ Sun, 02 Jun 2019 21:46:18: 4000000 INFO @ Sun, 02 Jun 2019 21:46:21: 4000000 INFO @ Sun, 02 Jun 2019 21:46:25: 4000000 INFO @ Sun, 02 Jun 2019 21:46:26: 5000000 INFO @ Sun, 02 Jun 2019 21:46:29: 5000000 INFO @ Sun, 02 Jun 2019 21:46:33: 6000000 INFO @ Sun, 02 Jun 2019 21:46:34: 5000000 INFO @ Sun, 02 Jun 2019 21:46:37: 6000000 INFO @ Sun, 02 Jun 2019 21:46:41: 7000000 INFO @ Sun, 02 Jun 2019 21:46:43: 6000000 INFO @ Sun, 02 Jun 2019 21:46:45: 7000000 INFO @ Sun, 02 Jun 2019 21:46:49: 8000000 INFO @ Sun, 02 Jun 2019 21:46:52: 7000000 INFO @ Sun, 02 Jun 2019 21:46:53: 8000000 INFO @ Sun, 02 Jun 2019 21:46:57: 9000000 INFO @ Sun, 02 Jun 2019 21:47:01: 8000000 INFO @ Sun, 02 Jun 2019 21:47:02: 9000000 INFO @ Sun, 02 Jun 2019 21:47:05: 10000000 INFO @ Sun, 02 Jun 2019 21:47:08: 9000000 INFO @ Sun, 02 Jun 2019 21:47:10: 10000000 INFO @ Sun, 02 Jun 2019 21:47:13: 11000000 INFO @ Sun, 02 Jun 2019 21:47:16: 10000000 INFO @ Sun, 02 Jun 2019 21:47:18: 11000000 INFO @ Sun, 02 Jun 2019 21:47:20: 12000000 INFO @ Sun, 02 Jun 2019 21:47:25: 12000000 INFO @ Sun, 02 Jun 2019 21:47:25: 11000000 INFO @ Sun, 02 Jun 2019 21:47:28: 13000000 INFO @ Sun, 02 Jun 2019 21:47:33: 13000000 INFO @ Sun, 02 Jun 2019 21:47:35: 12000000 INFO @ Sun, 02 Jun 2019 21:47:36: 14000000 INFO @ Sun, 02 Jun 2019 21:47:40: 14000000 INFO @ Sun, 02 Jun 2019 21:47:43: 15000000 INFO @ Sun, 02 Jun 2019 21:47:45: 13000000 INFO @ Sun, 02 Jun 2019 21:47:48: 15000000 INFO @ Sun, 02 Jun 2019 21:47:51: 16000000 INFO @ Sun, 02 Jun 2019 21:47:54: 14000000 INFO @ Sun, 02 Jun 2019 21:47:55: 16000000 INFO @ Sun, 02 Jun 2019 21:47:58: 17000000 INFO @ Sun, 02 Jun 2019 21:48:03: 17000000 INFO @ Sun, 02 Jun 2019 21:48:03: 15000000 INFO @ Sun, 02 Jun 2019 21:48:06: 18000000 INFO @ Sun, 02 Jun 2019 21:48:10: 18000000 INFO @ Sun, 02 Jun 2019 21:48:12: 16000000 INFO @ Sun, 02 Jun 2019 21:48:13: 19000000 INFO @ Sun, 02 Jun 2019 21:48:18: 19000000 INFO @ Sun, 02 Jun 2019 21:48:21: 20000000 INFO @ Sun, 02 Jun 2019 21:48:22: 17000000 INFO @ Sun, 02 Jun 2019 21:48:27: 20000000 INFO @ Sun, 02 Jun 2019 21:48:28: 21000000 INFO @ Sun, 02 Jun 2019 21:48:32: 18000000 INFO @ Sun, 02 Jun 2019 21:48:35: 21000000 INFO @ Sun, 02 Jun 2019 21:48:36: 22000000 INFO @ Sun, 02 Jun 2019 21:48:41: 19000000 INFO @ Sun, 02 Jun 2019 21:48:43: 22000000 INFO @ Sun, 02 Jun 2019 21:48:43: 23000000 INFO @ Sun, 02 Jun 2019 21:48:50: 20000000 INFO @ Sun, 02 Jun 2019 21:48:50: 23000000 INFO @ Sun, 02 Jun 2019 21:48:51: 24000000 INFO @ Sun, 02 Jun 2019 21:48:57: 24000000 INFO @ Sun, 02 Jun 2019 21:48:58: 25000000 INFO @ Sun, 02 Jun 2019 21:48:59: 21000000 INFO @ Sun, 02 Jun 2019 21:49:05: 25000000 INFO @ Sun, 02 Jun 2019 21:49:06: 26000000 INFO @ Sun, 02 Jun 2019 21:49:09: 22000000 INFO @ Sun, 02 Jun 2019 21:49:12: 26000000 INFO @ Sun, 02 Jun 2019 21:49:14: 27000000 INFO @ Sun, 02 Jun 2019 21:49:18: 23000000 INFO @ Sun, 02 Jun 2019 21:49:20: 27000000 INFO @ Sun, 02 Jun 2019 21:49:21: 28000000 INFO @ Sun, 02 Jun 2019 21:49:27: 28000000 INFO @ Sun, 02 Jun 2019 21:49:27: 24000000 INFO @ Sun, 02 Jun 2019 21:49:29: 29000000 