Job ID = 2007924 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:39:35 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 ) 2019-07-05T07:40:38 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' 2019-07-05T07:40:38 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/ERR506361/ERR506361.1' 2019-07-05T07:40:38 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'ERR506361', 'SEQUENCE', 'CMP_READ' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:43 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' 2019-07-05T07:40:43 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/ERR506361/ERR506361.1' 2019-07-05T07:40:43 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506361' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:48 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' 2019-07-05T07:40:48 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/ERR506361/ERR506361.1' 2019-07-05T07:40:48 fasterq-dump.2.9.6 err: invalid accession 'ERR506361' 2019-07-05T07:41:03 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' 2019-07-05T07:41:03 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/ERR506361/ERR506361.1' 2019-07-05T07:41:03 fasterq-dump.2.9.6 err: invalid accession 'ERR506361' 2019-07-05T07:41:18 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' 2019-07-05T07:41:18 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/ERR506361/ERR506361.1' 2019-07-05T07:41:18 fasterq-dump.2.9.6 err: invalid accession 'ERR506361' spots read : 1,990,662 reads read : 3,981,324 reads written : 3,981,324 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: 00:02:16 1990662 reads; of these: 1990662 (100.00%) were paired; of these: 285217 (14.33%) aligned concordantly 0 times 1563727 (78.55%) aligned concordantly exactly 1 time 141718 (7.12%) aligned concordantly >1 times ---- 285217 pairs aligned concordantly 0 times; of these: 163587 (57.36%) aligned discordantly 1 time ---- 121630 pairs aligned 0 times concordantly or discordantly; of these: 243260 mates make up the pairs; of these: 172337 (70.84%) aligned 0 times 36795 (15.13%) aligned exactly 1 time 34128 (14.03%) aligned >1 times 95.67% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 11292 / 1845749 = 0.0061 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 16:55:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.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 16:55:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:55:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:55:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.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 16:55:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:55:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:55:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.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 16:55:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:55:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:55:17: 1000000 INFO @ Fri, 05 Jul 2019 16:55:19: 1000000 INFO @ Fri, 05 Jul 2019 16:55:20: 1000000 INFO @ Fri, 05 Jul 2019 16:55:26: 2000000 INFO @ Fri, 05 Jul 2019 16:55:26: 2000000 INFO @ Fri, 05 Jul 2019 16:55:30: 2000000 INFO @ Fri, 05 Jul 2019 16:55:34: 3000000 INFO @ Fri, 05 Jul 2019 16:55:34: 3000000 INFO @ Fri, 05 Jul 2019 16:55:40: 3000000 INFO @ Fri, 05 Jul 2019 16:55:40: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:55:40: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:55:40: #1 total tags in treatment: 1694607 INFO @ Fri, 05 Jul 2019 16:55:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:55:40: #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 16:55:40: #1 tags after filtering in treatment: 1623058 INFO @ Fri, 05 Jul 2019 16:55:40: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:55:40: #1 finished! INFO @ Fri, 05 Jul 2019 16:55:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:55:40: #2 number of paired peaks: 21 WARNING @ Fri, 05 Jul 2019 16:55:40: Too few paired peaks (21) 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 16:55:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.20_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/ERX471718/ERX471718.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:55:41: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:55:41: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:55:41: #1 total tags in treatment: 1694607 INFO @ Fri, 05 Jul 2019 16:55:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:55:41: #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 16:55:41: #1 tags after filtering in treatment: 1623058 INFO @ Fri, 05 Jul 2019 16:55:41: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:55:41: #1 finished! INFO @ Fri, 05 Jul 2019 16:55:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:55:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:55:41: #2 number of paired peaks: 21 WARNING @ Fri, 05 Jul 2019 16:55:41: Too few paired peaks (21) 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 16:55:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.05_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/ERX471718/ERX471718.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:55:47: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:55:47: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:55:47: #1 total tags in treatment: 1694607 INFO @ Fri, 05 Jul 2019 16:55:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:55:47: #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 16:55:47: #1 tags after filtering in treatment: 1623058 INFO @ Fri, 05 Jul 2019 16:55:47: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:55:47: #1 finished! INFO @ Fri, 05 Jul 2019 16:55:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:55:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:55:48: #2 number of paired peaks: 21 WARNING @ Fri, 05 Jul 2019 16:55:48: Too few paired peaks (21) 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 16:55:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.10_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/ERX471718/ERX471718.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471718/ERX471718.10_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。