Job ID = 2010209 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T12:48:23 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 ) 2019-07-05T12:48:23 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' 2019-07-05T12:48:23 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' 2019-07-05T12:48:23 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/SRR6184433' (), 32768) from '172.19.7.77' 2019-07-05T12:48:23 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' 2019-07-05T12:48:23 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' 2019-07-05T12:48:23 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' 2019-07-05T12:48:23 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/SRR6184433' (), 32768) from '172.19.7.77' 2019-07-05T12:48:23 fasterq-dump.2.9.6 err: cmn_iter.c cmn_read_String( #1779713 ).VCursorCellDataDirect() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T12:48:23 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 ) 2019-07-05T12:48:23 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' 2019-07-05T12:48:23 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' 2019-07-05T12:48:23 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/SRR6184433' (), 32768) from '172.19.7.77' 2019-07-05T12:48:23 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' 2019-07-05T12:48:23 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' 2019-07-05T12:48:23 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' 2019-07-05T12:48:23 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/SRR6184433' (), 32768) from '172.19.7.77' 2019-07-05T12:48:23 fasterq-dump.2.9.6 err: cmn_iter.c cmn_read_String( #3725313 ).VCursorCellDataDirect() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T12:48:28 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' 2019-07-05T12:48:28 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/SRR6184433' 2019-07-05T12:48:28 fasterq-dump.2.9.6 err: invalid accession 'SRR6184433' 2019-07-05T12:48:43 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' 2019-07-05T12:48:43 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/traces/sra53/SRR/006039/SRR6184433' 2019-07-05T12:48:43 fasterq-dump.2.9.6 err: invalid accession 'SRR6184433' 2019-07-05T12:48:58 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' 2019-07-05T12:48:58 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/SRR6184433' 2019-07-05T12:48:58 fasterq-dump.2.9.6 err: invalid accession 'SRR6184433' spots read : 5,760,876 reads read : 11,521,752 reads written : 5,760,876 reads 0-length : 5,760,876 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: 00:02:00 5760876 reads; of these: 5760876 (100.00%) were unpaired; of these: 269142 (4.67%) aligned 0 times 4880793 (84.72%) aligned exactly 1 time 610941 (10.61%) aligned >1 times 95.33% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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_rmdupse_core] 1517644 / 5491734 = 0.2764 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 21:54:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.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 21:54:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:54:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:54:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.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 21:54:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:54:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:54:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.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 21:54:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:54:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:54:36: 1000000 INFO @ Fri, 05 Jul 2019 21:54:38: 1000000 INFO @ Fri, 05 Jul 2019 21:54:38: 1000000 INFO @ Fri, 05 Jul 2019 21:54:44: 2000000 INFO @ Fri, 05 Jul 2019 21:54:46: 2000000 INFO @ Fri, 05 Jul 2019 21:54:47: 2000000 INFO @ Fri, 05 Jul 2019 21:54:53: 3000000 INFO @ Fri, 05 Jul 2019 21:54:55: 3000000 INFO @ Fri, 05 Jul 2019 21:54:56: 3000000 INFO @ Fri, 05 Jul 2019 21:55:01: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:55:01: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:55:01: #1 total tags in treatment: 3974090 INFO @ Fri, 05 Jul 2019 21:55:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:55:01: #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 21:55:01: #1 tags after filtering in treatment: 3974090 INFO @ Fri, 05 Jul 2019 21:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:55:01: #1 finished! INFO @ Fri, 05 Jul 2019 21:55:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:55:01: #2 number of paired peaks: 37 WARNING @ Fri, 05 Jul 2019 21:55:01: Too few paired peaks (37) 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 21:55:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.05_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/SRX3294581/SRX3294581.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:55:03: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:55:03: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:55:03: #1 total tags in treatment: 3974090 INFO @ Fri, 05 Jul 2019 21:55:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:55:03: #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 21:55:03: #1 tags after filtering in treatment: 3974090 INFO @ Fri, 05 Jul 2019 21:55:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:55:03: #1 finished! INFO @ Fri, 05 Jul 2019 21:55:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:55:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:55:04: #2 number of paired peaks: 37 WARNING @ Fri, 05 Jul 2019 21:55:04: Too few paired peaks (37) 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 21:55:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.10_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/SRX3294581/SRX3294581.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:55:04: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:55:04: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:55:04: #1 total tags in treatment: 3974090 INFO @ Fri, 05 Jul 2019 21:55:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:55:04: #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 21:55:04: #1 tags after filtering in treatment: 3974090 INFO @ Fri, 05 Jul 2019 21:55:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:55:04: #1 finished! INFO @ Fri, 05 Jul 2019 21:55:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:55:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:55:04: #2 number of paired peaks: 37 WARNING @ Fri, 05 Jul 2019 21:55:04: Too few paired peaks (37) 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 21:55:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.20_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/SRX3294581/SRX3294581.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294581/SRX3294581.20_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。