Job ID = 2641247 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,299,011 reads read : 6,598,022 reads written : 6,598,022 spots read : 3,246,471 reads read : 6,492,942 reads written : 6,492,942 spots read : 3,268,931 reads read : 6,537,862 reads written : 6,537,862 spots read : 3,242,501 reads read : 6,485,002 reads written : 6,485,002 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: 00:05:47 13056914 reads; of these: 13056914 (100.00%) were paired; of these: 4663382 (35.72%) aligned concordantly 0 times 7764714 (59.47%) aligned concordantly exactly 1 time 628818 (4.82%) aligned concordantly >1 times ---- 4663382 pairs aligned concordantly 0 times; of these: 22896 (0.49%) aligned discordantly 1 time ---- 4640486 pairs aligned 0 times concordantly or discordantly; of these: 9280972 mates make up the pairs; of these: 7636349 (82.28%) aligned 0 times 1510401 (16.27%) aligned exactly 1 time 134222 (1.45%) aligned >1 times 70.76% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 256768 / 8411417 = 0.0305 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.bam'] # control file = None # effective genome size = 1.21e+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, 24 Aug 2019 22:31:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:31:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:31:40: 1000000 INFO @ Sat, 24 Aug 2019 22:31:46: 2000000 INFO @ Sat, 24 Aug 2019 22:31:52: 3000000 INFO @ Sat, 24 Aug 2019 22:31:58: 4000000 INFO @ Sat, 24 Aug 2019 22:32:04: 5000000 INFO @ Sat, 24 Aug 2019 22:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.bam'] # control file = None # effective genome size = 1.21e+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, 24 Aug 2019 22:32:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:32:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:32:10: 6000000 INFO @ Sat, 24 Aug 2019 22:32:11: 1000000 INFO @ Sat, 24 Aug 2019 22:32:16: 7000000 INFO @ Sat, 24 Aug 2019 22:32:18: 2000000 INFO @ Sat, 24 Aug 2019 22:32:22: 8000000 INFO @ Sat, 24 Aug 2019 22:32:25: 3000000 INFO @ Sat, 24 Aug 2019 22:32:28: 9000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:32:32: 4000000 INFO @ Sat, 24 Aug 2019 22:32:34: 10000000 INFO @ Sat, 24 Aug 2019 22:32:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.bam'] # control file = None # effective genome size = 1.21e+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, 24 Aug 2019 22:32:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:32:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:32:39: 5000000 INFO @ Sat, 24 Aug 2019 22:32:40: 11000000 INFO @ Sat, 24 Aug 2019 22:32:41: 1000000 INFO @ Sat, 24 Aug 2019 22:32:46: 6000000 INFO @ Sat, 24 Aug 2019 22:32:46: 12000000 INFO @ Sat, 24 Aug 2019 22:32:48: 2000000 INFO @ Sat, 24 Aug 2019 22:32:53: 13000000 INFO @ Sat, 24 Aug 2019 22:32:53: 7000000 INFO @ Sat, 24 Aug 2019 22:32:55: 3000000 INFO @ Sat, 24 Aug 2019 22:32:59: 14000000 INFO @ Sat, 24 Aug 2019 22:33:00: 8000000 INFO @ Sat, 24 Aug 2019 22:33:02: 4000000 INFO @ Sat, 24 Aug 2019 22:33:05: 15000000 INFO @ Sat, 24 Aug 2019 22:33:07: 9000000 INFO @ Sat, 24 Aug 2019 22:33:09: 5000000 INFO @ Sat, 24 Aug 2019 22:33:11: 16000000 INFO @ Sat, 24 Aug 2019 22:33:14: 10000000 INFO @ Sat, 24 Aug 2019 22:33:16: 6000000 INFO @ Sat, 24 Aug 2019 22:33:17: 17000000 INFO @ Sat, 24 Aug 2019 22:33:20: 11000000 INFO @ Sat, 24 Aug 2019 22:33:23: 7000000 INFO @ Sat, 24 Aug 2019 22:33:23: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:33:23: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:33:23: #1 total tags in treatment: 8136947 INFO @ Sat, 24 Aug 2019 22:33:23: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:33:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:33:23: #1 tags after filtering in treatment: 5949720 INFO @ Sat, 24 Aug 2019 22:33:23: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 22:33:23: #1 finished! INFO @ Sat, 24 Aug 2019 22:33:23: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:33:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:33:24: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:33:24: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 22:33:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:33:27: 12000000 INFO @ Sat, 24 Aug 2019 22:33:30: 8000000 INFO @ Sat, 24 Aug 2019 22:33:34: 13000000 INFO @ Sat, 24 Aug 2019 22:33:36: 9000000 INFO @ Sat, 24 Aug 2019 22:33:41: 14000000 INFO @ Sat, 24 Aug 2019 22:33:43: 10000000 INFO @ Sat, 24 Aug 2019 22:33:48: 15000000 INFO @ Sat, 24 Aug 2019 22:33:50: 11000000 INFO @ Sat, 24 Aug 2019 22:33:55: 16000000 INFO @ Sat, 24 Aug 2019 22:33:57: 12000000 INFO @ Sat, 24 Aug 2019 22:34:02: 17000000 INFO @ Sat, 24 Aug 2019 22:34:04: 13000000 INFO @ Sat, 24 Aug 2019 22:34:09: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:34:09: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:34:09: #1 total tags in treatment: 8136947 INFO @ Sat, 24 Aug 2019 22:34:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:34:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:34:09: #1 tags after filtering in treatment: 5949720 INFO @ Sat, 24 Aug 2019 22:34:09: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 22:34:09: #1 finished! INFO @ Sat, 24 Aug 2019 22:34:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:34:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:34:09: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:34:09: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 22:34:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:34:11: 14000000 INFO @ Sat, 24 Aug 2019 22:34:18: 15000000 INFO @ Sat, 24 Aug 2019 22:34:24: 16000000 INFO @ Sat, 24 Aug 2019 22:34:31: 17000000 INFO @ Sat, 24 Aug 2019 22:34:37: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:34:37: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:34:37: #1 total tags in treatment: 8136947 INFO @ Sat, 24 Aug 2019 22:34:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:34:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:34:37: #1 tags after filtering in treatment: 5949720 INFO @ Sat, 24 Aug 2019 22:34:37: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 22:34:37: #1 finished! INFO @ Sat, 24 Aug 2019 22:34:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:34:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:34:38: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:34:38: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 22:34:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403223/SRX6403223.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。