Job ID = 2010801 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T15:43:46 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 ) 2019-07-05T15:46:38 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 : 6,293,112 reads read : 12,586,224 reads written : 6,293,112 reads 0-length : 6,293,112 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: 00:02:19 6293112 reads; of these: 6293112 (100.00%) were unpaired; of these: 383761 (6.10%) aligned 0 times 5123612 (81.42%) aligned exactly 1 time 785739 (12.49%) aligned >1 times 93.90% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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] 1286822 / 5909351 = 0.2178 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 00:51:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.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 00:51:48: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:51:48: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.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 00:51:49: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:51:49: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:51:57: 1000000 INFO @ Sat, 06 Jul 2019 00:51:59: 1000000 INFO @ Sat, 06 Jul 2019 00:52:05: 2000000 INFO @ Sat, 06 Jul 2019 00:52:08: 2000000 INFO @ Sat, 06 Jul 2019 00:52:13: 3000000 INFO @ Sat, 06 Jul 2019 00:52:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.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 00:52:17: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:52:17: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:52:18: 3000000 INFO @ Sat, 06 Jul 2019 00:52:21: 4000000 INFO @ Sat, 06 Jul 2019 00:52:26: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 00:52:26: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 00:52:26: #1 total tags in treatment: 4622529 INFO @ Sat, 06 Jul 2019 00:52:26: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:26: #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 00:52:26: #1 tags after filtering in treatment: 4622529 INFO @ Sat, 06 Jul 2019 00:52:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:52:26: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:26: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:26: #2 number of paired peaks: 30 WARNING @ Sat, 06 Jul 2019 00:52:26: Too few paired peaks (30) 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 00:52:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.05_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/SRX4140912/SRX4140912.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:52:26: 4000000 INFO @ Sat, 06 Jul 2019 00:52:27: 1000000 INFO @ Sat, 06 Jul 2019 00:52:32: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 00:52:32: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 00:52:32: #1 total tags in treatment: 4622529 INFO @ Sat, 06 Jul 2019 00:52:32: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:32: #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 00:52:32: #1 tags after filtering in treatment: 4622529 INFO @ Sat, 06 Jul 2019 00:52:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:52:32: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:32: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:32: #2 number of paired peaks: 30 WARNING @ Sat, 06 Jul 2019 00:52:32: Too few paired peaks (30) 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 00:52:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.10_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/SRX4140912/SRX4140912.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:52:36: 2000000 INFO @ Sat, 06 Jul 2019 00:52:45: 3000000 INFO @ Sat, 06 Jul 2019 00:52:54: 4000000 INFO @ Sat, 06 Jul 2019 00:52:59: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 00:52:59: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 00:52:59: #1 total tags in treatment: 4622529 INFO @ Sat, 06 Jul 2019 00:52:59: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:59: #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 00:52:59: #1 tags after filtering in treatment: 4622529 INFO @ Sat, 06 Jul 2019 00:52:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:52:59: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:59: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:59: #2 number of paired peaks: 30 WARNING @ Sat, 06 Jul 2019 00:52:59: Too few paired peaks (30) 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 00:52:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.20_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/SRX4140912/SRX4140912.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140912/SRX4140912.20_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。