Job ID = 2010199 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T12:41:50 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 ) 2019-07-05T12:43:27 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 ) 2019-07-05T12:43:43 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 ) 2019-07-05T12:43:43 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 ) 2019-07-05T12:44:42 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 ) 2019-07-05T12:44:43 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 ) 2019-07-05T12:48:32 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 ) 2019-07-05T12:48:32 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' 2019-07-05T12:48:32 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' 2019-07-05T12:48:32 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/SRR6184424' (), 32768) from '172.19.7.55' 2019-07-05T12:48:32 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' 2019-07-05T12:48:32 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' 2019-07-05T12:48:32 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' 2019-07-05T12:48:32 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/SRR6184424' (), 32768) from '172.19.7.55' 2019-07-05T12:48:32 fasterq-dump.2.9.6 err: cmn_iter.c cmn_read_String( #2693121 ).VCursorCellDataDirect() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T12:49:41 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 ) 2019-07-05T12:51:19 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 20,600,557 reads read : 41,201,114 reads written : 20,600,557 reads 0-length : 20,600,557 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: 00:08:25 20600557 reads; of these: 20600557 (100.00%) were unpaired; of these: 1358987 (6.60%) aligned 0 times 16939965 (82.23%) aligned exactly 1 time 2301605 (11.17%) aligned >1 times 93.40% overall alignment rate Time searching: 00:08:25 Overall time: 00:08:25 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] 7424965 / 19241570 = 0.3859 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 22:09:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.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 22:09:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:09:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:09:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.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 22:09:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:09:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:09:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.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 22:09:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:09:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:09:14: 1000000 INFO @ Fri, 05 Jul 2019 22:09:15: 1000000 INFO @ Fri, 05 Jul 2019 22:09:17: 1000000 INFO @ Fri, 05 Jul 2019 22:09:21: 2000000 INFO @ Fri, 05 Jul 2019 22:09:23: 2000000 INFO @ Fri, 05 Jul 2019 22:09:25: 2000000 INFO @ Fri, 05 Jul 2019 22:09:28: 3000000 INFO @ Fri, 05 Jul 2019 22:09:30: 3000000 INFO @ Fri, 05 Jul 2019 22:09:32: 3000000 INFO @ Fri, 05 Jul 2019 22:09:34: 4000000 INFO @ Fri, 05 Jul 2019 22:09:37: 4000000 INFO @ Fri, 05 Jul 2019 22:09:40: 4000000 INFO @ Fri, 05 Jul 2019 22:09:41: 5000000 INFO @ Fri, 05 Jul 2019 22:09:44: 5000000 INFO @ Fri, 05 Jul 2019 22:09:47: 5000000 INFO @ Fri, 05 Jul 2019 22:09:48: 6000000 INFO @ Fri, 05 Jul 2019 22:09:51: 6000000 INFO @ Fri, 05 Jul 2019 22:09:54: 6000000 INFO @ Fri, 05 Jul 2019 22:09:54: 7000000 INFO @ Fri, 05 Jul 2019 22:09:58: 7000000 INFO @ Fri, 05 Jul 2019 22:10:01: 8000000 INFO @ Fri, 05 Jul 2019 22:10:02: 7000000 INFO @ Fri, 05 Jul 2019 22:10:05: 8000000 INFO @ Fri, 05 Jul 2019 22:10:08: 9000000 INFO @ Fri, 05 Jul 2019 22:10:09: 8000000 INFO @ Fri, 05 Jul 2019 22:10:12: 9000000 INFO @ Fri, 05 Jul 2019 22:10:14: 10000000 INFO @ Fri, 05 Jul 2019 22:10:16: 9000000 INFO @ Fri, 05 Jul 2019 22:10:19: 10000000 INFO @ Fri, 05 Jul 2019 22:10:21: 11000000 INFO @ Fri, 05 Jul 2019 22:10:24: 10000000 INFO @ Fri, 05 Jul 2019 22:10:25: 11000000 INFO @ Fri, 05 Jul 2019 22:10:26: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 22:10:26: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 22:10:26: #1 total tags in treatment: 11816605 INFO @ Fri, 05 Jul 2019 22:10:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:10:26: #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 22:10:27: #1 tags after filtering in treatment: 11816605 INFO @ Fri, 05 Jul 2019 22:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:10:27: #1 finished! INFO @ Fri, 05 Jul 2019 22:10:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:10:28: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:10:28: 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 22:10:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.05_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/SRX3294572/SRX3294572.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:10:31: 11000000 INFO @ Fri, 05 Jul 2019 22:10:31: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 22:10:31: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 22:10:31: #1 total tags in treatment: 11816605 INFO @ Fri, 05 Jul 2019 22:10:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:10:31: #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 22:10:31: #1 tags after filtering in treatment: 11816605 INFO @ Fri, 05 Jul 2019 22:10:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:10:31: #1 finished! INFO @ Fri, 05 Jul 2019 22:10:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:10:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:10:32: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:10:32: 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 22:10:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.10_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/SRX3294572/SRX3294572.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:10:37: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 22:10:37: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 22:10:37: #1 total tags in treatment: 11816605 INFO @ Fri, 05 Jul 2019 22:10:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:10:37: #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 22:10:37: #1 tags after filtering in treatment: 11816605 INFO @ Fri, 05 Jul 2019 22:10:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:10:37: #1 finished! INFO @ Fri, 05 Jul 2019 22:10:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:10:38: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:10:38: 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 22:10:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.20_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/SRX3294572/SRX3294572.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294572/SRX3294572.20_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。