Job ID = 1292366 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 28,529,693 reads read : 57,059,386 reads written : 57,059,386 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: 00:38:13 28529693 reads; of these: 28529693 (100.00%) were paired; of these: 2541465 (8.91%) aligned concordantly 0 times 24052087 (84.31%) aligned concordantly exactly 1 time 1936141 (6.79%) aligned concordantly >1 times ---- 2541465 pairs aligned concordantly 0 times; of these: 1087534 (42.79%) aligned discordantly 1 time ---- 1453931 pairs aligned 0 times concordantly or discordantly; of these: 2907862 mates make up the pairs; of these: 1960347 (67.42%) aligned 0 times 651175 (22.39%) aligned exactly 1 time 296340 (10.19%) aligned >1 times 96.56% overall alignment rate Time searching: 00:38:13 Overall time: 00:38:13 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 24 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] 10373255 / 26811286 = 0.3869 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 19:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.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 19:28:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:28:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.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 19:28:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:28:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.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 19:28:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:28:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:28:43: 1000000 INFO @ Sun, 02 Jun 2019 19:28:43: 1000000 INFO @ Sun, 02 Jun 2019 19:28:44: 1000000 INFO @ Sun, 02 Jun 2019 19:28:51: 2000000 INFO @ Sun, 02 Jun 2019 19:28:52: 2000000 INFO @ Sun, 02 Jun 2019 19:28:52: 2000000 INFO @ Sun, 02 Jun 2019 19:29:00: 3000000 INFO @ Sun, 02 Jun 2019 19:29:00: 3000000 INFO @ Sun, 02 Jun 2019 19:29:01: 3000000 INFO @ Sun, 02 Jun 2019 19:29:08: 4000000 INFO @ Sun, 02 Jun 2019 19:29:08: 4000000 INFO @ Sun, 02 Jun 2019 19:29:10: 4000000 INFO @ Sun, 02 Jun 2019 19:29:16: 5000000 INFO @ Sun, 02 Jun 2019 19:29:16: 5000000 INFO @ Sun, 02 Jun 2019 19:29:19: 5000000 INFO @ Sun, 02 Jun 2019 19:29:24: 6000000 INFO @ Sun, 02 Jun 2019 19:29:24: 6000000 INFO @ Sun, 02 Jun 2019 19:29:28: 6000000 INFO @ Sun, 02 Jun 2019 19:29:32: 7000000 INFO @ Sun, 02 Jun 2019 19:29:32: 7000000 INFO @ Sun, 02 Jun 2019 19:29:36: 7000000 INFO @ Sun, 02 Jun 2019 19:29:40: 8000000 INFO @ Sun, 02 Jun 2019 19:29:40: 8000000 INFO @ Sun, 02 Jun 2019 19:29:45: 8000000 INFO @ Sun, 02 Jun 2019 19:29:47: 9000000 INFO @ Sun, 02 Jun 2019 19:29:48: 9000000 INFO @ Sun, 02 Jun 2019 19:29:53: 9000000 INFO @ Sun, 02 Jun 2019 19:29:54: 10000000 INFO @ Sun, 02 Jun 2019 19:29:56: 10000000 INFO @ Sun, 02 Jun 2019 19:30:01: 10000000 INFO @ Sun, 02 Jun 2019 19:30:02: 11000000 INFO @ Sun, 02 Jun 2019 19:30:04: 11000000 INFO @ Sun, 02 Jun 2019 19:30:09: 12000000 INFO @ Sun, 02 Jun 2019 19:30:10: 11000000 INFO @ Sun, 02 Jun 2019 19:30:12: 12000000 INFO @ Sun, 02 Jun 2019 19:30:17: 13000000 INFO @ Sun, 02 Jun 2019 19:30:18: 12000000 INFO @ Sun, 02 Jun 2019 19:30:20: 13000000 INFO @ Sun, 02 Jun 2019 19:30:25: 14000000 INFO @ Sun, 02 Jun 2019 19:30:27: 13000000 INFO @ Sun, 02 Jun 2019 19:30:28: 14000000 INFO @ Sun, 02 Jun 2019 19:30:32: 15000000 INFO @ Sun, 02 Jun 2019 19:30:35: 14000000 INFO @ Sun, 02 Jun 2019 19:30:36: 15000000 INFO @ Sun, 02 Jun 2019 19:30:39: 16000000 INFO @ Sun, 02 Jun 2019 19:30:43: 15000000 INFO @ Sun, 02 Jun 2019 19:30:43: 16000000 INFO @ Sun, 02 Jun 2019 19:30:47: 17000000 INFO @ Sun, 02 Jun 2019 19:30:51: 