INFO @ Sun, 02 Jun 2019 21:49:34: 29000000 INFO @ Sun, 02 Jun 2019 21:49:36: 25000000 INFO @ Sun, 02 Jun 2019 21:49:36: 30000000 INFO @ Sun, 02 Jun 2019 21:49:41: 30000000 INFO @ Sun, 02 Jun 2019 21:49:43: 31000000 INFO @ Sun, 02 Jun 2019 21:49:45: 26000000 INFO @ Sun, 02 Jun 2019 21:49:49: 31000000 INFO @ Sun, 02 Jun 2019 21:49:51: 32000000 INFO @ Sun, 02 Jun 2019 21:49:54: 27000000 INFO @ Sun, 02 Jun 2019 21:49:56: 32000000 INFO @ Sun, 02 Jun 2019 21:49:58: 33000000 INFO @ Sun, 02 Jun 2019 21:50:03: 28000000 INFO @ Sun, 02 Jun 2019 21:50:04: 33000000 INFO @ Sun, 02 Jun 2019 21:50:06: 34000000 INFO @ Sun, 02 Jun 2019 21:50:11: 34000000 INFO @ Sun, 02 Jun 2019 21:50:12: 29000000 INFO @ Sun, 02 Jun 2019 21:50:13: 35000000 INFO @ Sun, 02 Jun 2019 21:50:18: 35000000 INFO @ Sun, 02 Jun 2019 21:50:21: 36000000 INFO @ Sun, 02 Jun 2019 21:50:21: 30000000 INFO @ Sun, 02 Jun 2019 21:50:26: 36000000 INFO @ Sun, 02 Jun 2019 21:50:28: 37000000 INFO @ Sun, 02 Jun 2019 21:50:30: 31000000 INFO @ Sun, 02 Jun 2019 21:50:33: 37000000 INFO @ Sun, 02 Jun 2019 21:50:36: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:50:36: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:50:36: #1 total tags in treatment: 17811221 INFO @ Sun, 02 Jun 2019 21:50:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:50:36: #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 21:50:36: #1 tags after filtering in treatment: 15660771 INFO @ Sun, 02 Jun 2019 21:50:36: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 02 Jun 2019 21:50:36: #1 finished! INFO @ Sun, 02 Jun 2019 21:50:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:50:37: #2 number of paired peaks: 434 WARNING @ Sun, 02 Jun 2019 21:50:37: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sun, 02 Jun 2019 21:50:37: start model_add_line... INFO @ Sun, 02 Jun 2019 21:50:37: start X-correlation... INFO @ Sun, 02 Jun 2019 21:50:38: end of X-cor INFO @ Sun, 02 Jun 2019 21:50:38: #2 finished! INFO @ Sun, 02 Jun 2019 21:50:38: #2 predicted fragment length is 126 bps INFO @ Sun, 02 Jun 2019 21:50:38: #2 alternative fragment length(s) may be 3,126 bps INFO @ Sun, 02 Jun 2019 21:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.05_model.r INFO @ Sun, 02 Jun 2019 21:50:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:50:39: 32000000 INFO @ Sun, 02 Jun 2019 21:50:40: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:50:40: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:50:40: #1 total tags in treatment: 17811221 INFO @ Sun, 02 Jun 2019 21:50:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:50:40: #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 21:50:41: #1 tags after filtering in treatment: 15660771 INFO @ Sun, 02 Jun 2019 21:50:41: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 02 Jun 2019 21:50:41: #1 finished! INFO @ Sun, 02 Jun 2019 21:50:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:50:42: #2 number of paired peaks: 434 WARNING @ Sun, 02 Jun 2019 21:50:42: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sun, 02 Jun 2019 21:50:42: start