Job ID = 2640985 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,586,745 reads read : 25,173,490 reads written : 25,173,490 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: 00:14:47 12586745 reads; of these: 12586745 (100.00%) were paired; of these: 907914 (7.21%) aligned concordantly 0 times 10707053 (85.07%) aligned concordantly exactly 1 time 971778 (7.72%) aligned concordantly >1 times ---- 907914 pairs aligned concordantly 0 times; of these: 100804 (11.10%) aligned discordantly 1 time ---- 807110 pairs aligned 0 times concordantly or discordantly; of these: 1614220 mates make up the pairs; of these: 1565294 (96.97%) aligned 0 times 26022 (1.61%) aligned exactly 1 time 22904 (1.42%) aligned >1 times 93.78% overall alignment rate Time searching: 00:14:47 Overall time: 00:14:47 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 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] 138531 / 11776180 = 0.0118 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:57:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.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 20:57:17: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:57:17: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:57:29: 1000000 INFO @ Sat, 24 Aug 2019 20:57:41: 2000000 INFO @ Sat, 24 Aug 2019 20:57:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.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 20:57:47: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:57:47: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:57:52: 3000000 INFO @ Sat, 24 Aug 2019 20:57:56: 1000000 INFO @ Sat, 24 Aug 2019 20:58:05: 4000000 INFO @ Sat, 24 Aug 2019 20:58:06: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:58:15: 3000000 INFO @ Sat, 24 Aug 2019 20:58:17: 5000000 INFO @ Sat, 24 Aug 2019 20:58:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.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 20:58:17: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:58:17: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:58:25: 4000000 INFO @ Sat, 24 Aug 2019 20:58:29: 6000000 INFO @ Sat, 24 Aug 2019 20:58:32: 1000000 INFO @ Sat, 24 Aug 2019 20:58:34: 5000000 INFO @ Sat, 24 Aug 2019 20:58:41: 7000000 INFO @ Sat, 24 Aug 2019 20:58:44: 6000000 INFO @ Sat, 24 Aug 2019 20:58:47: 2000000 INFO @ Sat, 24 Aug 2019 20:58:53: 7000000 INFO @ Sat, 24 Aug 2019 20:58:53: 8000000 INFO @ Sat, 24 Aug 2019 20:59:02: 3000000 INFO @ Sat, 24 Aug 2019 20:59:03: 8000000 INFO @ Sat, 24 Aug 2019 20:59:06: 9000000 INFO @ Sat, 24 Aug 2019 20:59:12: 9000000 INFO @ Sat, 24 Aug 2019 20:59:17: 4000000 INFO @ Sat, 24 Aug 2019 20:59:18: 10000000 INFO @ Sat, 24 Aug 2019 20:59:22: 10000000 INFO @ Sat, 24 Aug 2019 20:59:30: 11000000 INFO @ Sat, 24 Aug 2019 20:59:31: 5000000 INFO @ Sat, 24 Aug 2019 20:59:31: 11000000 INFO @ Sat, 24 Aug 2019 20:59:41: 12000000 INFO @ Sat, 24 Aug 2019 20:59:41: 12000000 INFO @ Sat, 24 Aug 2019 20:59:46: 6000000 INFO @ Sat, 24 Aug 2019 20:59:50: 13000000 INFO @ Sat, 24 Aug 2019 20:59:53: 13000000 INFO @ Sat, 24 Aug 2019 20:59:59: 14000000 INFO @ Sat, 24 Aug 2019 21:00:01: 7000000 INFO @ Sat, 24 Aug 2019 21:00:05: 14000000 INFO @ Sat, 24 Aug 2019 21:00:08: 15000000 INFO @ Sat, 24 Aug 2019 21:00:16: 8000000 INFO @ Sat, 24 Aug 2019 21:00:17: 15000000 INFO @ Sat, 24 Aug 2019 21:00:18: 16000000 INFO @ Sat, 24 Aug 2019 21:00:28: 17000000 INFO @ Sat, 24 Aug 2019 21:00:29: 16000000 INFO @ Sat, 24 Aug 2019 21:00:31: 9000000 INFO @ Sat, 24 Aug 2019 21:00:37: 18000000 INFO @ Sat, 24 Aug 2019 21:00:41: 17000000 INFO @ Sat, 24 Aug 2019 21:00:46: 19000000 INFO @ Sat, 24 Aug 2019 21:00:46: 10000000 INFO @ Sat, 24 Aug 2019 21:00:53: 18000000 INFO @ Sat, 24 Aug 2019 21:00:56: 20000000 INFO @ Sat, 24 Aug 2019 21:01:01: 11000000 INFO @ Sat, 24 Aug 2019 21:01:06: 19000000 INFO @ Sat, 24 Aug 2019 21:01:06: 21000000 INFO @ Sat, 24 Aug 2019 21:01:13: 12000000 INFO @ Sat, 24 Aug 2019 21:01:15: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:01:19: 20000000 INFO @ Sat, 24 Aug 2019 21:01:24: 23000000 INFO @ Sat, 24 Aug 2019 21:01:26: 13000000 INFO @ Sat, 24 Aug 2019 21:01:27: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:01:27: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:01:27: #1 total tags in treatment: 11540941 INFO @ Sat, 24 Aug 2019 21:01:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:01:27: #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 21:01:27: #1 tags after filtering in treatment: 8184562 INFO @ Sat, 24 Aug 2019 21:01:27: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:01:27: #1 finished! INFO @ Sat, 24 Aug 2019 21:01:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:01:28: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:01:28: 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 21:01:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.10_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/SRX4936091/SRX4936091.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:01:31: 21000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:01:39: 14000000 INFO @ Sat, 24 Aug 2019 21:01:44: 22000000 INFO @ Sat, 24 Aug 2019 21:01:52: 15000000 INFO @ Sat, 24 Aug 2019 21:01:57: 23000000 INFO @ Sat, 24 Aug 2019 21:02:01: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:02:01: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:02:01: #1 total tags in treatment: 11540941 INFO @ Sat, 24 Aug 2019 21:02:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:02:01: #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 21:02:01: #1 tags after filtering in treatment: 8184562 INFO @ Sat, 24 Aug 2019 21:02:01: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:02:01: #1 finished! INFO @ Sat, 24 Aug 2019 21:02:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:02:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:02:02: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:02:02: 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 21:02:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.05_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/SRX4936091/SRX4936091.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:02:04: 16000000 INFO @ Sat, 24 Aug 2019 21:02:16: 17000000 INFO @ Sat, 24 Aug 2019 21:02:27: 18000000 INFO @ Sat, 24 Aug 2019 21:02:39: 19000000 INFO @ Sat, 24 Aug 2019 21:02:51: 20000000 INFO @ Sat, 24 Aug 2019 21:03:02: 21000000 INFO @ Sat, 24 Aug 2019 21:03:14: 22000000 INFO @ Sat, 24 Aug 2019 21:03:25: 23000000 INFO @ Sat, 24 Aug 2019 21:03:29: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:03:29: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:03:29: #1 total tags in treatment: 11540941 INFO @ Sat, 24 Aug 2019 21:03:29: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:03:29: #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 21:03:29: #1 tags after filtering in treatment: 8184562 INFO @ Sat, 24 Aug 2019 21:03:29: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:03:29: #1 finished! INFO @ Sat, 24 Aug 2019 21:03:29: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:03:30: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:03:30: 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 21:03:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.20_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/SRX4936091/SRX4936091.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936091/SRX4936091.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling