Job ID = 2641126 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,980,618 reads read : 19,961,236 reads written : 19,961,236 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: 00:14:52 9980618 reads; of these: 9980618 (100.00%) were paired; of these: 3730262 (37.38%) aligned concordantly 0 times 5259232 (52.69%) aligned concordantly exactly 1 time 991124 (9.93%) aligned concordantly >1 times ---- 3730262 pairs aligned concordantly 0 times; of these: 2699033 (72.36%) aligned discordantly 1 time ---- 1031229 pairs aligned 0 times concordantly or discordantly; of these: 2062458 mates make up the pairs; of these: 847269 (41.08%) aligned 0 times 277829 (13.47%) aligned exactly 1 time 937360 (45.45%) aligned >1 times 95.76% overall alignment rate Time searching: 00:14:52 Overall time: 00:14:52 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] 299260 / 8947494 = 0.0334 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:05:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.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, 24 Aug 2019 22:05:58: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:05:58: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:06:07: 1000000 INFO @ Sat, 24 Aug 2019 22:06:17: 2000000 INFO @ Sat, 24 Aug 2019 22:06:26: 3000000 INFO @ Sat, 24 Aug 2019 22:06:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.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, 24 Aug 2019 22:06:27: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:06:27: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:06:35: 4000000 INFO @ Sat, 24 Aug 2019 22:06:36: 1000000 INFO @ Sat, 24 Aug 2019 22:06:45: 2000000 INFO @ Sat, 24 Aug 2019 22:06:45: 5000000 INFO @ Sat, 24 Aug 2019 22:06:53: 3000000 INFO @ Sat, 24 Aug 2019 22:06:54: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:06:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.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, 24 Aug 2019 22:06:57: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:06:57: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:07:02: 4000000 INFO @ Sat, 24 Aug 2019 22:07:04: 7000000 INFO @ Sat, 24 Aug 2019 22:07:08: 1000000 INFO @ Sat, 24 Aug 2019 22:07:11: 5000000 INFO @ Sat, 24 Aug 2019 22:07:13: 8000000 INFO @ Sat, 24 Aug 2019 22:07:18: 2000000 INFO @ Sat, 24 Aug 2019 22:07:20: 6000000 INFO @ Sat, 24 Aug 2019 22:07:23: 9000000 INFO @ Sat, 24 Aug 2019 22:07:28: 3000000 INFO @ Sat, 24 Aug 2019 22:07:28: 7000000 INFO @ Sat, 24 Aug 2019 22:07:33: 10000000 INFO @ Sat, 24 Aug 2019 22:07:37: 8000000 INFO @ Sat, 24 Aug 2019 22:07:38: 4000000 INFO @ Sat, 24 Aug 2019 22:07:42: 11000000 INFO @ Sat, 24 Aug 2019 22:07:46: 9000000 INFO @ Sat, 24 Aug 2019 22:07:48: 5000000 INFO @ Sat, 24 Aug 2019 22:07:52: 12000000 INFO @ Sat, 24 Aug 2019 22:07:55: 10000000 INFO @ Sat, 24 Aug 2019 22:07:58: 6000000 INFO @ Sat, 24 Aug 2019 22:08:02: 13000000 INFO @ Sat, 24 Aug 2019 22:08:04: 11000000 INFO @ Sat, 24 Aug 2019 22:08:08: 7000000 INFO @ Sat, 24 Aug 2019 22:08:12: 14000000 INFO @ Sat, 24 Aug 2019 22:08:13: 12000000 INFO @ Sat, 24 Aug 2019 22:08:18: 8000000 INFO @ Sat, 24 Aug 2019 22:08:21: 15000000 INFO @ Sat, 24 Aug 2019 22:08:21: 13000000 INFO @ Sat, 24 Aug 2019 22:08:29: 9000000 INFO @ Sat, 24 Aug 2019 22:08:30: 14000000 INFO @ Sat, 24 Aug 2019 22:08:31: 16000000 INFO @ Sat, 24 Aug 2019 22:08:39: 10000000 INFO @ Sat, 24 Aug 2019 22:08:39: 15000000 INFO @ Sat, 24 Aug 2019 22:08:41: 17000000 INFO @ Sat, 24 Aug 2019 22:08:48: 16000000 INFO @ Sat, 24 Aug 2019 22:08:49: 11000000 INFO @ Sat, 24 Aug 2019 22:08:50: 18000000 INFO @ Sat, 24 Aug 2019 22:08:56: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:08:56: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:08:56: #1 total tags in treatment: 6021333 INFO @ Sat, 24 Aug 2019 22:08:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:08:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:08:56: #1 tags after filtering in treatment: 4772303 INFO @ Sat, 24 Aug 2019 22:08:56: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 22:08:56: #1 finished! INFO @ Sat, 24 Aug 2019 22:08:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:08:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:08:56: #2 number of paired peaks: 27 WARNING @ Sat, 24 Aug 2019 22:08:56: Too few paired peaks (27) 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, 24 Aug 2019 22:08:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.05_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/SRX5546563/SRX5546563.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:08:57: 17000000 INFO @ Sat, 24 Aug 2019 22:08:59: 12000000 INFO @ Sat, 24 Aug 2019 22:09:05: 18000000 INFO @ Sat, 24 Aug 2019 22:09:08: 13000000 INFO @ Sat, 24 Aug 2019 22:09:10: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:09:10: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:09:10: #1 total tags in treatment: 6021333 INFO @ Sat, 24 Aug 2019 22:09:10: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:09:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:09:10: #1 tags after filtering in treatment: 4772303 INFO @ Sat, 24 Aug 2019 22:09:10: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 22:09:10: #1 finished! INFO @ Sat, 24 Aug 2019 22:09:10: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:09:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:09:10: #2 number of paired peaks: 27 WARNING @ Sat, 24 Aug 2019 22:09:10: Too few paired peaks (27) 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, 24 Aug 2019 22:09:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.10_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/SRX5546563/SRX5546563.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:09:18: 14000000 INFO @ Sat, 24 Aug 2019 22:09:27: 15000000 INFO @ Sat, 24 Aug 2019 22:09:37: 16000000 INFO @ Sat, 24 Aug 2019 22:09:46: 17000000 INFO @ Sat, 24 Aug 2019 22:09:56: 18000000 INFO @ Sat, 24 Aug 2019 22:10:01: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:10:01: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:10:01: #1 total tags in treatment: 6021333 INFO @ Sat, 24 Aug 2019 22:10:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:10:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:10:01: #1 tags after filtering in treatment: 4772303 INFO @ Sat, 24 Aug 2019 22:10:01: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 22:10:01: #1 finished! INFO @ Sat, 24 Aug 2019 22:10:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:10:01: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:10:01: #2 number of paired peaks: 27 WARNING @ Sat, 24 Aug 2019 22:10:01: Too few paired peaks (27) 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, 24 Aug 2019 22:10:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.20_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/SRX5546563/SRX5546563.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546563/SRX5546563.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。