Job ID = 4306420 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-12T13:44:53 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 ) 2019-12-12T13:44:53 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 ) 2019-12-12T13:44:53 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 ) 2019-12-12T13:44:53 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 ) 2019-12-12T13:45:22 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 : 7,999,313 reads read : 15,998,626 reads written : 7,999,313 reads 0-length : 7,999,313 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: 00:02:28 7999313 reads; of these: 7999313 (100.00%) were unpaired; of these: 1616947 (20.21%) aligned 0 times 5281325 (66.02%) aligned exactly 1 time 1101041 (13.76%) aligned >1 times 79.79% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 2121548 / 6382366 = 0.3324 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 22:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.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 @ Thu, 12 Dec 2019 22:52:47: #1 read tag files... INFO @ Thu, 12 Dec 2019 22:52:47: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 22:52:57: 1000000 INFO @ Thu, 12 Dec 2019 22:53:08: 2000000 INFO @ Thu, 12 Dec 2019 22:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.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 @ Thu, 12 Dec 2019 22:53:16: #1 read tag files... INFO @ Thu, 12 Dec 2019 22:53:16: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 22:53:20: 3000000 INFO @ Thu, 12 Dec 2019 22:53:26: 1000000 INFO @ Thu, 12 Dec 2019 22:53:32: 4000000 INFO @ Thu, 12 Dec 2019 22:53:35: #1 tag size is determined as 100 bps INFO @ Thu, 12 Dec 2019 22:53:35: #1 tag size = 100 INFO @ Thu, 12 Dec 2019 22:53:35: #1 total tags in treatment: 4260818 INFO @ Thu, 12 Dec 2019 22:53:35: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 22:53:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 22:53:35: #1 tags after filtering in treatment: 4260818 INFO @ Thu, 12 Dec 2019 22:53:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 22:53:35: #1 finished! INFO @ Thu, 12 Dec 2019 22:53:35: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 22:53:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 22:53:35: #2 number of paired peaks: 28 WARNING @ Thu, 12 Dec 2019 22:53:35: 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 @ Thu, 12 Dec 2019 22:53:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.05_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/SRX4140933/SRX4140933.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 22:53:36: 2000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 22:53:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.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 @ Thu, 12 Dec 2019 22:53:46: #1 read tag files... INFO @ Thu, 12 Dec 2019 22:53:46: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 22:53:46: 3000000 INFO @ Thu, 12 Dec 2019 22:53:56: 1000000 INFO @ Thu, 12 Dec 2019 22:53:57: 4000000 INFO @ Thu, 12 Dec 2019 22:53:59: #1 tag size is determined as 100 bps INFO @ Thu, 12 Dec 2019 22:53:59: #1 tag size = 100 INFO @ Thu, 12 Dec 2019 22:53:59: #1 total tags in treatment: 4260818 INFO @ Thu, 12 Dec 2019 22:53:59: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 22:53:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 22:53:59: #1 tags after filtering in treatment: 4260818 INFO @ Thu, 12 Dec 2019 22:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 22:53:59: #1 finished! INFO @ Thu, 12 Dec 2019 22:53:59: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 22:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 22:54:00: #2 number of paired peaks: 28 WARNING @ Thu, 12 Dec 2019 22:54:00: 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 @ Thu, 12 Dec 2019 22:54:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.10_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/SRX4140933/SRX4140933.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 22:54:06: 2000000 INFO @ Thu, 12 Dec 2019 22:54:16: 3000000 INFO @ Thu, 12 Dec 2019 22:54:26: 4000000 INFO @ Thu, 12 Dec 2019 22:54:28: #1 tag size is determined as 100 bps INFO @ Thu, 12 Dec 2019 22:54:28: #1 tag size = 100 INFO @ Thu, 12 Dec 2019 22:54:28: #1 total tags in treatment: 4260818 INFO @ Thu, 12 Dec 2019 22:54:28: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 22:54:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 22:54:28: #1 tags after filtering in treatment: 4260818 INFO @ Thu, 12 Dec 2019 22:54:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 22:54:28: #1 finished! INFO @ Thu, 12 Dec 2019 22:54:28: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 22:54:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 22:54:29: #2 number of paired peaks: 28 WARNING @ Thu, 12 Dec 2019 22:54:29: 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 @ Thu, 12 Dec 2019 22:54:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.20_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/SRX4140933/SRX4140933.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140933/SRX4140933.20_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。