Job ID = 2010345 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T13:06:58 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 ) 2019-07-05T13:06:58 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.51' 2019-07-05T13:06:58 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' (130.14.250.26) from '172.19.7.51' 2019-07-05T13:06:58 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/sra15/SRR/001005/SRR1029159' 2019-07-05T13:07:11 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1029159' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-07-05T13:07:11 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-07-05T13:09:31 fasterq-dump.2.9.6 sys: error unknown 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 ) 2019-07-05T13:15:44 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 ) spots read : 11,104,260 reads read : 11,104,260 reads written : 11,104,260 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1029159.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: 00:02:08 11104260 reads; of these: 11104260 (100.00%) were unpaired; of these: 1196538 (10.78%) aligned 0 times 8486659 (76.43%) aligned exactly 1 time 1421063 (12.80%) aligned >1 times 89.22% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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 8 files... [bam_rmdupse_core] 3572690 / 9907722 = 0.3606 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 22:30:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.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 22:30:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:30:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:30:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.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 22:30:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:30:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:30:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.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 22:30:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:30:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:30:19: 1000000 INFO @ Fri, 05 Jul 2019 22:30:21: 1000000 INFO @ Fri, 05 Jul 2019 22:30:21: 1000000 INFO @ Fri, 05 Jul 2019 22:30:27: 2000000 INFO @ Fri, 05 Jul 2019 22:30:29: 2000000 INFO @ Fri, 05 Jul 2019 22:30:30: 2000000 INFO @ Fri, 05 Jul 2019 22:30:35: 3000000 INFO @ Fri, 05 Jul 2019 22:30:37: 3000000 INFO @ Fri, 05 Jul 2019 22:30:39: 3000000 INFO @ Fri, 05 Jul 2019 22:30:42: 4000000 INFO @ Fri, 05 Jul 2019 22:30:45: 4000000 INFO @ Fri, 05 Jul 2019 22:30:47: 4000000 INFO @ Fri, 05 Jul 2019 22:30:50: 5000000 INFO @ Fri, 05 Jul 2019 22:30:52: 5000000 INFO @ Fri, 05 Jul 2019 22:30:56: 5000000 INFO @ Fri, 05 Jul 2019 22:30:58: 6000000 INFO @ Fri, 05 Jul 2019 22:31:00: 6000000 INFO @ Fri, 05 Jul 2019 22:31:01: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:31:01: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:31:01: #1 total tags in treatment: 6335032 INFO @ Fri, 05 Jul 2019 22:31:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:31:01: #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 22:31:01: #1 tags after filtering in treatment: 6335032 INFO @ Fri, 05 Jul 2019 22:31:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:31:01: #1 finished! INFO @ Fri, 05 Jul 2019 22:31:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:31:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:31:01: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:31:01: 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 22:31:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.05_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/SRX377002/SRX377002.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:31:03: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:31:03: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:31:03: #1 total tags in treatment: 6335032 INFO @ Fri, 05 Jul 2019 22:31:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:31:03: #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 22:31:03: #1 tags after filtering in treatment: 6335032 INFO @ Fri, 05 Jul 2019 22:31:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:31:03: #1 finished! INFO @ Fri, 05 Jul 2019 22:31:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:31:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:31:03: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:31:03: 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 22:31:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.20_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/SRX377002/SRX377002.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:31:04: 6000000 INFO @ Fri, 05 Jul 2019 22:31:07: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:31:07: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:31:07: #1 total tags in treatment: 6335032 INFO @ Fri, 05 Jul 2019 22:31:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:31:07: #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 22:31:07: #1 tags after filtering in treatment: 6335032 INFO @ Fri, 05 Jul 2019 22:31:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:31:07: #1 finished! INFO @ Fri, 05 Jul 2019 22:31:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:31:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:31:07: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:31:07: 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 22:31:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.10_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/SRX377002/SRX377002.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX377002/SRX377002.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。