Job ID = 2640998 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,417,645 reads read : 22,835,290 reads written : 22,835,290 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: 00:15:25 11417645 reads; of these: 11417645 (100.00%) were paired; of these: 300842 (2.63%) aligned concordantly 0 times 9817557 (85.99%) aligned concordantly exactly 1 time 1299246 (11.38%) aligned concordantly >1 times ---- 300842 pairs aligned concordantly 0 times; of these: 87574 (29.11%) aligned discordantly 1 time ---- 213268 pairs aligned 0 times concordantly or discordantly; of these: 426536 mates make up the pairs; of these: 371641 (87.13%) aligned 0 times 26222 (6.15%) aligned exactly 1 time 28673 (6.72%) aligned >1 times 98.37% overall alignment rate Time searching: 00:15:25 Overall time: 00:15:25 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] 130994 / 11201602 = 0.0117 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.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 21:01:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:01:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:01:46: 1000000 INFO @ Sat, 24 Aug 2019 21:02:00: 2000000 INFO @ Sat, 24 Aug 2019 21:02:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.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 21:02:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:02:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:02:13: 3000000 INFO @ Sat, 24 Aug 2019 21:02:20: 1000000 INFO @ Sat, 24 Aug 2019 21:02:26: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.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 21:02:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:02:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:02:36: 2000000 INFO @ Sat, 24 Aug 2019 21:02:38: 5000000 INFO @ Sat, 24 Aug 2019 21:02:47: 3000000 INFO @ Sat, 24 Aug 2019 21:02:47: 1000000 INFO @ Sat, 24 Aug 2019 21:02:49: 6000000 INFO @ Sat, 24 Aug 2019 21:02:58: 4000000 INFO @ Sat, 24 Aug 2019 21:02:59: 2000000 INFO @ Sat, 24 Aug 2019 21:03:00: 7000000 INFO @ Sat, 24 Aug 2019 21:03:09: 5000000 INFO @ Sat, 24 Aug 2019 21:03:12: 3000000 INFO @ Sat, 24 Aug 2019 21:03:12: 8000000 INFO @ Sat, 24 Aug 2019 21:03:20: 6000000 INFO @ Sat, 24 Aug 2019 21:03:23: 9000000 INFO @ Sat, 24 Aug 2019 21:03:24: 4000000 INFO @ Sat, 24 Aug 2019 21:03:32: 7000000 INFO @ Sat, 24 Aug 2019 21:03:35: 10000000 INFO @ Sat, 24 Aug 2019 21:03:36: 5000000 INFO @ Sat, 24 Aug 2019 21:03:43: 8000000 INFO @ Sat, 24 Aug 2019 21:03:46: 11000000 INFO @ Sat, 24 Aug 2019 21:03:48: 6000000 INFO @ Sat, 24 Aug 2019 21:03:54: 9000000 INFO @ Sat, 24 Aug 2019 21:03:57: 12000000 INFO @ Sat, 24 Aug 2019 21:04:01: 7000000 INFO @ Sat, 24 Aug 2019 21:04:05: 10000000 INFO @ Sat, 24 Aug 2019 21:04:09: 13000000 INFO @ Sat, 24 Aug 2019 21:04:13: 8000000 INFO @ Sat, 24 Aug 2019 21:04:16: 11000000 INFO @ Sat, 24 Aug 2019 21:04:20: 14000000 INFO @ Sat, 24 Aug 2019 21:04:25: 9000000 INFO @ Sat, 24 Aug 2019 21:04:27: 12000000 INFO @ Sat, 24 Aug 2019 21:04:30: 15000000 INFO @ Sat, 24 Aug 2019 21:04:37: 10000000 INFO @ Sat, 24 Aug 2019 21:04:39: 13000000 INFO @ Sat, 24 Aug 2019 21:04:40: 16000000 INFO @ Sat, 24 Aug 2019 21:04:49: 17000000 INFO @ Sat, 24 Aug 2019 21:04:50: 14000000 INFO @ Sat, 24 Aug 2019 21:04:51: 11000000 INFO @ Sat, 24 Aug 2019 21:04:59: 18000000 INFO @ Sat, 24 Aug 2019 21:05:02: 15000000 INFO @ Sat, 24 Aug 2019 21:05:06: 12000000 INFO @ Sat, 24 Aug 2019 21:05:08: 19000000 INFO @ Sat, 24 Aug 2019 21:05:16: 16000000 INFO @ Sat, 24 Aug 2019 21:05:17: 20000000 INFO @ Sat, 24 Aug 2019 21:05:20: 13000000 INFO @ Sat, 24 Aug 2019 21:05:27: 21000000 INFO @ Sat, 24 Aug 2019 21:05:30: 17000000 INFO @ Sat, 24 Aug 2019 21:05:33: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:05:36: 22000000 INFO @ Sat, 24 Aug 2019 21:05:38: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:05:38: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:05:38: #1 total tags in treatment: 10986288 INFO @ Sat, 24 Aug 2019 21:05:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:05:38: #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 21:05:38: #1 tags after filtering in treatment: 8326184 INFO @ Sat, 24 Aug 2019 21:05:38: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 24 Aug 2019 21:05:38: #1 finished! INFO @ Sat, 24 Aug 2019 21:05:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:05:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:05:39: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:05:39: 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 21:05:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.05_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/SRX4936104/SRX4936104.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:05:43: 18000000 INFO @ Sat, 24 Aug 2019 21:05:47: 15000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:05:57: 19000000 INFO @ Sat, 24 Aug 2019 21:06:02: 16000000 INFO @ Sat, 24 Aug 2019 21:06:12: 20000000 INFO @ Sat, 24 Aug 2019 21:06:17: 17000000 INFO @ Sat, 24 Aug 2019 21:06:26: 21000000 INFO @ Sat, 24 Aug 2019 21:06:31: 18000000 INFO @ Sat, 24 Aug 2019 21:06:39: 22000000 INFO @ Sat, 24 Aug 2019 21:06:41: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:06:41: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:06:41: #1 total tags in treatment: 10986288 INFO @ Sat, 24 Aug 2019 21:06:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:06:41: #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 21:06:42: #1 tags after filtering in treatment: 8326184 INFO @ Sat, 24 Aug 2019 21:06:42: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 24 Aug 2019 21:06:42: #1 finished! INFO @ Sat, 24 Aug 2019 21:06:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:06:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:06:42: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:06:42: 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 21:06:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.10_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/SRX4936104/SRX4936104.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:06:44: 19000000 INFO @ Sat, 24 Aug 2019 21:06:57: 20000000 INFO @ Sat, 24 Aug 2019 21:07:09: 21000000 INFO @ Sat, 24 Aug 2019 21:07:21: 22000000 INFO @ Sat, 24 Aug 2019 21:07:23: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:07:23: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:07:23: #1 total tags in treatment: 10986288 INFO @ Sat, 24 Aug 2019 21:07:23: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:07:23: #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 21:07:23: #1 tags after filtering in treatment: 8326184 INFO @ Sat, 24 Aug 2019 21:07:23: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 24 Aug 2019 21:07:23: #1 finished! INFO @ Sat, 24 Aug 2019 21:07:23: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:07:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:07:24: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:07:24: 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 21:07:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.20_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/SRX4936104/SRX4936104.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936104/SRX4936104.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling