Job ID = 2640788 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T10:11:23 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-08-24T10:11:23 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.235' from '172.19.7.83' 2019-08-24T10:11:23 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (165.112.9.235) from '172.19.7.83' 2019-08-24T10:11:23 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR3352712/SRR3352712.1' 2019-08-24T10:11:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR3352712' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 2,672,088 reads read : 2,672,088 reads written : 2,672,088 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR3352712.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:13 2672088 reads; of these: 2672088 (100.00%) were unpaired; of these: 2664310 (99.71%) aligned 0 times 1894 (0.07%) aligned exactly 1 time 5884 (0.22%) aligned >1 times 0.29% overall alignment rate Time searching: 00:00:14 Overall time: 00:00:14 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] 5396 / 7778 = 0.6938 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:13:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.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 @ Sat, 24 Aug 2019 19:13:43: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:13:43: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:13:43: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:13:43: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:13:43: #1 total tags in treatment: 2382 INFO @ Sat, 24 Aug 2019 19:13:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:13:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:13:43: #1 tags after filtering in treatment: 2380 INFO @ Sat, 24 Aug 2019 19:13:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:13:43: #1 finished! INFO @ Sat, 24 Aug 2019 19:13:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:13:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:13:43: #2 number of paired peaks: 22 WARNING @ Sat, 24 Aug 2019 19:13:43: Too few paired peaks (22) 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 @ Sat, 24 Aug 2019 19:13:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.05_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/SRX1630032/SRX1630032.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:14:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.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 @ Sat, 24 Aug 2019 19:14:13: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:14:13: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:14:13: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:14:13: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:14:13: #1 total tags in treatment: 2382 INFO @ Sat, 24 Aug 2019 19:14:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:14:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:14:13: #1 tags after filtering in treatment: 2380 INFO @ Sat, 24 Aug 2019 19:14:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:14:13: #1 finished! INFO @ Sat, 24 Aug 2019 19:14:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:14:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:14:13: #2 number of paired peaks: 22 WARNING @ Sat, 24 Aug 2019 19:14:13: Too few paired peaks (22) 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 @ Sat, 24 Aug 2019 19:14:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.10_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/SRX1630032/SRX1630032.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 19:14:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.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 @ Sat, 24 Aug 2019 19:14:43: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:14:43: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:14:43: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:14:43: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:14:43: #1 total tags in treatment: 2382 INFO @ Sat, 24 Aug 2019 19:14:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:14:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:14:43: #1 tags after filtering in treatment: 2380 INFO @ Sat, 24 Aug 2019 19:14:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:14:43: #1 finished! INFO @ Sat, 24 Aug 2019 19:14:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:14:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:14:43: #2 number of paired peaks: 22 WARNING @ Sat, 24 Aug 2019 19:14:43: Too few paired peaks (22) 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 @ Sat, 24 Aug 2019 19:14:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.20_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/SRX1630032/SRX1630032.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630032/SRX1630032.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling