Job ID = 4289013 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,819,243 reads read : 25,638,486 reads written : 25,638,486 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: 00:12:57 12819243 reads; of these: 12819243 (100.00%) were paired; of these: 1291768 (10.08%) aligned concordantly 0 times 10518148 (82.05%) aligned concordantly exactly 1 time 1009327 (7.87%) aligned concordantly >1 times ---- 1291768 pairs aligned concordantly 0 times; of these: 423753 (32.80%) aligned discordantly 1 time ---- 868015 pairs aligned 0 times concordantly or discordantly; of these: 1736030 mates make up the pairs; of these: 1472576 (84.82%) aligned 0 times 168176 (9.69%) aligned exactly 1 time 95278 (5.49%) aligned >1 times 94.26% overall alignment rate Time searching: 00:12:57 Overall time: 00:12:57 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] 2129032 / 11948702 = 0.1782 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:52:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.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 @ Tue, 10 Dec 2019 13:52:03: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:52:03: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:52:13: 1000000 INFO @ Tue, 10 Dec 2019 13:52:24: 2000000 INFO @ Tue, 10 Dec 2019 13:52:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.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 @ Tue, 10 Dec 2019 13:52:32: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:52:32: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:52:34: 3000000 INFO @ Tue, 10 Dec 2019 13:52:43: 1000000 INFO @ Tue, 10 Dec 2019 13:52:45: 4000000 INFO @ Tue, 10 Dec 2019 13:52:53: 2000000 INFO @ Tue, 10 Dec 2019 13:52:55: 5000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:53:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.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 @ Tue, 10 Dec 2019 13:53:02: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:53:02: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:53:04: 3000000 INFO @ Tue, 10 Dec 2019 13:53:06: 6000000 INFO @ Tue, 10 Dec 2019 13:53:10: 1000000 INFO @ Tue, 10 Dec 2019 13:53:15: 4000000 INFO @ Tue, 10 Dec 2019 13:53:17: 7000000 INFO @ Tue, 10 Dec 2019 13:53:18: 2000000 INFO @ Tue, 10 Dec 2019 13:53:26: 3000000 INFO @ Tue, 10 Dec 2019 13:53:26: 5000000 INFO @ Tue, 10 Dec 2019 13:53:28: 8000000 INFO @ Tue, 10 Dec 2019 13:53:34: 4000000 INFO @ Tue, 10 Dec 2019 13:53:37: 6000000 INFO @ Tue, 10 Dec 2019 13:53:39: 9000000 INFO @ Tue, 10 Dec 2019 13:53:41: 5000000 INFO @ Tue, 10 Dec 2019 13:53:48: 7000000 INFO @ Tue, 10 Dec 2019 13:53:49: 6000000 INFO @ Tue, 10 Dec 2019 13:53:50: 10000000 INFO @ Tue, 10 Dec 2019 13:53:57: 7000000 INFO @ Tue, 10 Dec 2019 13:53:59: 8000000 INFO @ Tue, 10 Dec 2019 13:54:01: 11000000 INFO @ Tue, 10 Dec 2019 13:54:05: 8000000 INFO @ Tue, 10 Dec 2019 13:54:10: 9000000 INFO @ Tue, 10 Dec 2019 13:54:12: 12000000 INFO @ Tue, 10 Dec 2019 13:54:12: 9000000 INFO @ Tue, 10 Dec 2019 13:54:20: 10000000 INFO @ Tue, 10 Dec 2019 13:54:21: 10000000 INFO @ Tue, 10 Dec 2019 13:54:23: 13000000 INFO @ Tue, 10 Dec 2019 13:54:28: 11000000 INFO @ Tue, 10 Dec 2019 13:54:32: 11000000 INFO @ Tue, 10 Dec 2019 13:54:33: 14000000 INFO @ Tue, 10 Dec 2019 13:54:36: 12000000 INFO @ Tue, 10 Dec 2019 13:54:43: 12000000 INFO @ Tue, 10 Dec 2019 13:54:44: 13000000 INFO @ Tue, 10 Dec 2019 13:54:44: 15000000 INFO @ Tue, 10 Dec 2019 13:54:51: 14000000 INFO @ Tue, 10 Dec 2019 13:54:54: 13000000 INFO @ Tue, 10 Dec 2019 13:54:55: 16000000 INFO @ Tue, 10 Dec 2019 13:54:59: 15000000 INFO @ Tue, 10 Dec 2019 13:55:04: 14000000 INFO @ Tue, 10 Dec 2019 13:55:05: 17000000 INFO @ Tue, 10 Dec 2019 13:55:07: 16000000 INFO @ Tue, 10 Dec 2019 13:55:15: 17000000 INFO @ Tue, 10 Dec 2019 13:55:15: 15000000 INFO @ Tue, 10 Dec 2019 13:55:16: 18000000 INFO @ Tue, 10 Dec 2019 13:55:22: 18000000 INFO @ Tue, 10 Dec 2019 13:55:26: 16000000 INFO @ Tue, 10 Dec 2019 13:55:27: 19000000 INFO @ Tue, 10 Dec 2019 13:55:30: 19000000 INFO @ Tue, 10 Dec 2019 13:55:37: 17000000 INFO @ Tue, 10 Dec 2019 13:55:37: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:55:37: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:55:37: #1 total tags in treatment: 9406143 INFO @ Tue, 10 Dec 2019 13:55:37: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:55:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:55:37: #1 tags after filtering in treatment: 6968981 INFO @ Tue, 10 Dec 2019 13:55:37: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 10 Dec 2019 13:55:37: #1 finished! INFO @ Tue, 10 Dec 2019 13:55:37: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:55:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:55:37: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:55:37: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:55:37: #1 total tags in treatment: 9406143 INFO @ Tue, 10 Dec 2019 13:55:37: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:55:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:55:37: #1 tags after filtering in treatment: 6968981 INFO @ Tue, 10 Dec 2019 13:55:37: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 10 Dec 2019 13:55:37: #1 finished! INFO @ Tue, 10 Dec 2019 13:55:37: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:55:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:55:37: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:55:37: 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 @ Tue, 10 Dec 2019 13:55:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.05_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/SRX3205549/SRX3205549.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:55:38: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:55:38: 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 @ Tue, 10 Dec 2019 13:55:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.20_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/SRX3205549/SRX3205549.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 13:55:47: 18000000 INFO @ Tue, 10 Dec 2019 13:55:57: 19000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 13:56:06: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:56:06: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:56:06: #1 total tags in treatment: 9406143 INFO @ Tue, 10 Dec 2019 13:56:06: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:56:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:56:07: #1 tags after filtering in treatment: 6968981 INFO @ Tue, 10 Dec 2019 13:56:07: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 10 Dec 2019 13:56:07: #1 finished! INFO @ Tue, 10 Dec 2019 13:56:07: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:56:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:56:07: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:56:07: 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 @ Tue, 10 Dec 2019 13:56:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.10_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/SRX3205549/SRX3205549.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205549/SRX3205549.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling