Job ID = 2011773 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T17:27:20 fasterq-dump.2.9.6 sys: timeout exhausted while creating file within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T17:27:20 fasterq-dump.2.9.6 err: timeout exhausted while creating file within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR8207207/SRR8207207.1' 2019-07-05T17:27:20 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR8207207', 'SEQUENCE', 'NAME' ).VDBManagerOpenDBRead() -> RC(rcNS,rcFile,rcCreating,rcTimeout,rcExhausted) 2019-07-05T17:31:56 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 ) 2019-07-05T17:31:56 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 ) 2019-07-05T17:31:56 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 ) 2019-07-05T17:31:56 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 ) 2019-07-05T17:32:32 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 : 6,478,206 reads read : 12,956,412 reads written : 6,478,206 reads 0-length : 6,478,206 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: 00:02:26 6478206 reads; of these: 6478206 (100.00%) were unpaired; of these: 272547 (4.21%) aligned 0 times 5270451 (81.36%) aligned exactly 1 time 935208 (14.44%) aligned >1 times 95.79% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 1990347 / 6205659 = 0.3207 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 @ Sat, 06 Jul 2019 02:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.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, 06 Jul 2019 02:39:07: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:39:07: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.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, 06 Jul 2019 02:39:07: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:39:07: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.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, 06 Jul 2019 02:39:07: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:39:07: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:39:16: 1000000 INFO @ Sat, 06 Jul 2019 02:39:18: 1000000 INFO @ Sat, 06 Jul 2019 02:39:20: 1000000 INFO @ Sat, 06 Jul 2019 02:39:25: 2000000 INFO @ Sat, 06 Jul 2019 02:39:27: 2000000 INFO @ Sat, 06 Jul 2019 02:39:32: 2000000 INFO @ Sat, 06 Jul 2019 02:39:33: 3000000 INFO @ Sat, 06 Jul 2019 02:39:37: 3000000 INFO @ Sat, 06 Jul 2019 02:39:42: 4000000 INFO @ Sat, 06 Jul 2019 02:39:44: #1 tag size is determined as 101 bps INFO @ Sat, 06 Jul 2019 02:39:44: #1 tag size = 101 INFO @ Sat, 06 Jul 2019 02:39:44: #1 total tags in treatment: 4215312 INFO @ Sat, 06 Jul 2019 02:39:44: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:39:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:39:44: #1 tags after filtering in treatment: 4215312 INFO @ Sat, 06 Jul 2019 02:39:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:39:44: #1 finished! INFO @ Sat, 06 Jul 2019 02:39:44: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:39:44: 3000000 INFO @ Sat, 06 Jul 2019 02:39:44: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 02:39:44: Too few paired peaks (28) 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, 06 Jul 2019 02:39:44: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:39:47: 4000000 INFO @ Sat, 06 Jul 2019 02:39:49: #1 tag size is determined as 101 bps INFO @ Sat, 06 Jul 2019 02:39:49: #1 tag size = 101 INFO @ Sat, 06 Jul 2019 02:39:49: #1 total tags in treatment: 4215312 INFO @ Sat, 06 Jul 2019 02:39:49: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:39:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:39:49: #1 tags after filtering in treatment: 4215312 INFO @ Sat, 06 Jul 2019 02:39:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:39:49: #1 finished! INFO @ Sat, 06 Jul 2019 02:39:49: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:39:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:39:49: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 02:39:49: Too few paired peaks (28) 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, 06 Jul 2019 02:39:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.20_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/SRX5026529/SRX5026529.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:39:55: 4000000 INFO @ Sat, 06 Jul 2019 02:39:58: #1 tag size is determined as 101 bps INFO @ Sat, 06 Jul 2019 02:39:58: #1 tag size = 101 INFO @ Sat, 06 Jul 2019 02:39:58: #1 total tags in treatment: 4215312 INFO @ Sat, 06 Jul 2019 02:39:58: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:39:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:39:58: #1 tags after filtering in treatment: 4215312 INFO @ Sat, 06 Jul 2019 02:39:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:39:58: #1 finished! INFO @ Sat, 06 Jul 2019 02:39:58: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:39:58: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 02:39:58: Too few paired peaks (28) 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, 06 Jul 2019 02:39:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.05_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/SRX5026529/SRX5026529.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5026529/SRX5026529.05_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。