Job ID = 2010657 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:48:39 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T14:48:39 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 3,647,981 reads read : 7,295,962 reads written : 7,295,962 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: 00:02:31 3647981 reads; of these: 3647981 (100.00%) were paired; of these: 759330 (20.82%) aligned concordantly 0 times 2471215 (67.74%) aligned concordantly exactly 1 time 417436 (11.44%) aligned concordantly >1 times ---- 759330 pairs aligned concordantly 0 times; of these: 52760 (6.95%) aligned discordantly 1 time ---- 706570 pairs aligned 0 times concordantly or discordantly; of these: 1413140 mates make up the pairs; of these: 1347952 (95.39%) aligned 0 times 43267 (3.06%) aligned exactly 1 time 21921 (1.55%) aligned >1 times 81.52% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 207747 / 2936149 = 0.0708 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 @ Fri, 05 Jul 2019 23:55:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.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 @ Fri, 05 Jul 2019 23:55:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:55:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:55:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.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 @ Fri, 05 Jul 2019 23:55:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:55:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.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 @ Fri, 05 Jul 2019 23:55:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:55:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:55:18: 1000000 INFO @ Fri, 05 Jul 2019 23:55:20: 1000000 INFO @ Fri, 05 Jul 2019 23:55:24: 1000000 INFO @ Fri, 05 Jul 2019 23:55:24: 2000000 INFO @ Fri, 05 Jul 2019 23:55:26: 2000000 INFO @ Fri, 05 Jul 2019 23:55:29: 2000000 INFO @ Fri, 05 Jul 2019 23:55:30: 3000000 INFO @ Fri, 05 Jul 2019 23:55:33: 3000000 INFO @ Fri, 05 Jul 2019 23:55:36: 3000000 INFO @ Fri, 05 Jul 2019 23:55:36: 4000000 INFO @ Fri, 05 Jul 2019 23:55:40: 4000000 INFO @ Fri, 05 Jul 2019 23:55:42: 4000000 INFO @ Fri, 05 Jul 2019 23:55:42: 5000000 INFO @ Fri, 05 Jul 2019 23:55:46: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:55:46: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:55:46: #1 total tags in treatment: 2683014 INFO @ Fri, 05 Jul 2019 23:55:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:55:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:55:46: #1 tags after filtering in treatment: 2044189 INFO @ Fri, 05 Jul 2019 23:55:46: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 05 Jul 2019 23:55:46: #1 finished! INFO @ Fri, 05 Jul 2019 23:55:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:55:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:55:46: #2 number of paired peaks: 44 WARNING @ Fri, 05 Jul 2019 23:55:46: Too few paired peaks (44) 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 @ Fri, 05 Jul 2019 23:55:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.05_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/SRX3865855/SRX3865855.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:55:47: 5000000 INFO @ Fri, 05 Jul 2019 23:55:48: 5000000 INFO @ Fri, 05 Jul 2019 23:55:51: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:55:51: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:55:51: #1 total tags in treatment: 2683014 INFO @ Fri, 05 Jul 2019 23:55:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:55:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:55:51: #1 tags after filtering in treatment: 2044189 INFO @ Fri, 05 Jul 2019 23:55:51: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 05 Jul 2019 23:55:51: #1 finished! INFO @ Fri, 05 Jul 2019 23:55:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:55:51: #2 number of paired peaks: 44 WARNING @ Fri, 05 Jul 2019 23:55:51: Too few paired peaks (44) 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 @ Fri, 05 Jul 2019 23:55:51: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:55:52: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:55:52: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:55:52: #1 total tags in treatment: 2683014 INFO @ Fri, 05 Jul 2019 23:55:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:55:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:55:52: #1 tags after filtering in treatment: 2044189 INFO @ Fri, 05 Jul 2019 23:55:52: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 05 Jul 2019 23:55:52: #1 finished! INFO @ Fri, 05 Jul 2019 23:55:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:55:52: #2 number of paired peaks: 44 WARNING @ Fri, 05 Jul 2019 23:55:52: Too few paired peaks (44) 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 @ Fri, 05 Jul 2019 23:55:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis pass1 - making usageList (0 chroms): 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/SRX3865855/SRX3865855.20_model.r’: No such file or directoryrm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.20_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865855/SRX3865855.10_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。