Job ID = 2007939 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:29 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 ) 2019-07-05T07:40:36 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' 2019-07-05T07:40:36 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/ERR506375/ERR506375.1' 2019-07-05T07:40:36 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506375' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:54 fasterq-dump.2.9.6 err: sorter.c run_producer_pool() : processed lookup rows: 2697500 of 3236995 2019-07-05T07:40:54 fasterq-dump.2.9.6 err: sorter.c execute_lookup_production() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-07-05T07:40:54 fasterq-dump.2.9.6 err: fasterq-dump.c produce_lookup_files() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-07-05T07:40:59 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' 2019-07-05T07:40:59 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/ERR506375/ERR506375.1' 2019-07-05T07:40:59 fasterq-dump.2.9.6 err: invalid accession 'ERR506375' 2019-07-05T07:41:14 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' 2019-07-05T07:41:14 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/ERR506375/ERR506375.1' 2019-07-05T07:41:14 fasterq-dump.2.9.6 err: invalid accession 'ERR506375' spots read : 1,732,216 reads read : 3,464,432 reads written : 3,464,432 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: 00:01:50 1732216 reads; of these: 1732216 (100.00%) were paired; of these: 256713 (14.82%) aligned concordantly 0 times 1379311 (79.63%) aligned concordantly exactly 1 time 96192 (5.55%) aligned concordantly >1 times ---- 256713 pairs aligned concordantly 0 times; of these: 120461 (46.92%) aligned discordantly 1 time ---- 136252 pairs aligned 0 times concordantly or discordantly; of these: 272504 mates make up the pairs; of these: 229005 (84.04%) aligned 0 times 23436 (8.60%) aligned exactly 1 time 20063 (7.36%) aligned >1 times 93.39% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 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] 71578 / 1589855 = 0.0450 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 16:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.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 16:53:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.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 16:53:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.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 16:53:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:54:01: 1000000 INFO @ Fri, 05 Jul 2019 16:54:04: 1000000 INFO @ Fri, 05 Jul 2019 16:54:05: 1000000 INFO @ Fri, 05 Jul 2019 16:54:10: 2000000 INFO @ Fri, 05 Jul 2019 16:54:19: 2000000 INFO @ Fri, 05 Jul 2019 16:54:20: 3000000 INFO @ Fri, 05 Jul 2019 16:54:20: 2000000 INFO @ Fri, 05 Jul 2019 16:54:21: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:21: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:21: #1 total tags in treatment: 1407099 INFO @ Fri, 05 Jul 2019 16:54:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:21: #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 16:54:21: #1 tags after filtering in treatment: 1325084 INFO @ Fri, 05 Jul 2019 16:54:21: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 16:54:21: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:21: #2 number of paired peaks: 26 WARNING @ Fri, 05 Jul 2019 16:54:21: Too few paired peaks (26) 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 16:54:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.20_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/ERX471732/ERX471732.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:54:33: 3000000 INFO @ Fri, 05 Jul 2019 16:54:33: 3000000 INFO @ Fri, 05 Jul 2019 16:54:34: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:34: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:34: #1 total tags in treatment: 1407099 INFO @ Fri, 05 Jul 2019 16:54:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:34: #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 16:54:34: #1 tags after filtering in treatment: 1325084 INFO @ Fri, 05 Jul 2019 16:54:34: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 16:54:34: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:34: #2 number of paired peaks: 26 WARNING @ Fri, 05 Jul 2019 16:54:34: Too few paired peaks (26) 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 16:54:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.05_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/ERX471732/ERX471732.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:54:34: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:34: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:34: #1 total tags in treatment: 1407099 INFO @ Fri, 05 Jul 2019 16:54:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:34: #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 16:54:34: #1 tags after filtering in treatment: 1325084 INFO @ Fri, 05 Jul 2019 16:54:34: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 16:54:34: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:34: #2 number of paired peaks: 26 WARNING @ Fri, 05 Jul 2019 16:54:34: Too few paired peaks (26) 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 16:54:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.10_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/ERX471732/ERX471732.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471732/ERX471732.10_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。