Job ID = 2011000 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,453,277 reads read : 8,906,554 reads written : 8,906,554 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: 00:02:24 4453277 reads; of these: 4453277 (100.00%) were paired; of these: 2013555 (45.22%) aligned concordantly 0 times 2345258 (52.66%) aligned concordantly exactly 1 time 94464 (2.12%) aligned concordantly >1 times ---- 2013555 pairs aligned concordantly 0 times; of these: 44425 (2.21%) aligned discordantly 1 time ---- 1969130 pairs aligned 0 times concordantly or discordantly; of these: 3938260 mates make up the pairs; of these: 2280416 (57.90%) aligned 0 times 1574153 (39.97%) aligned exactly 1 time 83691 (2.13%) aligned >1 times 74.40% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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_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] 73175 / 2483815 = 0.0295 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 06 Jul 2019 01:42:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.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, 06 Jul 2019 01:42:15: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:42:15: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:42:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.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, 06 Jul 2019 01:42:16: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:42:16: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.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, 06 Jul 2019 01:42:17: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:42:17: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:42:24: 1000000 INFO @ Sat, 06 Jul 2019 01:42:24: 1000000 INFO @ Sat, 06 Jul 2019 01:42:26: 1000000 INFO @ Sat, 06 Jul 2019 01:42:32: 2000000 INFO @ Sat, 06 Jul 2019 01:42:32: 2000000 INFO @ Sat, 06 Jul 2019 01:42:34: 2000000 INFO @ Sat, 06 Jul 2019 01:42:40: 3000000 INFO @ Sat, 06 Jul 2019 01:42:41: 3000000 INFO @ Sat, 06 Jul 2019 01:42:43: 3000000 INFO @ Sat, 06 Jul 2019 01:42:47: 4000000 INFO @ Sat, 06 Jul 2019 01:42:49: 4000000 INFO @ Sat, 06 Jul 2019 01:42:52: 4000000 INFO @ Sat, 06 Jul 2019 01:42:54: 5000000 INFO @ Sat, 06 Jul 2019 01:42:58: 5000000 INFO @ Sat, 06 Jul 2019 01:43:01: 5000000 INFO @ Sat, 06 Jul 2019 01:43:02: 6000000 INFO @ Sat, 06 Jul 2019 01:43:05: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:43:05: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:43:05: #1 total tags in treatment: 2366965 INFO @ Sat, 06 Jul 2019 01:43:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:43:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:43:05: #1 tags after filtering in treatment: 1690939 INFO @ Sat, 06 Jul 2019 01:43:05: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 01:43:05: #1 finished! INFO @ Sat, 06 Jul 2019 01:43:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:43:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:43:05: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:43:05: 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, 06 Jul 2019 01:43:05: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 01:43:06: 6000000 INFO @ Sat, 06 Jul 2019 01:43:10: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:43:10: 6000000 INFO @ Sat, 06 Jul 2019 01:43:10: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:43:10: #1 total tags in treatment: 2366965 INFO @ Sat, 06 Jul 2019 01:43:10: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:43:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:43:10: #1 tags after filtering in treatment: 1690939 INFO @ Sat, 06 Jul 2019 01:43:10: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 01:43:10: #1 finished! INFO @ Sat, 06 Jul 2019 01:43:10: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:43:10: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:43:10: 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, 06 Jul 2019 01:43:10: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 01:43:13: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:43:13: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:43:13: #1 total tags in treatment: 2366965 INFO @ Sat, 06 Jul 2019 01:43:13: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:43:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:43:14: #1 tags after filtering in treatment: 1690939 INFO @ Sat, 06 Jul 2019 01:43:14: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 01:43:14: #1 finished! INFO @ Sat, 06 Jul 2019 01:43:14: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:43:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:43:14: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:43:14: 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, 06 Jul 2019 01:43:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.20_model.r’rm: : No such file or directorycannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.10_*.xls’ : No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.10_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342946/SRX4342946.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。