Job ID = 4289570 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:50:31 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 ) 2019-12-10T06:00:43 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 ) 2019-12-10T06:13:33 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 ) 2019-12-10T06:18:25 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 ) 2019-12-10T06:30:47 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 ) 2019-12-10T06:33:34 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 : 85,640,912 reads read : 85,640,912 reads written : 85,640,912 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: 00:28:18 85640912 reads; of these: 85640912 (100.00%) were unpaired; of these: 795736 (0.93%) aligned 0 times 28030375 (32.73%) aligned exactly 1 time 56814801 (66.34%) aligned >1 times 99.07% overall alignment rate Time searching: 00:28:18 Overall time: 00:28:18 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 36 files... [bam_rmdupse_core] 74885537 / 84845176 = 0.8826 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 17:22:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.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 @ Tue, 10 Dec 2019 17:22:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 17:22:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 17:22:12: 1000000 INFO @ Tue, 10 Dec 2019 17:22:23: 2000000 INFO @ Tue, 10 Dec 2019 17:22:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.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 @ Tue, 10 Dec 2019 17:22:30: #1 read tag files... INFO @ Tue, 10 Dec 2019 17:22:30: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 17:22:35: 3000000 INFO @ Tue, 10 Dec 2019 17:22:43: 1000000 INFO @ Tue, 10 Dec 2019 17:22:48: 4000000 INFO @ Tue, 10 Dec 2019 17:22:56: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 17:23:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.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 @ Tue, 10 Dec 2019 17:23:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 17:23:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 17:23:01: 5000000 INFO @ Tue, 10 Dec 2019 17:23:09: 3000000 INFO @ Tue, 10 Dec 2019 17:23:11: 1000000 INFO @ Tue, 10 Dec 2019 17:23:14: 6000000 INFO @ Tue, 10 Dec 2019 17:23:22: 2000000 INFO @ Tue, 10 Dec 2019 17:23:22: 4000000 INFO @ Tue, 10 Dec 2019 17:23:27: 7000000 INFO @ Tue, 10 Dec 2019 17:23:33: 3000000 INFO @ Tue, 10 Dec 2019 17:23:36: 5000000 INFO @ Tue, 10 Dec 2019 17:23:41: 8000000 INFO @ Tue, 10 Dec 2019 17:23:44: 4000000 INFO @ Tue, 10 Dec 2019 17:23:48: 6000000 INFO @ Tue, 10 Dec 2019 17:23:53: 9000000 INFO @ Tue, 10 Dec 2019 17:23:55: 5000000 INFO @ Tue, 10 Dec 2019 17:24:00: 7000000 INFO @ Tue, 10 Dec 2019 17:24:04: #1 tag size is determined as 100 bps INFO @ Tue, 10 Dec 2019 17:24:04: #1 tag size = 100 INFO @ Tue, 10 Dec 2019 17:24:04: #1 total tags in treatment: 9959639 INFO @ Tue, 10 Dec 2019 17:24:04: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 17:24:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 17:24:05: #1 tags after filtering in treatment: 9959639 INFO @ Tue, 10 Dec 2019 17:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 17:24:05: #1 finished! INFO @ Tue, 10 Dec 2019 17:24:05: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 17:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 17:24:05: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 17:24:05: 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 @ Tue, 10 Dec 2019 17:24:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.05_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/SRX7037574/SRX7037574.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 17:24:06: 6000000 INFO @ Tue, 10 Dec 2019 17:24:12: 8000000 INFO @ Tue, 10 Dec 2019 17:24:16: 7000000 INFO @ Tue, 10 Dec 2019 17:24:23: 9000000 INFO @ Tue, 10 Dec 2019 17:24:27: 8000000 INFO @ Tue, 10 Dec 2019 17:24:34: #1 tag size is determined as 100 bps INFO @ Tue, 10 Dec 2019 17:24:34: #1 tag size = 100 INFO @ Tue, 10 Dec 2019 17:24:34: #1 total tags in treatment: 9959639 INFO @ Tue, 10 Dec 2019 17:24:34: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 17:24:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 17:24:34: #1 tags after filtering in treatment: 9959639 INFO @ Tue, 10 Dec 2019 17:24:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 17:24:34: #1 finished! INFO @ Tue, 10 Dec 2019 17:24:34: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 17:24:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 17:24:35: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 17:24:35: 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 @ Tue, 10 Dec 2019 17:24:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.10_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/SRX7037574/SRX7037574.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 17:24:37: 9000000 INFO @ Tue, 10 Dec 2019 17:24:47: #1 tag size is determined as 100 bps INFO @ Tue, 10 Dec 2019 17:24:47: #1 tag size = 100 INFO @ Tue, 10 Dec 2019 17:24:47: #1 total tags in treatment: 9959639 INFO @ Tue, 10 Dec 2019 17:24:47: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 17:24:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 17:24:47: #1 tags after filtering in treatment: 9959639 INFO @ Tue, 10 Dec 2019 17:24:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 17:24:47: #1 finished! INFO @ Tue, 10 Dec 2019 17:24:47: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 17:24:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 17:24:48: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 17:24:48: 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 @ Tue, 10 Dec 2019 17:24:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.20_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/SRX7037574/SRX7037574.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7037574/SRX7037574.20_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。