Job ID = 2011945 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,038,120 reads read : 20,076,240 reads written : 20,076,240 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: 00:06:57 10038120 reads; of these: 10038120 (100.00%) were paired; of these: 8485760 (84.54%) aligned concordantly 0 times 1284994 (12.80%) aligned concordantly exactly 1 time 267366 (2.66%) aligned concordantly >1 times ---- 8485760 pairs aligned concordantly 0 times; of these: 1394247 (16.43%) aligned discordantly 1 time ---- 7091513 pairs aligned 0 times concordantly or discordantly; of these: 14183026 mates make up the pairs; of these: 13280183 (93.63%) aligned 0 times 314160 (2.22%) aligned exactly 1 time 588683 (4.15%) aligned >1 times 33.85% overall alignment rate Time searching: 00:06:57 Overall time: 00:06:57 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] 339850 / 2863916 = 0.1187 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 03:43:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.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 03:43:41: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:43:41: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:43:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.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 03:43:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:43:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:43:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.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 03:43:43: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:43:43: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:43:50: 1000000 INFO @ Sat, 06 Jul 2019 03:43:51: 1000000 INFO @ Sat, 06 Jul 2019 03:43:54: 1000000 INFO @ Sat, 06 Jul 2019 03:43:58: 2000000 INFO @ Sat, 06 Jul 2019 03:44:01: 2000000 INFO @ Sat, 06 Jul 2019 03:44:05: 2000000 INFO @ Sat, 06 Jul 2019 03:44:05: 3000000 INFO @ Sat, 06 Jul 2019 03:44:10: 3000000 INFO @ Sat, 06 Jul 2019 03:44:13: 4000000 INFO @ Sat, 06 Jul 2019 03:44:16: 3000000 INFO @ Sat, 06 Jul 2019 03:44:19: 4000000 INFO @ Sat, 06 Jul 2019 03:44:20: 5000000 INFO @ Sat, 06 Jul 2019 03:44:27: 4000000 INFO @ Sat, 06 Jul 2019 03:44:28: 6000000 INFO @ Sat, 06 Jul 2019 03:44:29: 5000000 INFO @ Sat, 06 Jul 2019 03:44:29: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:44:29: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:44:29: #1 total tags in treatment: 1378957 INFO @ Sat, 06 Jul 2019 03:44:29: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:44:29: #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 03:44:29: #1 tags after filtering in treatment: 1160539 INFO @ Sat, 06 Jul 2019 03:44:29: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 03:44:29: #1 finished! INFO @ Sat, 06 Jul 2019 03:44:29: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:44:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:44:29: #2 number of paired peaks: 26 WARNING @ Sat, 06 Jul 2019 03:44:29: Too few paired peaks (26) 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 03:44:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.10_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/SRX5624304/SRX5624304.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:44:38: 5000000 INFO @ Sat, 06 Jul 2019 03:44:38: 6000000 INFO @ Sat, 06 Jul 2019 03:44:39: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:44:39: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:44:39: #1 total tags in treatment: 1378957 INFO @ Sat, 06 Jul 2019 03:44:39: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:44:39: #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 03:44:39: #1 tags after filtering in treatment: 1160539 INFO @ Sat, 06 Jul 2019 03:44:39: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 03:44:39: #1 finished! INFO @ Sat, 06 Jul 2019 03:44:39: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:44:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:44:39: #2 number of paired peaks: 26 WARNING @ Sat, 06 Jul 2019 03:44:39: Too few paired peaks (26) 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 03:44:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.05_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/SRX5624304/SRX5624304.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:44:48: 6000000 INFO @ Sat, 06 Jul 2019 03:44:49: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:44:49: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:44:49: #1 total tags in treatment: 1378957 INFO @ Sat, 06 Jul 2019 03:44:49: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:44:49: #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 03:44:50: #1 tags after filtering in treatment: 1160539 INFO @ Sat, 06 Jul 2019 03:44:50: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 03:44:50: #1 finished! INFO @ Sat, 06 Jul 2019 03:44:50: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:44:50: #2 number of paired peaks: 26 WARNING @ Sat, 06 Jul 2019 03:44:50: Too few paired peaks (26) 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 03:44:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.20_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/SRX5624304/SRX5624304.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624304/SRX5624304.20_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。