Job ID = 2009638 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T10:13:53 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 : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 2019-07-05T10:16:23 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 2,613,512 reads read : 2,613,512 reads written : 2,613,512 2019-07-05T10:24:44 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 ) 2019-07-05T10:24:44 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.80' 2019-07-05T10:24:44 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 '172.19.7.80' 2019-07-05T10:24:44 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/era11/ERR/ERR778/ERR778685' 2019-07-05T10:24:53 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'ERR778685' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-07-05T10:24:53 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-07-05T10:26:19 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 ) 2019-07-05T10:26:19 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 : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR778556.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR778591.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: 00:03:07 14613512 reads; of these: 14613512 (100.00%) were unpaired; of these: 5017309 (34.33%) aligned 0 times 8663336 (59.28%) aligned exactly 1 time 932867 (6.38%) aligned >1 times 65.67% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 5072411 / 9596203 = 0.5286 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 19:36:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.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 19:36:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:36:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:36:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.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 19:36:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:36:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:36:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.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 19:36:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:36:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:37:06: 1000000 INFO @ Fri, 05 Jul 2019 19:37:07: 1000000 INFO @ Fri, 05 Jul 2019 19:37:08: 1000000 INFO @ Fri, 05 Jul 2019 19:37:16: 2000000 INFO @ Fri, 05 Jul 2019 19:37:17: 2000000 INFO @ Fri, 05 Jul 2019 19:37:18: 2000000 INFO @ Fri, 05 Jul 2019 19:37:25: 3000000 INFO @ Fri, 05 Jul 2019 19:37:26: 3000000 INFO @ Fri, 05 Jul 2019 19:37:27: 3000000 INFO @ Fri, 05 Jul 2019 19:37:34: 4000000 INFO @ Fri, 05 Jul 2019 19:37:35: 4000000 INFO @ Fri, 05 Jul 2019 19:37:36: 4000000 INFO @ Fri, 05 Jul 2019 19:37:39: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:37:39: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:37:39: #1 total tags in treatment: 4523792 INFO @ Fri, 05 Jul 2019 19:37:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:37:39: #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 19:37:39: #1 tags after filtering in treatment: 4523792 INFO @ Fri, 05 Jul 2019 19:37:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:37:39: #1 finished! INFO @ Fri, 05 Jul 2019 19:37:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:37:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:37:39: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 19:37:39: 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 19:37:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.05_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/ERX769119/ERX769119.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:37:40: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:37:40: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:37:40: #1 total tags in treatment: 4523792 INFO @ Fri, 05 Jul 2019 19:37:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:37:40: #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 19:37:40: #1 tags after filtering in treatment: 4523792 INFO @ Fri, 05 Jul 2019 19:37:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:37:40: #1 finished! INFO @ Fri, 05 Jul 2019 19:37:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:37:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:37:40: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 19:37:40: 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 19:37:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.10_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/ERX769119/ERX769119.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:37:41: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:37:41: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:37:41: #1 total tags in treatment: 4523792 INFO @ Fri, 05 Jul 2019 19:37:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:37:41: #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 19:37:41: #1 tags after filtering in treatment: 4523792 INFO @ Fri, 05 Jul 2019 19:37:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:37:41: #1 finished! INFO @ Fri, 05 Jul 2019 19:37:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:37:41: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 19:37:41: 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 @ Fri, 05 Jul 2019 19:37:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.20_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/ERX769119/ERX769119.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769119/ERX769119.20_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。