Job ID = 2640997 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,587,628 reads read : 23,175,256 reads written : 23,175,256 rm: cannot remove ‘[DSE]RR*’: 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: 00:13:49 11587628 reads; of these: 11587628 (100.00%) were paired; of these: 828370 (7.15%) aligned concordantly 0 times 9903705 (85.47%) aligned concordantly exactly 1 time 855553 (7.38%) aligned concordantly >1 times ---- 828370 pairs aligned concordantly 0 times; of these: 97746 (11.80%) aligned discordantly 1 time ---- 730624 pairs aligned 0 times concordantly or discordantly; of these: 1461248 mates make up the pairs; of these: 1415572 (96.87%) aligned 0 times 24347 (1.67%) aligned exactly 1 time 21329 (1.46%) aligned >1 times 93.89% overall alignment rate Time searching: 00:13:49 Overall time: 00:13:49 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] 108974 / 10852810 = 0.0100 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:57:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.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 20:57:58: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:57:58: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:58:07: 1000000 INFO @ Sat, 24 Aug 2019 20:58:16: 2000000 INFO @ Sat, 24 Aug 2019 20:58:24: 3000000 INFO @ Sat, 24 Aug 2019 20:58:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.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 20:58:28: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:58:28: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:58:33: 4000000 INFO @ Sat, 24 Aug 2019 20:58:37: 1000000 INFO @ Sat, 24 Aug 2019 20:58:42: 5000000 INFO @ Sat, 24 Aug 2019 20:58:46: 2000000 INFO @ Sat, 24 Aug 2019 20:58:51: 6000000 INFO @ Sat, 24 Aug 2019 20:58:55: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:58:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.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 20:58:58: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:58:58: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:59:00: 7000000 INFO @ Sat, 24 Aug 2019 20:59:04: 4000000 INFO @ Sat, 24 Aug 2019 20:59:09: 8000000 INFO @ Sat, 24 Aug 2019 20:59:09: 1000000 INFO @ Sat, 24 Aug 2019 20:59:13: 5000000 INFO @ Sat, 24 Aug 2019 20:59:18: 9000000 INFO @ Sat, 24 Aug 2019 20:59:20: 2000000 INFO @ Sat, 24 Aug 2019 20:59:22: 6000000 INFO @ Sat, 24 Aug 2019 20:59:27: 10000000 INFO @ Sat, 24 Aug 2019 20:59:31: 3000000 INFO @ Sat, 24 Aug 2019 20:59:31: 7000000 INFO @ Sat, 24 Aug 2019 20:59:36: 11000000 INFO @ Sat, 24 Aug 2019 20:59:40: 8000000 INFO @ Sat, 24 Aug 2019 20:59:42: 4000000 INFO @ Sat, 24 Aug 2019 20:59:45: 12000000 INFO @ Sat, 24 Aug 2019 20:59:49: 9000000 INFO @ Sat, 24 Aug 2019 20:59:53: 5000000 INFO @ Sat, 24 Aug 2019 20:59:54: 13000000 INFO @ Sat, 24 Aug 2019 20:59:58: 10000000 INFO @ Sat, 24 Aug 2019 21:00:03: 14000000 INFO @ Sat, 24 Aug 2019 21:00:03: 6000000 INFO @ Sat, 24 Aug 2019 21:00:07: 11000000 INFO @ Sat, 24 Aug 2019 21:00:12: 15000000 INFO @ Sat, 24 Aug 2019 21:00:14: 7000000 INFO @ Sat, 24 Aug 2019 21:00:16: 12000000 INFO @ Sat, 24 Aug 2019 21:00:21: 16000000 INFO @ Sat, 24 Aug 2019 21:00:25: 8000000 INFO @ Sat, 24 Aug 2019 21:00:25: 13000000 INFO @ Sat, 24 Aug 2019 21:00:30: 17000000 INFO @ Sat, 24 Aug 2019 21:00:34: 14000000 INFO @ Sat, 24 Aug 2019 21:00:36: 9000000 INFO @ Sat, 24 Aug 2019 21:00:39: 18000000 INFO @ Sat, 24 Aug 2019 21:00:43: 15000000 INFO @ Sat, 24 Aug 2019 21:00:47: 10000000 INFO @ Sat, 24 Aug 2019 21:00:48: 19000000 INFO @ Sat, 24 Aug 2019 21:00:52: 16000000 INFO @ Sat, 24 Aug 2019 21:00:57: 20000000 INFO @ Sat, 24 Aug 2019 21:00:58: 11000000 INFO @ Sat, 24 Aug 2019 21:01:01: 17000000 INFO @ Sat, 24 Aug 2019 21:01:06: 21000000 INFO @ Sat, 24 Aug 2019 21:01:08: 12000000 INFO @ Sat, 24 Aug 2019 21:01:10: 18000000 INFO @ Sat, 24 Aug 2019 21:01:10: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:01:10: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:01:10: #1 total tags in treatment: 10650804 INFO @ Sat, 24 Aug 2019 21:01:10: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:01:10: #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 21:01:11: #1 tags after filtering in treatment: 7617586 INFO @ Sat, 24 Aug 2019 21:01:11: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 21:01:11: #1 finished! INFO @ Sat, 24 Aug 2019 21:01:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:01:11: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:01:11: 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 21:01:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.05_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/SRX4936103/SRX4936103.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:01:19: 13000000 INFO @ Sat, 24 Aug 2019 21:01:19: 19000000 INFO @ Sat, 24 Aug 2019 21:01:28: 20000000 INFO @ Sat, 24 Aug 2019 21:01:30: 14000000 INFO @ Sat, 24 Aug 2019 21:01:37: 21000000 INFO @ Sat, 24 Aug 2019 21:01:40: 15000000 INFO @ Sat, 24 Aug 2019 21:01:42: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:01:42: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:01:42: #1 total tags in treatment: 10650804 INFO @ Sat, 24 Aug 2019 21:01:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:01:42: #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 21:01:42: #1 tags after filtering in treatment: 7617586 INFO @ Sat, 24 Aug 2019 21:01:42: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 21:01:42: #1 finished! INFO @ Sat, 24 Aug 2019 21:01:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:01:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:01:43: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:01:43: 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 21:01:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.10_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/SRX4936103/SRX4936103.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:01:51: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:02:01: 17000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:02:12: 18000000 INFO @ Sat, 24 Aug 2019 21:02:22: 19000000 INFO @ Sat, 24 Aug 2019 21:02:33: 20000000 INFO @ Sat, 24 Aug 2019 21:02:43: 21000000 INFO @ Sat, 24 Aug 2019 21:02:49: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:02:49: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:02:49: #1 total tags in treatment: 10650804 INFO @ Sat, 24 Aug 2019 21:02:49: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:02:49: #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 21:02:49: #1 tags after filtering in treatment: 7617586 INFO @ Sat, 24 Aug 2019 21:02:49: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 21:02:49: #1 finished! INFO @ Sat, 24 Aug 2019 21:02:49: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:02:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:02:50: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:02:50: 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 21:02:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.20_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/SRX4936103/SRX4936103.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936103/SRX4936103.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling