Job ID = 2010203 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T12:41:36 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 ) 2019-07-05T12:41:49 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 ) 2019-07-05T12:43:02 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 ) 2019-07-05T12:43:56 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 ) 2019-07-05T12:43:56 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 ) 2019-07-05T12:44:52 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 ) 2019-07-05T12:48:24 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 ) 2019-07-05T12:48:24 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' 2019-07-05T12:48:24 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' 2019-07-05T12:48:24 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra53/SRR/006039/SRR6184427' (), 32768) from '172.19.7.74' 2019-07-05T12:48:24 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' 2019-07-05T12:48:24 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' 2019-07-05T12:48:24 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' 2019-07-05T12:48:24 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra53/SRR/006039/SRR6184427' (), 32768) from '172.19.7.74' 2019-07-05T12:48:24 fasterq-dump.2.9.6 err: cmn_iter.c cmn_read_String( #18094081 ).VCursorCellDataDirect() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T12:48:44 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' 2019-07-05T12:48:44 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/traces/sra53/SRR/006039/SRR6184427' 2019-07-05T12:48:44 fasterq-dump.2.9.6 err: invalid accession 'SRR6184427' 2019-07-05T12:48:59 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' 2019-07-05T12:48:59 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/traces/sra53/SRR/006039/SRR6184427' 2019-07-05T12:48:59 fasterq-dump.2.9.6 err: invalid accession 'SRR6184427' spots read : 18,755,363 reads read : 37,510,726 reads written : 18,755,363 reads 0-length : 18,755,363 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: 00:06:42 18755363 reads; of these: 18755363 (100.00%) were unpaired; of these: 1188809 (6.34%) aligned 0 times 15200838 (81.05%) aligned exactly 1 time 2365716 (12.61%) aligned >1 times 93.66% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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_sort_core] merging from 8 files... [bam_rmdupse_core] 8504367 / 17566554 = 0.4841 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 22:03:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.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 22:03:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:03:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:03:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.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 22:03:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:03:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:03:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.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 22:03:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:03:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:03:43: 1000000 INFO @ Fri, 05 Jul 2019 22:03:43: 1000000 INFO @ Fri, 05 Jul 2019 22:03:45: 1000000 INFO @ Fri, 05 Jul 2019 22:03:50: 2000000 INFO @ Fri, 05 Jul 2019 22:03:51: 2000000 INFO @ Fri, 05 Jul 2019 22:03:53: 2000000 INFO @ Fri, 05 Jul 2019 22:03:56: 3000000 INFO @ Fri, 05 Jul 2019 22:03:59: 3000000 INFO @ Fri, 05 Jul 2019 22:04:01: 3000000 INFO @ Fri, 05 Jul 2019 22:04:03: 4000000 INFO @ Fri, 05 Jul 2019 22:04:07: 4000000 INFO @ Fri, 05 Jul 2019 22:04:09: 4000000 INFO @ Fri, 05 Jul 2019 22:04:09: 5000000 INFO @ Fri, 05 Jul 2019 22:04:15: 5000000 INFO @ Fri, 05 Jul 2019 22:04:16: 6000000 INFO @ Fri, 05 Jul 2019 22:04:16: 5000000 INFO @ Fri, 05 Jul 2019 22:04:22: 7000000 INFO @ Fri, 05 Jul 2019 22:04:22: 6000000 INFO @ Fri, 05 Jul 2019 22:04:23: 6000000 INFO @ Fri, 05 Jul 2019 22:04:29: 8000000 INFO @ Fri, 05 Jul 2019 22:04:30: 7000000 INFO @ Fri, 05 Jul 2019 22:04:30: 7000000 INFO @ Fri, 05 Jul 2019 22:04:35: 9000000 INFO @ Fri, 05 Jul 2019 22:04:36: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 22:04:36: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 22:04:36: #1 total tags in treatment: 9062187 INFO @ Fri, 05 Jul 2019 22:04:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:04:36: #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 22:04:36: #1 tags after filtering in treatment: 9062187 INFO @ Fri, 05 Jul 2019 22:04:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:04:36: #1 finished! INFO @ Fri, 05 Jul 2019 22:04:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:04:36: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:04:36: Too few paired peaks (0) 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 22:04:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.10_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/SRX3294575/SRX3294575.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:04:37: 8000000 INFO @ Fri, 05 Jul 2019 22:04:38: 8000000 INFO @ Fri, 05 Jul 2019 22:04:45: 9000000 INFO @ Fri, 05 Jul 2019 22:04:45: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 22:04:45: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 22:04:45: #1 total tags in treatment: 9062187 INFO @ Fri, 05 Jul 2019 22:04:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:04:45: #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 22:04:46: #1 tags after filtering in treatment: 9062187 INFO @ Fri, 05 Jul 2019 22:04:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:04:46: #1 finished! INFO @ Fri, 05 Jul 2019 22:04:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:04:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:04:46: 9000000 INFO @ Fri, 05 Jul 2019 22:04:46: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 22:04:46: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 22:04:46: #1 total tags in treatment: 9062187 INFO @ Fri, 05 Jul 2019 22:04:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:04:46: #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 22:04:46: #1 tags after filtering in treatment: 9062187 INFO @ Fri, 05 Jul 2019 22:04:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:04:46: #1 finished! INFO @ Fri, 05 Jul 2019 22:04:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:04:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:04:46: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:04:46: Too few paired peaks (0) 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 22:04:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.05_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/SRX3294575/SRX3294575.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:04:47: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:04:47: Too few paired peaks (0) 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 22:04:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.20_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/SRX3294575/SRX3294575.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294575/SRX3294575.20_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。