Job ID = 2007928 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:35 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' 2019-07-05T07:40:35 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/ERR506364/ERR506364.1' 2019-07-05T07:40:35 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'ERR506364', 'SEQUENCE', 'NAME' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 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' 2019-07-05T07:40:40 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/ERR506364/ERR506364.1' 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506364' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:47 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' 2019-07-05T07:40:47 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/ERR506364/ERR506364.1' 2019-07-05T07:40:47 fasterq-dump.2.9.6 err: invalid accession 'ERR506364' 2019-07-05T07:41:02 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' 2019-07-05T07:41:02 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/ERR506364/ERR506364.1' 2019-07-05T07:41:02 fasterq-dump.2.9.6 err: invalid accession 'ERR506364' 2019-07-05T07:41:17 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' 2019-07-05T07:41:17 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/ERR506364/ERR506364.1' 2019-07-05T07:41:17 fasterq-dump.2.9.6 err: invalid accession 'ERR506364' spots read : 1,805,572 reads read : 3,611,144 reads written : 3,611,144 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: 00:02:21 1805572 reads; of these: 1805572 (100.00%) were paired; of these: 246801 (13.67%) aligned concordantly 0 times 1430796 (79.24%) aligned concordantly exactly 1 time 127975 (7.09%) aligned concordantly >1 times ---- 246801 pairs aligned concordantly 0 times; of these: 151696 (61.46%) aligned discordantly 1 time ---- 95105 pairs aligned 0 times concordantly or discordantly; of these: 190210 mates make up the pairs; of these: 129134 (67.89%) aligned 0 times 29279 (15.39%) aligned exactly 1 time 31797 (16.72%) aligned >1 times 96.42% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 10640 / 1706276 = 0.0062 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 16:54:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.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 16:54:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:54:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:54:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.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 16:54:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:54:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.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 16:54:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:54:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:54:21: 1000000 INFO @ Fri, 05 Jul 2019 16:54:22: 1000000 INFO @ Fri, 05 Jul 2019 16:54:23: 1000000 INFO @ Fri, 05 Jul 2019 16:54:32: 2000000 INFO @ Fri, 05 Jul 2019 16:54:32: 2000000 INFO @ Fri, 05 Jul 2019 16:54:37: 2000000 INFO @ Fri, 05 Jul 2019 16:54:41: 3000000 INFO @ Fri, 05 Jul 2019 16:54:42: 3000000 INFO @ Fri, 05 Jul 2019 16:54:45: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:45: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:45: #1 total tags in treatment: 1548667 INFO @ Fri, 05 Jul 2019 16:54:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:45: #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 16:54:45: #1 tags after filtering in treatment: 1490625 INFO @ Fri, 05 Jul 2019 16:54:45: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:54:45: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:45: #2 number of paired peaks: 22 WARNING @ Fri, 05 Jul 2019 16:54:45: Too few paired peaks (22) 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 16:54:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.20_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/ERX471721/ERX471721.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:54:47: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:47: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:47: #1 total tags in treatment: 1548667 INFO @ Fri, 05 Jul 2019 16:54:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:47: #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 16:54:47: #1 tags after filtering in treatment: 1490625 INFO @ Fri, 05 Jul 2019 16:54:47: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:54:47: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:47: #2 number of paired peaks: 22 WARNING @ Fri, 05 Jul 2019 16:54:47: Too few paired peaks (22) 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 16:54:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.10_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/ERX471721/ERX471721.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:54:51: 3000000 INFO @ Fri, 05 Jul 2019 16:54:58: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:58: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:58: #1 total tags in treatment: 1548667 INFO @ Fri, 05 Jul 2019 16:54:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:58: #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 16:54:58: #1 tags after filtering in treatment: 1490625 INFO @ Fri, 05 Jul 2019 16:54:58: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:54:58: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:58: #2 number of paired peaks: 22 WARNING @ Fri, 05 Jul 2019 16:54:58: Too few paired peaks (22) 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 16:54:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.05_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/ERX471721/ERX471721.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471721/ERX471721.05_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。