model_add_line... INFO @ Sun, 02 Jun 2019 21:50:42: start X-correlation... INFO @ Sun, 02 Jun 2019 21:50:42: end of X-cor INFO @ Sun, 02 Jun 2019 21:50:42: #2 finished! INFO @ Sun, 02 Jun 2019 21:50:42: #2 predicted fragment length is 126 bps INFO @ Sun, 02 Jun 2019 21:50:42: #2 alternative fragment length(s) may be 3,126 bps INFO @ Sun, 02 Jun 2019 21:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.10_model.r INFO @ Sun, 02 Jun 2019 21:50:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:50:48: 33000000 INFO @ Sun, 02 Jun 2019 21:50:57: 34000000 INFO @ Sun, 02 Jun 2019 21:51:05: 35000000 INFO @ Sun, 02 Jun 2019 21:51:14: 36000000 INFO @ Sun, 02 Jun 2019 21:51:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:51:23: 37000000 INFO @ Sun, 02 Jun 2019 21:51:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:51:31: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:51:31: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:51:31: #1 total tags in treatment: 17811221 INFO @ Sun, 02 Jun 2019 21:51:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:51:31: #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 21:51:31: #1 tags after filtering in treatment: 15660771 INFO @ Sun, 02 Jun 2019 21:51:31: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 02 Jun 2019 21:51:31: #1 finished! INFO @ Sun, 02 Jun 2019 21:51:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:51:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:51:33: #2 number of paired peaks: 434 WARNING @ Sun, 02 Jun 2019 21:51:33: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sun, 02 Jun 2019 21:51:33: start model_add_line... INFO @ Sun, 02 Jun 2019 21:51:33: start X-correlation... INFO @ Sun, 02 Jun 2019 21:51:33: end of X-cor INFO @ Sun, 02 Jun 2019 21:51:33: #2 finished! INFO @ Sun, 02 Jun 2019 21:51:33: #2 predicted fragment length is 126 bps INFO @ Sun, 02 Jun 2019 21:51:33: #2 alternative fragment length(s) may be 3,126 bps INFO @ Sun, 02 Jun 2019 21:51:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.20_model.r INFO @ Sun, 02 Jun 2019 21:51:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:51:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:51:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:51:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:51:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.05_summits.bed INFO @ Sun, 02 Jun 2019 21:51:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (465 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.10_summits.bed INFO @ Sun, 02 Jun 2019 21:51:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 257 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:52:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:52:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:52:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:52:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996803/SRX4996803.20_summits.bed INFO @ Sun, 02 Jun 2019 21:52:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (235 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。