Job ID = 4289573 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T06:04:16 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 ) 1900-01-00T00:00:00 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 ) 2019-12-10T06:11:34 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 ) 2019-12-10T06:11:34 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 ) 2019-12-10T06:28:17 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 : 85,998,778 reads read : 85,998,778 reads written : 85,998,778 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: 00:00:01 Multiseed full-index search: 00:28:00 85998778 reads; of these: 85998778 (100.00%) were unpaired; of these: 1810323 (2.11%) aligned 0 times 28984348 (33.70%) aligned exactly 1 time 55204107 (64.19%) aligned >1 times 97.89% overall alignment rate Time searching: 00:28:01 Overall time: 00:28:01 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] 75579601 / 84188455 = 0.8977 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 17:20:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.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 17:20:25: #1 read tag files... INFO @ Tue, 10 Dec 2019 17:20:25: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 17:20:37: 1000000 INFO @ Tue, 10 Dec 2019 17:20:50: 2000000 INFO @ Tue, 10 Dec 2019 17:20:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.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 17:20:54: #1 read tag files... INFO @ Tue, 10 Dec 2019 17:20:54: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 17:21:02: 3000000 INFO @ Tue, 10 Dec 2019 17:21:07: 1000000 INFO @ Tue, 10 Dec 2019 17:21:15: 4000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 17:21:21: 2000000 INFO @ Tue, 10 Dec 2019 17:21:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.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 17:21:24: #1 read tag files... INFO @ Tue, 10 Dec 2019 17:21:24: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 17:21:29: 5000000 INFO @ Tue, 10 Dec 2019 17:21:35: 3000000 INFO @ Tue, 10 Dec 2019 17:21:39: 1000000 INFO @ Tue, 10 Dec 2019 17:21:44: 6000000 INFO @ Tue, 10 Dec 2019 17:21:49: 4000000 INFO @ Tue, 10 Dec 2019 17:21:54: 2000000 INFO @ Tue, 10 Dec 2019 17:22:00: 7000000 INFO @ Tue, 10 Dec 2019 17:22:03: 5000000 INFO @ Tue, 10 Dec 2019 17:22:09: 3000000 INFO @ Tue, 10 Dec 2019 17:22:15: 8000000 INFO @ Tue, 10 Dec 2019 17:22:17: 6000000 INFO @ Tue, 10 Dec 2019 17:22:24: #1 tag size is determined as 100 bps INFO @ Tue, 10 Dec 2019 17:22:24: #1 tag size = 100 INFO @ Tue, 10 Dec 2019 17:22:24: #1 total tags in treatment: 8608854 INFO @ Tue, 10 Dec 2019 17:22:24: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 17:22:24: #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 17:22:24: #1 tags after filtering in treatment: 8608854 INFO @ Tue, 10 Dec 2019 17:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 17:22:24: #1 finished! INFO @ Tue, 10 Dec 2019 17:22:24: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 17:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 17:22:24: 4000000 INFO @ Tue, 10 Dec 2019 17:22:25: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 17:22:25: 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 17:22:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.05_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/SRX7037575/SRX7037575.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 17:22:31: 7000000 INFO @ Tue, 10 Dec 2019 17:22:37: 5000000 INFO @ Tue, 10 Dec 2019 17:22:44: 8000000 INFO @ Tue, 10 Dec 2019 17:22:49: 6000000 INFO @ Tue, 10 Dec 2019 17:22:53: #1 tag size is determined as 100 bps INFO @ Tue, 10 Dec 2019 17:22:53: #1 tag size = 100 INFO @ Tue, 10 Dec 2019 17:22:53: #1 total tags in treatment: 8608854 INFO @ Tue, 10 Dec 2019 17:22:53: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 17:22:53: #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 17:22:53: #1 tags after filtering in treatment: 8608854 INFO @ Tue, 10 Dec 2019 17:22:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 17:22:53: #1 finished! INFO @ Tue, 10 Dec 2019 17:22:53: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 17:22:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 17:22:53: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 17:22:53: 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 17:22:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.10_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/SRX7037575/SRX7037575.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 17:23:01: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 17:23:14: 8000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 17:23:21: #1 tag size is determined as 100 bps INFO @ Tue, 10 Dec 2019 17:23:21: #1 tag size = 100 INFO @ Tue, 10 Dec 2019 17:23:21: #1 total tags in treatment: 8608854 INFO @ Tue, 10 Dec 2019 17:23:21: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 17:23:21: #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 17:23:21: #1 tags after filtering in treatment: 8608854 INFO @ Tue, 10 Dec 2019 17:23:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 17:23:21: #1 finished! INFO @ Tue, 10 Dec 2019 17:23:21: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 17:23:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 17:23:22: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 17:23:22: 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 17:23:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.20_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/SRX7037575/SRX7037575.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7037575/SRX7037575.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling