Job ID = 2640994 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,694,266 reads read : 27,388,532 reads written : 27,388,532 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: 00:16:54 13694266 reads; of these: 13694266 (100.00%) were paired; of these: 1886076 (13.77%) aligned concordantly 0 times 10831583 (79.10%) aligned concordantly exactly 1 time 976607 (7.13%) aligned concordantly >1 times ---- 1886076 pairs aligned concordantly 0 times; of these: 217694 (11.54%) aligned discordantly 1 time ---- 1668382 pairs aligned 0 times concordantly or discordantly; of these: 3336764 mates make up the pairs; of these: 3235388 (96.96%) aligned 0 times 52409 (1.57%) aligned exactly 1 time 48967 (1.47%) aligned >1 times 88.19% overall alignment rate Time searching: 00:16:54 Overall time: 00:16:54 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] 178213 / 12023091 = 0.0148 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:15:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.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 21:15:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:15:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:15:49: 1000000 INFO @ Sat, 24 Aug 2019 21:15:59: 2000000 INFO @ Sat, 24 Aug 2019 21:16:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.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 21:16:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:16:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:16:09: 3000000 INFO @ Sat, 24 Aug 2019 21:16:18: 1000000 INFO @ Sat, 24 Aug 2019 21:16:19: 4000000 INFO @ Sat, 24 Aug 2019 21:16:27: 2000000 INFO @ Sat, 24 Aug 2019 21:16:30: 5000000 INFO @ Sat, 24 Aug 2019 21:16:36: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:16:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.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 21:16:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:16:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:16:40: 6000000 INFO @ Sat, 24 Aug 2019 21:16:45: 4000000 INFO @ Sat, 24 Aug 2019 21:16:50: 7000000 INFO @ Sat, 24 Aug 2019 21:16:53: 1000000 INFO @ Sat, 24 Aug 2019 21:16:54: 5000000 INFO @ Sat, 24 Aug 2019 21:17:00: 8000000 INFO @ Sat, 24 Aug 2019 21:17:03: 6000000 INFO @ Sat, 24 Aug 2019 21:17:06: 2000000 INFO @ Sat, 24 Aug 2019 21:17:11: 9000000 INFO @ Sat, 24 Aug 2019 21:17:12: 7000000 INFO @ Sat, 24 Aug 2019 21:17:19: 3000000 INFO @ Sat, 24 Aug 2019 21:17:21: 10000000 INFO @ Sat, 24 Aug 2019 21:17:21: 8000000 INFO @ Sat, 24 Aug 2019 21:17:30: 9000000 INFO @ Sat, 24 Aug 2019 21:17:31: 11000000 INFO @ Sat, 24 Aug 2019 21:17:32: 4000000 INFO @ Sat, 24 Aug 2019 21:17:39: 10000000 INFO @ Sat, 24 Aug 2019 21:17:41: 12000000 INFO @ Sat, 24 Aug 2019 21:17:45: 5000000 INFO @ Sat, 24 Aug 2019 21:17:48: 11000000 INFO @ Sat, 24 Aug 2019 21:17:51: 13000000 INFO @ Sat, 24 Aug 2019 21:17:57: 12000000 INFO @ Sat, 24 Aug 2019 21:17:58: 6000000 INFO @ Sat, 24 Aug 2019 21:18:02: 14000000 INFO @ Sat, 24 Aug 2019 21:18:06: 13000000 INFO @ Sat, 24 Aug 2019 21:18:11: 7000000 INFO @ Sat, 24 Aug 2019 21:18:12: 15000000 INFO @ Sat, 24 Aug 2019 21:18:15: 14000000 INFO @ Sat, 24 Aug 2019 21:18:22: 16000000 INFO @ Sat, 24 Aug 2019 21:18:24: 8000000 INFO @ Sat, 24 Aug 2019 21:18:24: 15000000 INFO @ Sat, 24 Aug 2019 21:18:32: 17000000 INFO @ Sat, 24 Aug 2019 21:18:33: 16000000 INFO @ Sat, 24 Aug 2019 21:18:37: 9000000 INFO @ Sat, 24 Aug 2019 21:18:42: 17000000 INFO @ Sat, 24 Aug 2019 21:18:43: 18000000 INFO @ Sat, 24 Aug 2019 21:18:50: 10000000 INFO @ Sat, 24 Aug 2019 21:18:51: 18000000 INFO @ Sat, 24 Aug 2019 21:18:53: 19000000 INFO @ Sat, 24 Aug 2019 21:19:00: 19000000 INFO @ Sat, 24 Aug 2019 21:19:02: 11000000 INFO @ Sat, 24 Aug 2019 21:19:03: 20000000 INFO @ Sat, 24 Aug 2019 21:19:09: 20000000 INFO @ Sat, 24 Aug 2019 21:19:13: 21000000 INFO @ Sat, 24 Aug 2019 21:19:15: 12000000 INFO @ Sat, 24 Aug 2019 21:19:18: 21000000 INFO @ Sat, 24 Aug 2019 21:19:23: 22000000 INFO @ Sat, 24 Aug 2019 21:19:27: 22000000 INFO @ Sat, 24 Aug 2019 21:19:28: 13000000 INFO @ Sat, 24 Aug 2019 21:19:34: 23000000 INFO @ Sat, 24 Aug 2019 21:19:36: 23000000 INFO @ Sat, 24 Aug 2019 21:19:40: 14000000 INFO @ Sat, 24 Aug 2019 21:19:42: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:19:42: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:19:42: #1 total tags in treatment: 11632779 INFO @ Sat, 24 Aug 2019 21:19:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:19:42: #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 21:19:42: #1 tags after filtering in treatment: 8642770 INFO @ Sat, 24 Aug 2019 21:19:42: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 24 Aug 2019 21:19:42: #1 finished! INFO @ Sat, 24 Aug 2019 21:19:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:19:43: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:19:43: 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 21:19:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.05_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/SRX4936100/SRX4936100.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:19:43: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:19:43: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:19:43: #1 total tags in treatment: 11632779 INFO @ Sat, 24 Aug 2019 21:19:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:19:43: #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 21:19:43: #1 tags after filtering in treatment: 8642770 INFO @ Sat, 24 Aug 2019 21:19:43: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 24 Aug 2019 21:19:43: #1 finished! INFO @ Sat, 24 Aug 2019 21:19:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:19:44: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:19:44: 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 21:19:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.10_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/SRX4936100/SRX4936100.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:19:52: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:20:04: 16000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:20:15: 17000000 INFO @ Sat, 24 Aug 2019 21:20:27: 18000000 INFO @ Sat, 24 Aug 2019 21:20:38: 19000000 INFO @ Sat, 24 Aug 2019 21:20:50: 20000000 INFO @ Sat, 24 Aug 2019 21:21:01: 21000000 INFO @ Sat, 24 Aug 2019 21:21:13: 22000000 INFO @ Sat, 24 Aug 2019 21:21:25: 23000000 INFO @ Sat, 24 Aug 2019 21:21:34: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:21:34: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:21:34: #1 total tags in treatment: 11632779 INFO @ Sat, 24 Aug 2019 21:21:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:21:34: #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 21:21:34: #1 tags after filtering in treatment: 8642770 INFO @ Sat, 24 Aug 2019 21:21:34: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 24 Aug 2019 21:21:34: #1 finished! INFO @ Sat, 24 Aug 2019 21:21:34: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:21:35: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:21:35: 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 21:21:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.20_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/SRX4936100/SRX4936100.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936100/SRX4936100.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling