Job ID = 2640928 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T10:55:11 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 ) 2019-08-24T10:58:16 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 ) 2019-08-24T10:58:18 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 : 19,357,802 reads read : 19,357,802 reads written : 19,357,802 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: 00:05:08 19357802 reads; of these: 19357802 (100.00%) were unpaired; of these: 4247579 (21.94%) aligned 0 times 10904144 (56.33%) aligned exactly 1 time 4206079 (21.73%) aligned >1 times 78.06% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 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] 8929739 / 15110223 = 0.5910 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.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 20:20:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:20:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:20:22: 1000000 INFO @ Sat, 24 Aug 2019 20:20:30: 2000000 INFO @ Sat, 24 Aug 2019 20:20:37: 3000000 INFO @ Sat, 24 Aug 2019 20:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.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 20:20:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:20:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:20:45: 4000000 INFO @ Sat, 24 Aug 2019 20:20:52: 1000000 INFO @ Sat, 24 Aug 2019 20:20:53: 5000000 INFO @ Sat, 24 Aug 2019 20:21:00: 2000000 INFO @ Sat, 24 Aug 2019 20:21:00: 6000000 INFO @ Sat, 24 Aug 2019 20:21:02: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:21:02: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:21:02: #1 total tags in treatment: 6180484 INFO @ Sat, 24 Aug 2019 20:21:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:21:02: #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 20:21:02: #1 tags after filtering in treatment: 6180484 INFO @ Sat, 24 Aug 2019 20:21:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:21:02: #1 finished! INFO @ Sat, 24 Aug 2019 20:21:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:21:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:21:02: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:21:02: 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 @ Sat, 24 Aug 2019 20:21:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.05_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/SRX4703451/SRX4703451.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:21:08: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:21:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.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 20:21:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:21:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:21:15: 4000000 INFO @ Sat, 24 Aug 2019 20:21:22: 1000000 INFO @ Sat, 24 Aug 2019 20:21:23: 5000000 INFO @ Sat, 24 Aug 2019 20:21:31: 2000000 INFO @ Sat, 24 Aug 2019 20:21:31: 6000000 INFO @ Sat, 24 Aug 2019 20:21:32: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:21:32: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:21:32: #1 total tags in treatment: 6180484 INFO @ Sat, 24 Aug 2019 20:21:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:21:32: #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 20:21:32: #1 tags after filtering in treatment: 6180484 INFO @ Sat, 24 Aug 2019 20:21:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:21:32: #1 finished! INFO @ Sat, 24 Aug 2019 20:21:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:21:33: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:21:33: 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 20:21:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.10_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/SRX4703451/SRX4703451.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:21:40: 3000000 INFO @ Sat, 24 Aug 2019 20:21:48: 4000000 INFO @ Sat, 24 Aug 2019 20:21:57: 5000000 INFO @ Sat, 24 Aug 2019 20:22:05: 6000000 INFO @ Sat, 24 Aug 2019 20:22:07: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:22:07: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:22:07: #1 total tags in treatment: 6180484 INFO @ Sat, 24 Aug 2019 20:22:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:22:07: #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 20:22:07: #1 tags after filtering in treatment: 6180484 INFO @ Sat, 24 Aug 2019 20:22:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:22:07: #1 finished! INFO @ Sat, 24 Aug 2019 20:22:07: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:22:07: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:22:07: 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 @ Sat, 24 Aug 2019 20:22:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.20_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/SRX4703451/SRX4703451.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703451/SRX4703451.20_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。