Job ID = 2640792 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T10:12:08 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 ) 2019-08-24T10:12:08 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.235' from '172.19.7.42' 2019-08-24T10:12:08 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 '172.19.7.42' 2019-08-24T10:12:08 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/SRR3351889/SRR3351889.1' 2019-08-24T10:12:08 fasterq-dump.2.9.6 err: invalid accession 'SRR3351889' spots read : 1,200,296 reads read : 1,200,296 reads written : 1,200,296 spots read : 993,170 reads read : 993,170 reads written : 993,170 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR3351889.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR3351890.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:14 2193466 reads; of these: 2193466 (100.00%) were unpaired; of these: 2188099 (99.76%) aligned 0 times 228 (0.01%) aligned exactly 1 time 5139 (0.23%) aligned >1 times 0.24% 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] 2358 / 5367 = 0.4394 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:15:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.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 19:15:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:15:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:15:31: #1 tag size is determined as 76 bps INFO @ Sat, 24 Aug 2019 19:15:31: #1 tag size = 76 INFO @ Sat, 24 Aug 2019 19:15:31: #1 total tags in treatment: 3009 INFO @ Sat, 24 Aug 2019 19:15:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:15:31: #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 19:15:31: #1 tags after filtering in treatment: 3003 INFO @ Sat, 24 Aug 2019 19:15:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:15:31: #1 finished! INFO @ Sat, 24 Aug 2019 19:15:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:15:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:15:31: #2 number of paired peaks: 9 WARNING @ Sat, 24 Aug 2019 19:15:31: Too few paired peaks (9) 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 19:15:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.05_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/SRX1630038/SRX1630038.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:16:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.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 19:16:00: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:16:00: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:16:00: #1 tag size is determined as 76 bps INFO @ Sat, 24 Aug 2019 19:16:00: #1 tag size = 76 INFO @ Sat, 24 Aug 2019 19:16:00: #1 total tags in treatment: 3009 INFO @ Sat, 24 Aug 2019 19:16:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:16:00: #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 19:16:00: #1 tags after filtering in treatment: 3003 INFO @ Sat, 24 Aug 2019 19:16:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:16:00: #1 finished! INFO @ Sat, 24 Aug 2019 19:16:00: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:16:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:16:00: #2 number of paired peaks: 9 WARNING @ Sat, 24 Aug 2019 19:16:00: Too few paired peaks (9) 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 19:16:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.10_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/SRX1630038/SRX1630038.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.10_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 19:16:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.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 19:16:30: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:16:30: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:16:30: #1 tag size is determined as 76 bps INFO @ Sat, 24 Aug 2019 19:16:30: #1 tag size = 76 INFO @ Sat, 24 Aug 2019 19:16:30: #1 total tags in treatment: 3009 INFO @ Sat, 24 Aug 2019 19:16:30: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:16:30: #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 19:16:30: #1 tags after filtering in treatment: 3003 INFO @ Sat, 24 Aug 2019 19:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:16:30: #1 finished! INFO @ Sat, 24 Aug 2019 19:16:30: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:16:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:16:30: #2 number of paired peaks: 9 WARNING @ Sat, 24 Aug 2019 19:16:30: Too few paired peaks (9) 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 19:16:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.20_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/SRX1630038/SRX1630038.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1630038/SRX1630038.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling