Job ID = 2640789 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T10:12:07 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 ) 2019-08-24T10:12:07 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.235' from '172.19.7.43' 2019-08-24T10:12:07 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 '172.19.7.43' 2019-08-24T10:12:07 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/traces/sra40/SRR/003274/SRR3352711' 2019-08-24T10:12:21 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR3352711', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 2,834,347 reads read : 2,834,347 reads written : 2,834,347 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: 00:00:14 2834347 reads; of these: 2834347 (100.00%) were unpaired; of these: 2829211 (99.82%) aligned 0 times 359 (0.01%) aligned exactly 1 time 4777 (0.17%) aligned >1 times 0.18% 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] 3228 / 5136 = 0.6285 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:15:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.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 19:15:32: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:15:32: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:15:32: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:15:32: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:15:32: #1 total tags in treatment: 1908 INFO @ Sat, 24 Aug 2019 19:15:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:15:32: #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 19:15:32: #1 tags after filtering in treatment: 1906 INFO @ Sat, 24 Aug 2019 19:15:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:15:32: #1 finished! INFO @ Sat, 24 Aug 2019 19:15:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:15:32: #2 number of paired peaks: 7 WARNING @ Sat, 24 Aug 2019 19:15:32: Too few paired peaks (7) 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 19:15:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.05_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/SRX1630033/SRX1630033.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:16:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.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 19:16:02: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:16:02: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:16:02: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:16:02: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:16:02: #1 total tags in treatment: 1908 INFO @ Sat, 24 Aug 2019 19:16:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:16:02: #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 19:16:02: #1 tags after filtering in treatment: 1906 INFO @ Sat, 24 Aug 2019 19:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:16:02: #1 finished! INFO @ Sat, 24 Aug 2019 19:16:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:16:02: #2 number of paired peaks: 7 WARNING @ Sat, 24 Aug 2019 19:16:02: Too few paired peaks (7) 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 19:16:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.10_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/SRX1630033/SRX1630033.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.10_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 19:16:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.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 19:16:32: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:16:32: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:16:32: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:16:32: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:16:32: #1 total tags in treatment: 1908 INFO @ Sat, 24 Aug 2019 19:16:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:16:32: #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 19:16:32: #1 tags after filtering in treatment: 1906 INFO @ Sat, 24 Aug 2019 19:16:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:16:32: #1 finished! INFO @ Sat, 24 Aug 2019 19:16:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:16:32: #2 number of paired peaks: 7 WARNING @ Sat, 24 Aug 2019 19:16:32: Too few paired peaks (7) 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 19:16:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.20_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/SRX1630033/SRX1630033.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630033/SRX1630033.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling