Job ID = 2007946 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:37 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR506382/ERR506382.1' 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506382' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: sorter.c run_producer_pool() : processed lookup rows: 0 of 3209436 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: sorter.c execute_lookup_production() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: fasterq-dump.c produce_lookup_files() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-07-05T07:40:42 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:40:42 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR506382/ERR506382.1' 2019-07-05T07:40:42 fasterq-dump.2.9.6 err: invalid accession 'ERR506382' 2019-07-05T07:40:57 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:40:57 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR506382/ERR506382.1' 2019-07-05T07:40:57 fasterq-dump.2.9.6 err: invalid accession 'ERR506382' 2019-07-05T07:41:12 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:41:12 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR506382/ERR506382.1' 2019-07-05T07:41:12 fasterq-dump.2.9.6 err: invalid accession 'ERR506382' spots read : 1,740,027 reads read : 3,480,054 reads written : 3,480,054 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: 00:01:49 1740027 reads; of these: 1740027 (100.00%) were paired; of these: 274324 (15.77%) aligned concordantly 0 times 1368341 (78.64%) aligned concordantly exactly 1 time 97362 (5.60%) aligned concordantly >1 times ---- 274324 pairs aligned concordantly 0 times; of these: 112602 (41.05%) aligned discordantly 1 time ---- 161722 pairs aligned 0 times concordantly or discordantly; of these: 323444 mates make up the pairs; of these: 274107 (84.75%) aligned 0 times 29669 (9.17%) aligned exactly 1 time 19668 (6.08%) aligned >1 times 92.12% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 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] 101114 / 1563679 = 0.0647 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 16:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.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 16:52:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.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 16:52:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.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 16:52:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:57: 1000000 INFO @ Fri, 05 Jul 2019 16:52:59: 1000000 INFO @ Fri, 05 Jul 2019 16:52:59: 1000000 INFO @ Fri, 05 Jul 2019 16:53:07: 2000000 INFO @ Fri, 05 Jul 2019 16:53:10: 2000000 INFO @ Fri, 05 Jul 2019 16:53:10: 2000000 INFO @ Fri, 05 Jul 2019 16:53:17: 3000000 INFO @ Fri, 05 Jul 2019 16:53:17: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:17: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:17: #1 total tags in treatment: 1368457 INFO @ Fri, 05 Jul 2019 16:53:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:17: #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 16:53:17: #1 tags after filtering in treatment: 1267251 INFO @ Fri, 05 Jul 2019 16:53:17: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 16:53:17: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:17: #2 number of paired peaks: 78 WARNING @ Fri, 05 Jul 2019 16:53:17: Too few paired peaks (78) 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 16:53:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.05_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/ERX471739/ERX471739.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:53:20: 3000000 INFO @ Fri, 05 Jul 2019 16:53:20: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:20: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:20: #1 total tags in treatment: 1368457 INFO @ Fri, 05 Jul 2019 16:53:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:20: #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 16:53:20: #1 tags after filtering in treatment: 1267251 INFO @ Fri, 05 Jul 2019 16:53:20: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 16:53:20: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:20: #2 number of paired peaks: 78 WARNING @ Fri, 05 Jul 2019 16:53:20: Too few paired peaks (78) 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 16:53:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.20_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/ERX471739/ERX471739.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:53:21: 3000000 INFO @ Fri, 05 Jul 2019 16:53:21: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:21: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:21: #1 total tags in treatment: 1368457 INFO @ Fri, 05 Jul 2019 16:53:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:21: #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 16:53:21: #1 tags after filtering in treatment: 1267251 INFO @ Fri, 05 Jul 2019 16:53:21: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 16:53:21: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:21: #2 number of paired peaks: 78 WARNING @ Fri, 05 Jul 2019 16:53:21: Too few paired peaks (78) 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 16:53:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.10_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/ERX471739/ERX471739.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471739/ERX471739.10_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。