Job ID = 2641041 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T11:54:13 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 ) 2019-08-24T11:54:13 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.232' from '172.19.7.77' 2019-08-24T11:54:13 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' (165.112.9.232) from '172.19.7.77' 2019-08-24T11:54:13 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/sra75/SRR/008252/SRR8450267' 2019-08-24T11:54:13 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR8450267', 'SEQUENCE', 'NAME' ).VDBManagerOpenDBRead() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) spots read : 27,513,945 reads read : 55,027,890 reads written : 27,513,945 reads 0-length : 27,513,945 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: 00:04:48 27513945 reads; of these: 27513945 (100.00%) were unpaired; of these: 1410062 (5.12%) aligned 0 times 23611127 (85.82%) aligned exactly 1 time 2492756 (9.06%) aligned >1 times 94.88% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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 12 files... [bam_rmdupse_core] 15362711 / 26103883 = 0.5885 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:14:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.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 21:14:00: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:14:00: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:14:08: 1000000 INFO @ Sat, 24 Aug 2019 21:14:16: 2000000 INFO @ Sat, 24 Aug 2019 21:14:23: 3000000 INFO @ Sat, 24 Aug 2019 21:14:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.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 21:14:30: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:14:30: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:14:31: 4000000 INFO @ Sat, 24 Aug 2019 21:14:38: 1000000 INFO @ Sat, 24 Aug 2019 21:14:39: 5000000 INFO @ Sat, 24 Aug 2019 21:14:46: 2000000 INFO @ Sat, 24 Aug 2019 21:14:46: 6000000 INFO @ Sat, 24 Aug 2019 21:14:54: 3000000 INFO @ Sat, 24 Aug 2019 21:14:54: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:15:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.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 21:15:00: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:15:00: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:15:02: 4000000 INFO @ Sat, 24 Aug 2019 21:15:02: 8000000 INFO @ Sat, 24 Aug 2019 21:15:10: 5000000 INFO @ Sat, 24 Aug 2019 21:15:10: 1000000 INFO @ Sat, 24 Aug 2019 21:15:10: 9000000 INFO @ Sat, 24 Aug 2019 21:15:18: 6000000 INFO @ Sat, 24 Aug 2019 21:15:18: 10000000 INFO @ Sat, 24 Aug 2019 21:15:20: 2000000 INFO @ Sat, 24 Aug 2019 21:15:24: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:15:24: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:15:24: #1 total tags in treatment: 10741172 INFO @ Sat, 24 Aug 2019 21:15:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:15:24: #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 21:15:24: #1 tags after filtering in treatment: 10741172 INFO @ Sat, 24 Aug 2019 21:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:15:24: #1 finished! INFO @ Sat, 24 Aug 2019 21:15:24: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:15:25: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:15:25: 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 @ Sat, 24 Aug 2019 21:15:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.05_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/SRX5257238/SRX5257238.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:15:26: 7000000 INFO @ Sat, 24 Aug 2019 21:15:29: 3000000 INFO @ Sat, 24 Aug 2019 21:15:34: 8000000 INFO @ Sat, 24 Aug 2019 21:15:38: 4000000 INFO @ Sat, 24 Aug 2019 21:15:42: 9000000 INFO @ Sat, 24 Aug 2019 21:15:48: 5000000 INFO @ Sat, 24 Aug 2019 21:15:50: 10000000 INFO @ Sat, 24 Aug 2019 21:15:55: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:15:55: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:15:55: #1 total tags in treatment: 10741172 INFO @ Sat, 24 Aug 2019 21:15:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:15:55: #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 21:15:55: #1 tags after filtering in treatment: 10741172 INFO @ Sat, 24 Aug 2019 21:15:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:15:55: #1 finished! INFO @ Sat, 24 Aug 2019 21:15:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:15:56: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:15:56: 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 @ Sat, 24 Aug 2019 21:15:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.10_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/SRX5257238/SRX5257238.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:15:57: 6000000 INFO @ Sat, 24 Aug 2019 21:16:06: 7000000 INFO @ Sat, 24 Aug 2019 21:16:15: 8000000 INFO @ Sat, 24 Aug 2019 21:16:24: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:16:33: 10000000 INFO @ Sat, 24 Aug 2019 21:16:40: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:16:40: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:16:40: #1 total tags in treatment: 10741172 INFO @ Sat, 24 Aug 2019 21:16:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:16:40: #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 21:16:40: #1 tags after filtering in treatment: 10741172 INFO @ Sat, 24 Aug 2019 21:16:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:16:40: #1 finished! INFO @ Sat, 24 Aug 2019 21:16:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:16:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:16:41: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:16:41: 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 @ Sat, 24 Aug 2019 21:16:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.20_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/SRX5257238/SRX5257238.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257238/SRX5257238.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。