Job ID = 2011949 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 17,502,194 reads read : 35,004,388 reads written : 35,004,388 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: 00:10:29 17502194 reads; of these: 17502194 (100.00%) were paired; of these: 15533066 (88.75%) aligned concordantly 0 times 1649322 (9.42%) aligned concordantly exactly 1 time 319806 (1.83%) aligned concordantly >1 times ---- 15533066 pairs aligned concordantly 0 times; of these: 2001446 (12.89%) aligned discordantly 1 time ---- 13531620 pairs aligned 0 times concordantly or discordantly; of these: 27063240 mates make up the pairs; of these: 25805584 (95.35%) aligned 0 times 466873 (1.73%) aligned exactly 1 time 790783 (2.92%) aligned >1 times 26.28% overall alignment rate Time searching: 00:10:29 Overall time: 00:10:29 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] 566633 / 3858218 = 0.1469 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 03:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.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 03:57:01: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:57:01: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:57:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.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 03:57:02: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:57:02: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:57:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.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 03:57:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:57:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:57:10: 1000000 INFO @ Sat, 06 Jul 2019 03:57:12: 1000000 INFO @ Sat, 06 Jul 2019 03:57:14: 1000000 INFO @ Sat, 06 Jul 2019 03:57:18: 2000000 INFO @ Sat, 06 Jul 2019 03:57:21: 2000000 INFO @ Sat, 06 Jul 2019 03:57:27: 2000000 INFO @ Sat, 06 Jul 2019 03:57:27: 3000000 INFO @ Sat, 06 Jul 2019 03:57:29: 3000000 INFO @ Sat, 06 Jul 2019 03:57:35: 4000000 INFO @ Sat, 06 Jul 2019 03:57:38: 4000000 INFO @ Sat, 06 Jul 2019 03:57:39: 3000000 INFO @ Sat, 06 Jul 2019 03:57:43: 5000000 INFO @ Sat, 06 Jul 2019 03:57:46: 5000000 INFO @ Sat, 06 Jul 2019 03:57:51: 4000000 INFO @ Sat, 06 Jul 2019 03:57:52: 6000000 INFO @ Sat, 06 Jul 2019 03:57:54: 6000000 INFO @ Sat, 06 Jul 2019 03:58:00: 7000000 INFO @ Sat, 06 Jul 2019 03:58:02: 5000000 INFO @ Sat, 06 Jul 2019 03:58:03: 7000000 INFO @ Sat, 06 Jul 2019 03:58:08: 8000000 INFO @ Sat, 06 Jul 2019 03:58:09: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:58:09: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:58:09: #1 total tags in treatment: 1716054 INFO @ Sat, 06 Jul 2019 03:58:09: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:58:09: #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 03:58:09: #1 tags after filtering in treatment: 1414623 INFO @ Sat, 06 Jul 2019 03:58:09: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 06 Jul 2019 03:58:09: #1 finished! INFO @ Sat, 06 Jul 2019 03:58:09: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:58:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:58:09: #2 number of paired peaks: 35 WARNING @ Sat, 06 Jul 2019 03:58:09: Too few paired peaks (35) 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 03:58:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.05_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/SRX5624308/SRX5624308.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:58:11: 8000000 INFO @ Sat, 06 Jul 2019 03:58:11: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:58:11: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:58:11: #1 total tags in treatment: 1716054 INFO @ Sat, 06 Jul 2019 03:58:11: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:58:11: #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 03:58:11: #1 tags after filtering in treatment: 1414623 INFO @ Sat, 06 Jul 2019 03:58:11: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 06 Jul 2019 03:58:11: #1 finished! INFO @ Sat, 06 Jul 2019 03:58:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:58:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:58:12: #2 number of paired peaks: 35 WARNING @ Sat, 06 Jul 2019 03:58:12: Too few paired peaks (35) 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 03:58:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.20_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/SRX5624308/SRX5624308.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:58:14: 6000000 INFO @ Sat, 06 Jul 2019 03:58:25: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:58:36: 8000000 INFO @ Sat, 06 Jul 2019 03:58:37: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:58:37: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:58:37: #1 total tags in treatment: 1716054 INFO @ Sat, 06 Jul 2019 03:58:37: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:58:37: #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 03:58:37: #1 tags after filtering in treatment: 1414623 INFO @ Sat, 06 Jul 2019 03:58:37: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 06 Jul 2019 03:58:37: #1 finished! INFO @ Sat, 06 Jul 2019 03:58:37: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:58:37: #2 number of paired peaks: 35 WARNING @ Sat, 06 Jul 2019 03:58:37: Too few paired peaks (35) 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 03:58:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.10_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/SRX5624308/SRX5624308.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624308/SRX5624308.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。