Job ID = 2010978 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T16:32:40 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 ) 2019-07-05T16:32:40 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 : 5,375,405 reads read : 10,750,810 reads written : 5,375,405 reads 0-length : 5,375,405 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: 00:01:14 5375405 reads; of these: 5375405 (100.00%) were unpaired; of these: 813072 (15.13%) aligned 0 times 3945980 (73.41%) aligned exactly 1 time 616353 (11.47%) aligned >1 times 84.87% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 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] 932393 / 4562333 = 0.2044 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 01:36:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.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 01:36:02: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:36:02: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.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 01:36:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:36:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:36:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.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 01:36:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:36:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:36:11: 1000000 INFO @ Sat, 06 Jul 2019 01:36:13: 1000000 INFO @ Sat, 06 Jul 2019 01:36:14: 1000000 INFO @ Sat, 06 Jul 2019 01:36:20: 2000000 INFO @ Sat, 06 Jul 2019 01:36:22: 2000000 INFO @ Sat, 06 Jul 2019 01:36:23: 2000000 INFO @ Sat, 06 Jul 2019 01:36:28: 3000000 INFO @ Sat, 06 Jul 2019 01:36:32: 3000000 INFO @ Sat, 06 Jul 2019 01:36:32: 3000000 INFO @ Sat, 06 Jul 2019 01:36:33: #1 tag size is determined as 65 bps INFO @ Sat, 06 Jul 2019 01:36:33: #1 tag size = 65 INFO @ Sat, 06 Jul 2019 01:36:33: #1 total tags in treatment: 3629940 INFO @ Sat, 06 Jul 2019 01:36:33: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:36:33: #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 01:36:33: #1 tags after filtering in treatment: 3629940 INFO @ Sat, 06 Jul 2019 01:36:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:36:33: #1 finished! INFO @ Sat, 06 Jul 2019 01:36:33: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:36:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:36:34: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 01:36:34: 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 01:36:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.05_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/SRX4342628/SRX4342628.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:36:37: #1 tag size is determined as 65 bps INFO @ Sat, 06 Jul 2019 01:36:37: #1 tag size = 65 INFO @ Sat, 06 Jul 2019 01:36:37: #1 total tags in treatment: 3629940 INFO @ Sat, 06 Jul 2019 01:36:37: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:36:37: #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 01:36:37: #1 tags after filtering in treatment: 3629940 INFO @ Sat, 06 Jul 2019 01:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:36:37: #1 finished! INFO @ Sat, 06 Jul 2019 01:36:37: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:36:37: #1 tag size is determined as 65 bps INFO @ Sat, 06 Jul 2019 01:36:37: #1 tag size = 65 INFO @ Sat, 06 Jul 2019 01:36:37: #1 total tags in treatment: 3629940 INFO @ Sat, 06 Jul 2019 01:36:37: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:36:37: #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 01:36:37: #1 tags after filtering in treatment: 3629940 INFO @ Sat, 06 Jul 2019 01:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:36:37: #1 finished! INFO @ Sat, 06 Jul 2019 01:36:37: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:36:38: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 01:36:38: 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 01:36:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.20_peaks.narrowPeak: No such file or directory INFO @ Sat, 06 Jul 2019 01:36:38: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 01:36:38: 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 01:36:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.10_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/SRX4342628/SRX4342628.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.20_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/SRX4342628/SRX4342628.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342628/SRX4342628.10_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。