Job ID = 2010777 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T15:37:10 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 ) 2019-07-05T15:38:54 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 6,194,590 reads read : 6,194,590 reads written : 6,194,590 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: 00:00:55 6194590 reads; of these: 6194590 (100.00%) were unpaired; of these: 1854160 (29.93%) aligned 0 times 4109622 (66.34%) aligned exactly 1 time 230808 (3.73%) aligned >1 times 70.07% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 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] 933311 / 4340430 = 0.2150 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 00:41:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.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 00:41:58: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:41:58: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:41:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.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 00:41:59: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:41:59: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:42:07: 1000000 INFO @ Sat, 06 Jul 2019 00:42:08: 1000000 INFO @ Sat, 06 Jul 2019 00:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.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 00:42:14: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:42:14: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:42:15: 2000000 INFO @ Sat, 06 Jul 2019 00:42:17: 2000000 INFO @ Sat, 06 Jul 2019 00:42:22: 3000000 INFO @ Sat, 06 Jul 2019 00:42:23: 1000000 INFO @ Sat, 06 Jul 2019 00:42:25: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:42:25: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:42:25: #1 total tags in treatment: 3407119 INFO @ Sat, 06 Jul 2019 00:42:25: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:42:25: #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 00:42:26: #1 tags after filtering in treatment: 3407119 INFO @ Sat, 06 Jul 2019 00:42:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:42:26: #1 finished! INFO @ Sat, 06 Jul 2019 00:42:26: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:42:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:42:26: #2 number of paired peaks: 5 WARNING @ Sat, 06 Jul 2019 00:42:26: Too few paired peaks (5) 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 00:42:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.10_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/SRX390622/SRX390622.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:42:27: 3000000 INFO @ Sat, 06 Jul 2019 00:42:31: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:42:31: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:42:31: #1 total tags in treatment: 3407119 INFO @ Sat, 06 Jul 2019 00:42:31: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:42:31: #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 00:42:31: #1 tags after filtering in treatment: 3407119 INFO @ Sat, 06 Jul 2019 00:42:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:42:31: #1 finished! INFO @ Sat, 06 Jul 2019 00:42:31: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:42:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:42:31: #2 number of paired peaks: 5 WARNING @ Sat, 06 Jul 2019 00:42:31: Too few paired peaks (5) 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 00:42:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.05_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/SRX390622/SRX390622.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:42:33: 2000000 INFO @ Sat, 06 Jul 2019 00:42:42: 3000000 INFO @ Sat, 06 Jul 2019 00:42:46: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:42:46: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:42:46: #1 total tags in treatment: 3407119 INFO @ Sat, 06 Jul 2019 00:42:46: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:42:46: #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 00:42:46: #1 tags after filtering in treatment: 3407119 INFO @ Sat, 06 Jul 2019 00:42:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:42:46: #1 finished! INFO @ Sat, 06 Jul 2019 00:42:46: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:42:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:42:46: #2 number of paired peaks: 5 WARNING @ Sat, 06 Jul 2019 00:42:46: Too few paired peaks (5) 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 00:42:46: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.20_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX390622/SRX390622.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。