Job ID = 2011665 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,409,379 reads read : 10,818,758 reads written : 10,818,758 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1146733.sra.cache’: 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: 00:04:20 5409379 reads; of these: 5409379 (100.00%) were paired; of these: 363496 (6.72%) aligned concordantly 0 times 4083112 (75.48%) aligned concordantly exactly 1 time 962771 (17.80%) aligned concordantly >1 times ---- 363496 pairs aligned concordantly 0 times; of these: 138070 (37.98%) aligned discordantly 1 time ---- 225426 pairs aligned 0 times concordantly or discordantly; of these: 450852 mates make up the pairs; of these: 295004 (65.43%) aligned 0 times 63692 (14.13%) aligned exactly 1 time 92156 (20.44%) aligned >1 times 97.27% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 612924 / 5107709 = 0.1200 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 02:01:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.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 02:01:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:01:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:01:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.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 02:01:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:01:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:01:12: 1000000 INFO @ Sat, 06 Jul 2019 02:01:13: 1000000 INFO @ Sat, 06 Jul 2019 02:01:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.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 02:01:17: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:01:17: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:01:18: 2000000 INFO @ Sat, 06 Jul 2019 02:01:21: 2000000 INFO @ Sat, 06 Jul 2019 02:01:24: 1000000 INFO @ Sat, 06 Jul 2019 02:01:25: 3000000 INFO @ Sat, 06 Jul 2019 02:01:29: 3000000 INFO @ Sat, 06 Jul 2019 02:01:32: 2000000 INFO @ Sat, 06 Jul 2019 02:01:32: 4000000 INFO @ Sat, 06 Jul 2019 02:01:36: 4000000 INFO @ Sat, 06 Jul 2019 02:01:39: 5000000 INFO @ Sat, 06 Jul 2019 02:01:40: 3000000 INFO @ Sat, 06 Jul 2019 02:01:44: 5000000 INFO @ Sat, 06 Jul 2019 02:01:46: 6000000 INFO @ Sat, 06 Jul 2019 02:01:47: 4000000 INFO @ Sat, 06 Jul 2019 02:01:52: 6000000 INFO @ Sat, 06 Jul 2019 02:01:53: 7000000 INFO @ Sat, 06 Jul 2019 02:01:55: 5000000 INFO @ Sat, 06 Jul 2019 02:01:59: 8000000 INFO @ Sat, 06 Jul 2019 02:01:59: 7000000 INFO @ Sat, 06 Jul 2019 02:02:03: 6000000 INFO @ Sat, 06 Jul 2019 02:02:06: 9000000 INFO @ Sat, 06 Jul 2019 02:02:07: 8000000 INFO @ Sat, 06 Jul 2019 02:02:08: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:02:08: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:02:08: #1 total tags in treatment: 4442169 INFO @ Sat, 06 Jul 2019 02:02:08: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:02:08: #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 02:02:08: #1 tags after filtering in treatment: 3564890 INFO @ Sat, 06 Jul 2019 02:02:08: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 02:02:08: #1 finished! INFO @ Sat, 06 Jul 2019 02:02:08: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:02:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:02:09: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 02:02:09: Too few paired peaks (28) 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 02:02:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.05_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/SRX455443/SRX455443.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:02:10: 7000000 INFO @ Sat, 06 Jul 2019 02:02:15: 9000000 INFO @ Sat, 06 Jul 2019 02:02:17: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:02:17: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:02:17: #1 total tags in treatment: 4442169 INFO @ Sat, 06 Jul 2019 02:02:17: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:02:17: #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 02:02:17: #1 tags after filtering in treatment: 3564890 INFO @ Sat, 06 Jul 2019 02:02:17: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 02:02:17: #1 finished! INFO @ Sat, 06 Jul 2019 02:02:17: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:02:17: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 02:02:17: Too few paired peaks (28) 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 02:02:17: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:02:18: 8000000 INFO @ Sat, 06 Jul 2019 02:02:26: 9000000 INFO @ Sat, 06 Jul 2019 02:02:28: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:02:28: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:02:28: #1 total tags in treatment: 4442169 INFO @ Sat, 06 Jul 2019 02:02:28: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:02:28: #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 02:02:28: #1 tags after filtering in treatment: 3564890 INFO @ Sat, 06 Jul 2019 02:02:28: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 02:02:28: #1 finished! INFO @ Sat, 06 Jul 2019 02:02:28: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:02:28: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 02:02:28: Too few paired peaks (28) 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 02:02:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms)pass1 - making usageList (0 chroms): 2 millis : 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.20_model.r’: No such file or directory rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.10_model.r’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.20_*.xls’: No such file or directory: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.20_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455443/SRX455443.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。