17000000 INFO @ Sun, 02 Jun 2019 19:30:51: 16000000 INFO @ Sun, 02 Jun 2019 19:30:54: 18000000 INFO @ Sun, 02 Jun 2019 19:30:58: 18000000 INFO @ Sun, 02 Jun 2019 19:30:59: 17000000 INFO @ Sun, 02 Jun 2019 19:31:02: 19000000 INFO @ Sun, 02 Jun 2019 19:31:06: 19000000 INFO @ Sun, 02 Jun 2019 19:31:07: 18000000 INFO @ Sun, 02 Jun 2019 19:31:09: 20000000 INFO @ Sun, 02 Jun 2019 19:31:13: 20000000 INFO @ Sun, 02 Jun 2019 19:31:16: 19000000 INFO @ Sun, 02 Jun 2019 19:31:16: 21000000 INFO @ Sun, 02 Jun 2019 19:31:21: 21000000 INFO @ Sun, 02 Jun 2019 19:31:23: 22000000 INFO @ Sun, 02 Jun 2019 19:31:25: 20000000 INFO @ Sun, 02 Jun 2019 19:31:28: 22000000 INFO @ Sun, 02 Jun 2019 19:31:31: 23000000 INFO @ Sun, 02 Jun 2019 19:31:33: 21000000 INFO @ Sun, 02 Jun 2019 19:31:36: 23000000 INFO @ Sun, 02 Jun 2019 19:31:38: 24000000 INFO @ Sun, 02 Jun 2019 19:31:42: 22000000 INFO @ Sun, 02 Jun 2019 19:31:43: 24000000 INFO @ Sun, 02 Jun 2019 19:31:45: 25000000 INFO @ Sun, 02 Jun 2019 19:31:50: 23000000 INFO @ Sun, 02 Jun 2019 19:31:50: 25000000 INFO @ Sun, 02 Jun 2019 19:31:52: 26000000 INFO @ Sun, 02 Jun 2019 19:31:58: 26000000 INFO @ Sun, 02 Jun 2019 19:32:00: 27000000 INFO @ Sun, 02 Jun 2019 19:32:00: 24000000 INFO @ Sun, 02 Jun 2019 19:32:05: 27000000 INFO @ Sun, 02 Jun 2019 19:32:07: 28000000 INFO @ Sun, 02 Jun 2019 19:32:09: 25000000 INFO @ Sun, 02 Jun 2019 19:32:13: 28000000 INFO @ Sun, 02 Jun 2019 19:32:14: 29000000 INFO @ Sun, 02 Jun 2019 19:32:19: 26000000 INFO @ Sun, 02 Jun 2019 19:32:20: 29000000 INFO @ Sun, 02 Jun 2019 19:32:21: 30000000 INFO @ Sun, 02 Jun 2019 19:32:28: 30000000 INFO @ Sun, 02 Jun 2019 19:32:28: 27000000 INFO @ Sun, 02 Jun 2019 19:32:29: 31000000 INFO @ Sun, 02 Jun 2019 19:32:35: 31000000 INFO @ Sun, 02 Jun 2019 19:32:36: 32000000 INFO @ Sun, 02 Jun 2019 19:32:37: 28000000 INFO @ Sun, 02 Jun 2019 19:32:42: 32000000 INFO @ Sun, 02 Jun 2019 19:32:43: 33000000 INFO @ Sun, 02 Jun 2019 19:32:47: 29000000 INFO @ Sun, 02 Jun 2019 19:32:50: 33000000 INFO @ Sun, 02 Jun 2019 19:32:50: 34000000 INFO @ Sun, 02 Jun 2019 19:32:53: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:32:53: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:32:53: #1 total tags in treatment: 15840738 INFO @ Sun, 02 Jun 2019 19:32:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:32:53: #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 19:32:53: #1 tags after filtering in treatment: 13702361 INFO @ Sun, 02 Jun 2019 19:32:53: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 02 Jun 2019 19:32:53: #1 finished! INFO @ Sun, 02 Jun 2019 19:32:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:32:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:32:55: #2 number of paired peaks: 420 WARNING @ Sun, 02 Jun 2019 19:32:55: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Sun, 02 Jun 2019 19:32:55: start model_add_line... INFO @ Sun, 02 Jun 2019 19:32:55: start X-correlation... INFO @ Sun, 02 Jun 2019 19:32:55: end of X-cor INFO @ Sun, 02 Jun 2019 19:32:55: #2 finished! INFO @ Sun, 02 Jun 2019 19:32:55: #2 predicted fragment length is 192 bps INFO @ Sun, 02 Jun 2019 19:32:55: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 02 Jun 2019 19:32:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.05_model.r INFO @ Sun, 02 Jun 2019 19:32:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:32:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:32:56: 30000000 INFO @ Sun, 02 Jun 2019 19:32:57: 34000000 INFO @ Sun, 02 Jun 2019 19:33:00: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:33:00: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:33:00: #1 total tags in treatment: 15840738 INFO @ Sun, 02 Jun 2019 19:33:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:33:00: #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 19:33:00: #1 tags after filtering in treatment: 13702361 INFO @ Sun, 02 Jun 2019 19:33:00: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 02 Jun 2019 19:33:00: #1 finished! INFO @ Sun, 02 Jun 2019 19:33:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:33:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:33:01: #2 number of paired peaks: 420 WARNING @ Sun, 02 Jun 2019 19:33:01: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Sun, 02 Jun 2019 19:33:01: start model_add_line... INFO @ Sun, 02 Jun 2019 19:33:01: start X-correlation... INFO @ Sun, 02 Jun 2019 19:33:01: end of X-cor INFO @ Sun, 02 Jun 2019 19:33:01: #2 finished! INFO @ Sun, 02 Jun 2019 19:33:01: #2 predicted fragment length is 192 bps INFO @ Sun, 02 Jun 2019 19:33:01: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 02 Jun 2019 19:33:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.10_model.r INFO @ Sun, 02 Jun 2019 19:33:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:33:05: 31000000 INFO @ Sun, 02 Jun 2019 19:33:15: 32000000 INFO @ Sun, 02 Jun 2019 19:33:24: 33000000 INFO @ Sun, 02 Jun 2019 19:33:32: 34000000 INFO @ Sun, 02 Jun 2019 19:33:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:33:36: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:33:36: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:33:36: #1 total tags in treatment: 15840738 INFO @ Sun, 02 Jun 2019 19:33:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:33:36: #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 19:33:36: #1 tags after filtering in treatment: 13702361 INFO @ Sun, 02 Jun 2019 19:33:36: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 02 Jun 2019 19:33:36: #1 finished! INFO @ Sun, 02 Jun 2019 19:33:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:33:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:33:37: #2 number of paired peaks: 420 WARNING @ Sun, 02 Jun 2019 19:33:37: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Sun, 02 Jun 2019 19:33:37: start model_add_line... INFO @ Sun, 02 Jun 2019 19:33:38: start X-correlation... INFO @ Sun, 02 Jun 2019 19:33:38: end of X-cor INFO @ Sun, 02 Jun 2019 19:33:38: #2 finished! INFO @ Sun, 02 Jun 2019 19:33:38: #2 predicted fragment length is 192 bps INFO @ Sun, 02 Jun 2019 19:33:38: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 02 Jun 2019 19:33:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.20_model.r INFO @ Sun, 02 Jun 2019 19:33:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:33:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:33:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.05_summits.bed INFO @ Sun, 02 Jun 2019 19:33:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3628 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:33:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:33:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:33:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.10_summits.bed INFO @ Sun, 02 Jun 2019 19:33:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2001 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:34:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:34:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:34:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733153/SRX3733153.20_summits.bed INFO @ Sun, 02 Jun 2019 19:34:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (839 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。