Job ID = 2011942 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,445,783 reads read : 16,891,566 reads written : 16,891,566 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: 00:06:59 8445783 reads; of these: 8445783 (100.00%) were paired; of these: 5134862 (60.80%) aligned concordantly 0 times 2786670 (32.99%) aligned concordantly exactly 1 time 524251 (6.21%) aligned concordantly >1 times ---- 5134862 pairs aligned concordantly 0 times; of these: 1481539 (28.85%) aligned discordantly 1 time ---- 3653323 pairs aligned 0 times concordantly or discordantly; of these: 7306646 mates make up the pairs; of these: 6426358 (87.95%) aligned 0 times 297349 (4.07%) aligned exactly 1 time 582939 (7.98%) aligned >1 times 61.96% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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 8 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] 620810 / 4693396 = 0.1323 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 03:45:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.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 03:45:24: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:45:24: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:45:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.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 03:45:25: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:45:25: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:45:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.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 03:45:26: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:45:26: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:45:34: 1000000 INFO @ Sat, 06 Jul 2019 03:45:34: 1000000 INFO @ Sat, 06 Jul 2019 03:45:36: 1000000 INFO @ Sat, 06 Jul 2019 03:45:44: 2000000 INFO @ Sat, 06 Jul 2019 03:45:44: 2000000 INFO @ Sat, 06 Jul 2019 03:45:46: 2000000 INFO @ Sat, 06 Jul 2019 03:45:53: 3000000 INFO @ Sat, 06 Jul 2019 03:45:53: 3000000 INFO @ Sat, 06 Jul 2019 03:45:54: 3000000 INFO @ Sat, 06 Jul 2019 03:46:01: 4000000 INFO @ Sat, 06 Jul 2019 03:46:02: 4000000 INFO @ Sat, 06 Jul 2019 03:46:03: 4000000 INFO @ Sat, 06 Jul 2019 03:46:09: 5000000 INFO @ Sat, 06 Jul 2019 03:46:11: 5000000 INFO @ Sat, 06 Jul 2019 03:46:13: 5000000 INFO @ Sat, 06 Jul 2019 03:46:17: 6000000 INFO @ Sat, 06 Jul 2019 03:46:19: 6000000 INFO @ Sat, 06 Jul 2019 03:46:22: 6000000 INFO @ Sat, 06 Jul 2019 03:46:25: 7000000 INFO @ Sat, 06 Jul 2019 03:46:27: 7000000 INFO @ Sat, 06 Jul 2019 03:46:33: 7000000 INFO @ Sat, 06 Jul 2019 03:46:33: 8000000 INFO @ Sat, 06 Jul 2019 03:46:35: 8000000 INFO @ Sat, 06 Jul 2019 03:46:41: 9000000 INFO @ Sat, 06 Jul 2019 03:46:43: 8000000 INFO @ Sat, 06 Jul 2019 03:46:43: 9000000 INFO @ Sat, 06 Jul 2019 03:46:43: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:46:43: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:46:43: #1 total tags in treatment: 2872943 INFO @ Sat, 06 Jul 2019 03:46:43: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:46:43: #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 03:46:43: #1 tags after filtering in treatment: 2130536 INFO @ Sat, 06 Jul 2019 03:46:43: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:46:43: #1 finished! INFO @ Sat, 06 Jul 2019 03:46:43: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:46:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:46:43: #2 number of paired peaks: 29 WARNING @ Sat, 06 Jul 2019 03:46:43: Too few paired peaks (29) 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 03:46:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.10_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/SRX5624301/SRX5624301.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:46:44: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:46:44: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:46:44: #1 total tags in treatment: 2872943 INFO @ Sat, 06 Jul 2019 03:46:44: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:46:44: #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 03:46:44: #1 tags after filtering in treatment: 2130536 INFO @ Sat, 06 Jul 2019 03:46:44: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:46:44: #1 finished! INFO @ Sat, 06 Jul 2019 03:46:44: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:46:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:46:45: #2 number of paired peaks: 29 WARNING @ Sat, 06 Jul 2019 03:46:45: Too few paired peaks (29) 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 03:46:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.20_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/SRX5624301/SRX5624301.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:46:52: 9000000 INFO @ Sat, 06 Jul 2019 03:46:54: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:46:54: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:46:54: #1 total tags in treatment: 2872943 INFO @ Sat, 06 Jul 2019 03:46:54: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:46:54: #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 03:46:54: #1 tags after filtering in treatment: 2130536 INFO @ Sat, 06 Jul 2019 03:46:54: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:46:54: #1 finished! INFO @ Sat, 06 Jul 2019 03:46:54: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:46:54: #2 number of paired peaks: 29 WARNING @ Sat, 06 Jul 2019 03:46:54: Too few paired peaks (29) 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 03:46:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.05_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/SRX5624301/SRX5624301.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624301/SRX5624301.05_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。