Job ID = 2010797 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T15:41:00 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 ) 2019-07-05T15:43:37 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 : 6,430,192 reads read : 12,860,384 reads written : 6,430,192 reads 0-length : 6,430,192 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: 00:02:42 6430192 reads; of these: 6430192 (100.00%) were unpaired; of these: 1153291 (17.94%) aligned 0 times 4642110 (72.19%) aligned exactly 1 time 634791 (9.87%) aligned >1 times 82.06% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 1011310 / 5276901 = 0.1916 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 00:51:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.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 00:51:32: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:51:32: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:51:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.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 00:51:33: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:51:33: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:51:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.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 00:51:34: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:51:34: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:51:43: 1000000 INFO @ Sat, 06 Jul 2019 00:51:45: 1000000 INFO @ Sat, 06 Jul 2019 00:51:46: 1000000 INFO @ Sat, 06 Jul 2019 00:51:53: 2000000 INFO @ Sat, 06 Jul 2019 00:51:56: 2000000 INFO @ Sat, 06 Jul 2019 00:51:57: 2000000 INFO @ Sat, 06 Jul 2019 00:52:04: 3000000 INFO @ Sat, 06 Jul 2019 00:52:06: 3000000 INFO @ Sat, 06 Jul 2019 00:52:09: 3000000 INFO @ Sat, 06 Jul 2019 00:52:15: 4000000 INFO @ Sat, 06 Jul 2019 00:52:17: 4000000 INFO @ Sat, 06 Jul 2019 00:52:17: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 00:52:17: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 00:52:17: #1 total tags in treatment: 4265591 INFO @ Sat, 06 Jul 2019 00:52:17: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:17: #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 00:52:17: #1 tags after filtering in treatment: 4265591 INFO @ Sat, 06 Jul 2019 00:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:52:17: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:17: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:18: #2 number of paired peaks: 42 WARNING @ Sat, 06 Jul 2019 00:52:18: Too few paired peaks (42) 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 00:52:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.05_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/SRX4140908/SRX4140908.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:52:20: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 00:52:20: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 00:52:20: #1 total tags in treatment: 4265591 INFO @ Sat, 06 Jul 2019 00:52:20: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:20: #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 00:52:20: #1 tags after filtering in treatment: 4265591 INFO @ Sat, 06 Jul 2019 00:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:52:20: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:20: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:20: #2 number of paired peaks: 42 WARNING @ Sat, 06 Jul 2019 00:52:20: Too few paired peaks (42) 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 00:52:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.20_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/SRX4140908/SRX4140908.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:52:21: 4000000 INFO @ Sat, 06 Jul 2019 00:52:24: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 00:52:24: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 00:52:24: #1 total tags in treatment: 4265591 INFO @ Sat, 06 Jul 2019 00:52:24: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:24: #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 00:52:24: #1 tags after filtering in treatment: 4265591 INFO @ Sat, 06 Jul 2019 00:52:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:52:24: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:24: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:24: #2 number of paired peaks: 42 WARNING @ Sat, 06 Jul 2019 00:52:24: Too few paired peaks (42) 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 00:52:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.10_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/SRX4140908/SRX4140908.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140908/SRX4140908.10_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。