Job ID = 2641001 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,389,449 reads read : 26,778,898 reads written : 26,778,898 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: 00:17:06 13389449 reads; of these: 13389449 (100.00%) were paired; of these: 1960420 (14.64%) aligned concordantly 0 times 9481126 (70.81%) aligned concordantly exactly 1 time 1947903 (14.55%) aligned concordantly >1 times ---- 1960420 pairs aligned concordantly 0 times; of these: 634784 (32.38%) aligned discordantly 1 time ---- 1325636 pairs aligned 0 times concordantly or discordantly; of these: 2651272 mates make up the pairs; of these: 2264449 (85.41%) aligned 0 times 124799 (4.71%) aligned exactly 1 time 262024 (9.88%) aligned >1 times 91.54% overall alignment rate Time searching: 00:17:06 Overall time: 00:17:06 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] 1122340 / 12060653 = 0.0931 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.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 21:05:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:05:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:05:51: 1000000 INFO @ Sat, 24 Aug 2019 21:06:00: 2000000 INFO @ Sat, 24 Aug 2019 21:06:09: 3000000 INFO @ Sat, 24 Aug 2019 21:06:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.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 21:06:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:06:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:06:18: 4000000 INFO @ Sat, 24 Aug 2019 21:06:24: 1000000 INFO @ Sat, 24 Aug 2019 21:06:27: 5000000 INFO @ Sat, 24 Aug 2019 21:06:36: 6000000 INFO @ Sat, 24 Aug 2019 21:06:37: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:06:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.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 21:06:41: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:06:41: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:06:45: 7000000 INFO @ Sat, 24 Aug 2019 21:06:50: 3000000 INFO @ Sat, 24 Aug 2019 21:06:51: 1000000 INFO @ Sat, 24 Aug 2019 21:06:54: 8000000 INFO @ Sat, 24 Aug 2019 21:07:00: 2000000 INFO @ Sat, 24 Aug 2019 21:07:02: 4000000 INFO @ Sat, 24 Aug 2019 21:07:03: 9000000 INFO @ Sat, 24 Aug 2019 21:07:09: 3000000 INFO @ Sat, 24 Aug 2019 21:07:12: 10000000 INFO @ Sat, 24 Aug 2019 21:07:14: 5000000 INFO @ Sat, 24 Aug 2019 21:07:19: 4000000 INFO @ Sat, 24 Aug 2019 21:07:21: 11000000 INFO @ Sat, 24 Aug 2019 21:07:26: 6000000 INFO @ Sat, 24 Aug 2019 21:07:28: 5000000 INFO @ Sat, 24 Aug 2019 21:07:31: 12000000 INFO @ Sat, 24 Aug 2019 21:07:37: 6000000 INFO @ Sat, 24 Aug 2019 21:07:38: 7000000 INFO @ Sat, 24 Aug 2019 21:07:40: 13000000 INFO @ Sat, 24 Aug 2019 21:07:46: 7000000 INFO @ Sat, 24 Aug 2019 21:07:49: 14000000 INFO @ Sat, 24 Aug 2019 21:07:50: 8000000 INFO @ Sat, 24 Aug 2019 21:07:55: 8000000 INFO @ Sat, 24 Aug 2019 21:07:58: 15000000 INFO @ Sat, 24 Aug 2019 21:08:01: 9000000 INFO @ Sat, 24 Aug 2019 21:08:04: 9000000 INFO @ Sat, 24 Aug 2019 21:08:07: 16000000 INFO @ Sat, 24 Aug 2019 21:08:13: 10000000 INFO @ Sat, 24 Aug 2019 21:08:14: 10000000 INFO @ Sat, 24 Aug 2019 21:08:16: 17000000 INFO @ Sat, 24 Aug 2019 21:08:23: 11000000 INFO @ Sat, 24 Aug 2019 21:08:25: 11000000 INFO @ Sat, 24 Aug 2019 21:08:25: 18000000 INFO @ Sat, 24 Aug 2019 21:08:32: 12000000 INFO @ Sat, 24 Aug 2019 21:08:35: 19000000 INFO @ Sat, 24 Aug 2019 21:08:37: 12000000 INFO @ Sat, 24 Aug 2019 21:08:41: 13000000 INFO @ Sat, 24 Aug 2019 21:08:44: 20000000 INFO @ Sat, 24 Aug 2019 21:08:49: 13000000 INFO @ Sat, 24 Aug 2019 21:08:50: 14000000 INFO @ Sat, 24 Aug 2019 21:08:53: 21000000 INFO @ Sat, 24 Aug 2019 21:08:59: 15000000 INFO @ Sat, 24 Aug 2019 21:09:01: 14000000 INFO @ Sat, 24 Aug 2019 21:09:02: 22000000 INFO @ Sat, 24 Aug 2019 21:09:04: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:09:04: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:09:04: #1 total tags in treatment: 10333435 INFO @ Sat, 24 Aug 2019 21:09:04: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:09:04: #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 21:09:05: #1 tags after filtering in treatment: 7500757 INFO @ Sat, 24 Aug 2019 21:09:05: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 21:09:05: #1 finished! INFO @ Sat, 24 Aug 2019 21:09:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:09:05: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:09:05: 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 21:09:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.05_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/SRX4936107/SRX4936107.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:09:08: 16000000 INFO @ Sat, 24 Aug 2019 21:09:12: 15000000 INFO @ Sat, 24 Aug 2019 21:09:17: 17000000 INFO @ Sat, 24 Aug 2019 21:09:24: 16000000 INFO @ Sat, 24 Aug 2019 21:09:26: 18000000 INFO @ Sat, 24 Aug 2019 21:09:35: 19000000 INFO @ Sat, 24 Aug 2019 21:09:36: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:09:44: 20000000 INFO @ Sat, 24 Aug 2019 21:09:48: 18000000 INFO @ Sat, 24 Aug 2019 21:09:53: 21000000 INFO @ Sat, 24 Aug 2019 21:10:00: 19000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:10:02: 22000000 INFO @ Sat, 24 Aug 2019 21:10:04: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:10:04: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:10:04: #1 total tags in treatment: 10333435 INFO @ Sat, 24 Aug 2019 21:10:04: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:10:04: #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 21:10:05: #1 tags after filtering in treatment: 7500757 INFO @ Sat, 24 Aug 2019 21:10:05: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 21:10:05: #1 finished! INFO @ Sat, 24 Aug 2019 21:10:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:10:05: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:10:05: 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 21:10:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.20_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/SRX4936107/SRX4936107.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:10:12: 20000000 INFO @ Sat, 24 Aug 2019 21:10:24: 21000000 INFO @ Sat, 24 Aug 2019 21:10:36: 22000000 INFO @ Sat, 24 Aug 2019 21:10:39: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:10:39: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:10:39: #1 total tags in treatment: 10333435 INFO @ Sat, 24 Aug 2019 21:10:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:10:39: #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 21:10:39: #1 tags after filtering in treatment: 7500757 INFO @ Sat, 24 Aug 2019 21:10:39: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 21:10:39: #1 finished! INFO @ Sat, 24 Aug 2019 21:10:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:10:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:10:40: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:10:40: 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 21:10:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.10_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/SRX4936107/SRX4936107.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936107/SRX4936107.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling