Job ID = 2011690 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 15,233,560 reads read : 30,467,120 reads written : 30,467,120 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1157188.sra.cache’: 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: 00:18:14 15233560 reads; of these: 15233560 (100.00%) were paired; of these: 2729296 (17.92%) aligned concordantly 0 times 10319613 (67.74%) aligned concordantly exactly 1 time 2184651 (14.34%) aligned concordantly >1 times ---- 2729296 pairs aligned concordantly 0 times; of these: 288253 (10.56%) aligned discordantly 1 time ---- 2441043 pairs aligned 0 times concordantly or discordantly; of these: 4882086 mates make up the pairs; of these: 4405490 (90.24%) aligned 0 times 262123 (5.37%) aligned exactly 1 time 214473 (4.39%) aligned >1 times 85.54% overall alignment rate Time searching: 00:18:14 Overall time: 00:18:14 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 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 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] 1312379 / 12747150 = 0.1030 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, 06 Jul 2019 02:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.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, 06 Jul 2019 02:40:10: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:40:10: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:40:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.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, 06 Jul 2019 02:40:11: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:40:11: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.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, 06 Jul 2019 02:40:12: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:40:12: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:40:20: 1000000 INFO @ Sat, 06 Jul 2019 02:40:21: 1000000 INFO @ Sat, 06 Jul 2019 02:40:21: 1000000 INFO @ Sat, 06 Jul 2019 02:40:30: 2000000 INFO @ Sat, 06 Jul 2019 02:40:30: 2000000 INFO @ Sat, 06 Jul 2019 02:40:31: 2000000 INFO @ Sat, 06 Jul 2019 02:40:40: 3000000 INFO @ Sat, 06 Jul 2019 02:40:40: 3000000 INFO @ Sat, 06 Jul 2019 02:40:41: 3000000 INFO @ Sat, 06 Jul 2019 02:40:49: 4000000 INFO @ Sat, 06 Jul 2019 02:40:50: 4000000 INFO @ Sat, 06 Jul 2019 02:40:50: 4000000 INFO @ Sat, 06 Jul 2019 02:40:59: 5000000 INFO @ Sat, 06 Jul 2019 02:41:00: 5000000 INFO @ Sat, 06 Jul 2019 02:41:01: 5000000 INFO @ Sat, 06 Jul 2019 02:41:08: 6000000 INFO @ Sat, 06 Jul 2019 02:41:10: 6000000 INFO @ Sat, 06 Jul 2019 02:41:11: 6000000 INFO @ Sat, 06 Jul 2019 02:41:18: 7000000 INFO @ Sat, 06 Jul 2019 02:41:20: 7000000 INFO @ Sat, 06 Jul 2019 02:41:20: 7000000 INFO @ Sat, 06 Jul 2019 02:41:28: 8000000 INFO @ Sat, 06 Jul 2019 02:41:30: 8000000 INFO @ Sat, 06 Jul 2019 02:41:33: 8000000 INFO @ Sat, 06 Jul 2019 02:41:37: 9000000 INFO @ Sat, 06 Jul 2019 02:41:40: 9000000 INFO @ Sat, 06 Jul 2019 02:41:46: 9000000 INFO @ Sat, 06 Jul 2019 02:41:47: 10000000 INFO @ Sat, 06 Jul 2019 02:41:49: 10000000 INFO @ Sat, 06 Jul 2019 02:41:56: 11000000 INFO @ Sat, 06 Jul 2019 02:41:58: 10000000 INFO @ Sat, 06 Jul 2019 02:41:59: 11000000 INFO @ Sat, 06 Jul 2019 02:42:06: 12000000 INFO @ Sat, 06 Jul 2019 02:42:09: 12000000 INFO @ Sat, 06 Jul 2019 02:42:11: 11000000 INFO @ Sat, 06 Jul 2019 02:42:16: 13000000 INFO @ Sat, 06 Jul 2019 02:42:18: 13000000 INFO @ Sat, 06 Jul 2019 02:42:23: 12000000 INFO @ Sat, 06 Jul 2019 02:42:25: 14000000 INFO @ Sat, 06 Jul 2019 02:42:28: 14000000 INFO @ Sat, 06 Jul 2019 02:42:35: 15000000 INFO @ Sat, 06 Jul 2019 02:42:35: 13000000 INFO @ Sat, 06 Jul 2019 02:42:38: 15000000 INFO @ Sat, 06 Jul 2019 02:42:44: 16000000 INFO @ Sat, 06 Jul 2019 02:42:45: 14000000 INFO @ Sat, 06 Jul 2019 02:42:47: 16000000 INFO @ Sat, 06 Jul 2019 02:42:54: 17000000 INFO @ Sat, 06 Jul 2019 02:42:57: 15000000 INFO @ Sat, 06 Jul 2019 02:42:57: 17000000 INFO @ Sat, 06 Jul 2019 02:43:03: 18000000 INFO @ Sat, 06 Jul 2019 02:43:07: 18000000 INFO @ Sat, 06 Jul 2019 02:43:08: 16000000 INFO @ Sat, 06 Jul 2019 02:43:13: 19000000 INFO @ Sat, 06 Jul 2019 02:43:16: 19000000 INFO @ Sat, 06 Jul 2019 02:43:20: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:43:23: 20000000 INFO @ Sat, 06 Jul 2019 02:43:26: 20000000 INFO @ Sat, 06 Jul 2019 02:43:31: 18000000 INFO @ Sat, 06 Jul 2019 02:43:32: 21000000 INFO @ Sat, 06 Jul 2019 02:43:36: 21000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 02:43:42: 22000000 INFO @ Sat, 06 Jul 2019 02:43:43: 19000000 INFO @ Sat, 06 Jul 2019 02:43:45: 22000000 INFO @ Sat, 06 Jul 2019 02:43:52: 23000000 INFO @ Sat, 06 Jul 2019 02:43:54: 20000000 INFO @ Sat, 06 Jul 2019 02:43:55: 23000000 INFO @ Sat, 06 Jul 2019 02:43:56: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 02:43:56: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 02:43:56: #1 total tags in treatment: 11197101 INFO @ Sat, 06 Jul 2019 02:43:56: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:43:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:43:56: #1 tags after filtering in treatment: 7760130 INFO @ Sat, 06 Jul 2019 02:43:56: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 06 Jul 2019 02:43:56: #1 finished! INFO @ Sat, 06 Jul 2019 02:43:56: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:43:57: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:43:57: 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, 06 Jul 2019 02:43:57: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:43:59: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 02:43:59: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 02:43:59: #1 total tags in treatment: 11197101 INFO @ Sat, 06 Jul 2019 02:43:59: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:43:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:43:59: #1 tags after filtering in treatment: 7760130 INFO @ Sat, 06 Jul 2019 02:43:59: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 06 Jul 2019 02:43:59: #1 finished! INFO @ Sat, 06 Jul 2019 02:43:59: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:43:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:44:00: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:44:00: 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, 06 Jul 2019 02:44:00: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:44:06: 21000000 INFO @ Sat, 06 Jul 2019 02:44:17: 22000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.10_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/SRX461382/SRX461382.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:44:28: 23000000 INFO @ Sat, 06 Jul 2019 02:44:33: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 02:44:33: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 02:44:33: #1 total tags in treatment: 11197101 INFO @ Sat, 06 Jul 2019 02:44:33: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:44:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:44:33: #1 tags after filtering in treatment: 7760130 INFO @ Sat, 06 Jul 2019 02:44:33: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 06 Jul 2019 02:44:33: #1 finished! INFO @ Sat, 06 Jul 2019 02:44:33: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:44:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:44:34: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:44:34: 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, 06 Jul 2019 02:44:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.20_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/SRX461382/SRX461382.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX461382/SRX461382.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling