Job ID = 2010309 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T13:03:17 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 ) 2019-07-05T13:03:17 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.69' 2019-07-05T13:03:17 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' (130.14.250.24) from '172.19.7.69' 2019-07-05T13:03:17 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/sra53/SRR/006079/SRR6225426' 2019-07-05T13:03:17 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR6225426' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T13:03:17 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T13:03:17 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 ) 2019-07-05T13:03:17 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.69' 2019-07-05T13:03:17 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' (130.14.250.24) from '172.19.7.69' 2019-07-05T13:03:17 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/sra53/SRR/006079/SRR6225426' 2019-07-05T13:03:17 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR6225426' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T13:03:17 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T13:11:27 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 ) 2019-07-05T13:15:44 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 ) 2019-07-05T13:15:55 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 ) spots read : 59,471,823 reads read : 118,943,646 reads written : 59,471,823 reads 0-length : 59,471,823 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: 00:10:05 59471823 reads; of these: 59471823 (100.00%) were unpaired; of these: 6082725 (10.23%) aligned 0 times 42697781 (71.79%) aligned exactly 1 time 10691317 (17.98%) aligned >1 times 89.77% overall alignment rate Time searching: 00:10:05 Overall time: 00:10:05 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 24 files... [bam_rmdupse_core] 34989452 / 53389098 = 0.6554 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 23:10:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.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 23:10:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:10:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:10:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.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 23:10:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:10:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:11:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.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 23:11:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:11:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:11:06: 1000000 INFO @ Fri, 05 Jul 2019 23:11:07: 1000000 INFO @ Fri, 05 Jul 2019 23:11:09: 1000000 INFO @ Fri, 05 Jul 2019 23:11:14: 2000000 INFO @ Fri, 05 Jul 2019 23:11:14: 2000000 INFO @ Fri, 05 Jul 2019 23:11:18: 2000000 INFO @ Fri, 05 Jul 2019 23:11:20: 3000000 INFO @ Fri, 05 Jul 2019 23:11:21: 3000000 INFO @ Fri, 05 Jul 2019 23:11:27: 3000000 INFO @ Fri, 05 Jul 2019 23:11:27: 4000000 INFO @ Fri, 05 Jul 2019 23:11:28: 4000000 INFO @ Fri, 05 Jul 2019 23:11:33: 5000000 INFO @ Fri, 05 Jul 2019 23:11:35: 4000000 INFO @ Fri, 05 Jul 2019 23:11:35: 5000000 INFO @ Fri, 05 Jul 2019 23:11:40: 6000000 INFO @ Fri, 05 Jul 2019 23:11:42: 6000000 INFO @ Fri, 05 Jul 2019 23:11:44: 5000000 INFO @ Fri, 05 Jul 2019 23:11:46: 7000000 INFO @ Fri, 05 Jul 2019 23:11:50: 7000000 INFO @ Fri, 05 Jul 2019 23:11:53: 8000000 INFO @ Fri, 05 Jul 2019 23:11:53: 6000000 INFO @ Fri, 05 Jul 2019 23:11:57: 8000000 INFO @ Fri, 05 Jul 2019 23:11:59: 9000000 INFO @ Fri, 05 Jul 2019 23:12:01: 7000000 INFO @ Fri, 05 Jul 2019 23:12:04: 9000000 INFO @ Fri, 05 Jul 2019 23:12:05: 10000000 INFO @ Fri, 05 Jul 2019 23:12:10: 8000000 INFO @ Fri, 05 Jul 2019 23:12:11: 10000000 INFO @ Fri, 05 Jul 2019 23:12:12: 11000000 INFO @ Fri, 05 Jul 2019 23:12:18: 9000000 INFO @ Fri, 05 Jul 2019 23:12:19: 11000000 INFO @ Fri, 05 Jul 2019 23:12:19: 12000000 INFO @ Fri, 05 Jul 2019 23:12:26: 13000000 INFO @ Fri, 05 Jul 2019 23:12:27: 12000000 INFO @ Fri, 05 Jul 2019 23:12:27: 10000000 INFO @ Fri, 05 Jul 2019 23:12:32: 14000000 INFO @ Fri, 05 Jul 2019 23:12:34: 13000000 INFO @ Fri, 05 Jul 2019 23:12:35: 11000000 INFO @ Fri, 05 Jul 2019 23:12:39: 15000000 INFO @ Fri, 05 Jul 2019 23:12:41: 14000000 INFO @ Fri, 05 Jul 2019 23:12:43: 12000000 INFO @ Fri, 05 Jul 2019 23:12:45: 16000000 INFO @ Fri, 05 Jul 2019 23:12:48: 15000000 INFO @ Fri, 05 Jul 2019 23:12:51: 17000000 INFO @ Fri, 05 Jul 2019 23:12:52: 13000000 INFO @ Fri, 05 Jul 2019 23:12:55: 16000000 INFO @ Fri, 05 Jul 2019 23:12:58: 18000000 INFO @ Fri, 05 Jul 2019 23:13:00: 14000000 INFO @ Fri, 05 Jul 2019 23:13:00: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:13:00: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:13:00: #1 total tags in treatment: 18399646 INFO @ Fri, 05 Jul 2019 23:13:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:13:00: #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 23:13:01: #1 tags after filtering in treatment: 18399646 INFO @ Fri, 05 Jul 2019 23:13:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 23:13:01: #1 finished! INFO @ Fri, 05 Jul 2019 23:13:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:13:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:13:02: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:13:02: 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 23:13:02: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:13:02: 17000000 BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 23:13:09: 15000000 INFO @ Fri, 05 Jul 2019 23:13:09: 18000000 INFO @ Fri, 05 Jul 2019 23:13:12: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:13:12: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:13:12: #1 total tags in treatment: 18399646 INFO @ Fri, 05 Jul 2019 23:13:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:13:12: #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 23:13:12: #1 tags after filtering in treatment: 18399646 INFO @ Fri, 05 Jul 2019 23:13:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 23:13:12: #1 finished! INFO @ Fri, 05 Jul 2019 23:13:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:13:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:13:14: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:13:14: 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 23:13:14: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:13:17: 16000000 INFO @ Fri, 05 Jul 2019 23:13:26: 17000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.20_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.05_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.20_peaks.narrowPeak’: No such file or directory rm: CompletedMACS2peakCalling cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:13:34: 18000000 INFO @ Fri, 05 Jul 2019 23:13:37: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:13:37: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:13:37: #1 total tags in treatment: 18399646 INFO @ Fri, 05 Jul 2019 23:13:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:13:37: #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 23:13:38: #1 tags after filtering in treatment: 18399646 INFO @ Fri, 05 Jul 2019 23:13:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 23:13:38: #1 finished! INFO @ Fri, 05 Jul 2019 23:13:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:13:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:13:39: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:13:39: 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 23:13:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.10_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/SRX3334034/SRX3334034.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334034/SRX3334034.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。