Job ID = 2641048 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T12:03:50 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 ) 2019-08-24T12:03:50 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 : 28,794,292 reads read : 57,588,584 reads written : 28,794,292 reads 0-length : 28,794,292 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: 00:04:53 28794292 reads; of these: 28794292 (100.00%) were unpaired; of these: 869399 (3.02%) aligned 0 times 25430300 (88.32%) aligned exactly 1 time 2494593 (8.66%) aligned >1 times 96.98% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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 12 files... [bam_rmdupse_core] 16752982 / 27924893 = 0.5999 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:16:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.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 21:16:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:16:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:16:16: 1000000 INFO @ Sat, 24 Aug 2019 21:16:23: 2000000 INFO @ Sat, 24 Aug 2019 21:16:29: 3000000 INFO @ Sat, 24 Aug 2019 21:16:36: 4000000 INFO @ Sat, 24 Aug 2019 21:16:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.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 21:16:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:16:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:16:43: 5000000 INFO @ Sat, 24 Aug 2019 21:16:46: 1000000 INFO @ Sat, 24 Aug 2019 21:16:49: 6000000 INFO @ Sat, 24 Aug 2019 21:16:53: 2000000 INFO @ Sat, 24 Aug 2019 21:16:56: 7000000 INFO @ Sat, 24 Aug 2019 21:16:59: 3000000 INFO @ Sat, 24 Aug 2019 21:17:02: 8000000 INFO @ Sat, 24 Aug 2019 21:17:06: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:17:09: 9000000 INFO @ Sat, 24 Aug 2019 21:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.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 21:17:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:17:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:17:13: 5000000 INFO @ Sat, 24 Aug 2019 21:17:16: 10000000 INFO @ Sat, 24 Aug 2019 21:17:16: 1000000 INFO @ Sat, 24 Aug 2019 21:17:19: 6000000 INFO @ Sat, 24 Aug 2019 21:17:22: 11000000 INFO @ Sat, 24 Aug 2019 21:17:23: 2000000 INFO @ Sat, 24 Aug 2019 21:17:23: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:17:23: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:17:23: #1 total tags in treatment: 11171911 INFO @ Sat, 24 Aug 2019 21:17:23: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:17:23: #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 21:17:23: #1 tags after filtering in treatment: 11171911 INFO @ Sat, 24 Aug 2019 21:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:17:23: #1 finished! INFO @ Sat, 24 Aug 2019 21:17:23: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:17:24: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:17:24: 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 21:17:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.05_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/SRX5257244/SRX5257244.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:17:26: 7000000 INFO @ Sat, 24 Aug 2019 21:17:30: 3000000 INFO @ Sat, 24 Aug 2019 21:17:33: 8000000 INFO @ Sat, 24 Aug 2019 21:17:37: 4000000 INFO @ Sat, 24 Aug 2019 21:17:40: 9000000 INFO @ Sat, 24 Aug 2019 21:17:44: 5000000 INFO @ Sat, 24 Aug 2019 21:17:47: 10000000 INFO @ Sat, 24 Aug 2019 21:17:51: 6000000 INFO @ Sat, 24 Aug 2019 21:17:53: 11000000 INFO @ Sat, 24 Aug 2019 21:17:55: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:17:55: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:17:55: #1 total tags in treatment: 11171911 INFO @ Sat, 24 Aug 2019 21:17:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:17:55: #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 21:17:55: #1 tags after filtering in treatment: 11171911 INFO @ Sat, 24 Aug 2019 21:17:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:17:55: #1 finished! INFO @ Sat, 24 Aug 2019 21:17:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:17:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:17:56: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:17:56: 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 21:17:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.10_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/SRX5257244/SRX5257244.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:17:58: 7000000 INFO @ Sat, 24 Aug 2019 21:18:05: 8000000 INFO @ Sat, 24 Aug 2019 21:18:11: 9000000 INFO @ Sat, 24 Aug 2019 21:18:18: 10000000 INFO @ Sat, 24 Aug 2019 21:18:24: 11000000 INFO @ Sat, 24 Aug 2019 21:18:25: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:18:25: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:18:25: #1 total tags in treatment: 11171911 INFO @ Sat, 24 Aug 2019 21:18:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:18:25: #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 21:18:25: #1 tags after filtering in treatment: 11171911 INFO @ Sat, 24 Aug 2019 21:18:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:18:25: #1 finished! INFO @ Sat, 24 Aug 2019 21:18:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:18:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:18:26: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:18:26: 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 21:18:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.20_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/SRX5257244/SRX5257244.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257244/SRX5257244.20_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。