Job ID = 4289168 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:45:31 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 ) 2019-12-10T04:45:31 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 ) 2019-12-10T04:55:25 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 ) 2019-12-10T04:55:25 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 : 17,809,952 reads read : 35,619,904 reads written : 17,809,952 reads 0-length : 17,809,952 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: 00:08:25 17809952 reads; of these: 17809952 (100.00%) were unpaired; of these: 2516366 (14.13%) aligned 0 times 12197738 (68.49%) aligned exactly 1 time 3095848 (17.38%) aligned >1 times 85.87% overall alignment rate Time searching: 00:08:25 Overall time: 00:08:25 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 8 files... [bam_rmdupse_core] 7791478 / 15293586 = 0.5095 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:11:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.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 14:11:11: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:11:11: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:11:28: 1000000 INFO @ Tue, 10 Dec 2019 14:11:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.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 14:11:41: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:11:41: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:11:44: 2000000 INFO @ Tue, 10 Dec 2019 14:11:59: 1000000 INFO @ Tue, 10 Dec 2019 14:12:01: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:12:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.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 14:12:11: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:12:11: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:12:17: 2000000 INFO @ Tue, 10 Dec 2019 14:12:19: 4000000 INFO @ Tue, 10 Dec 2019 14:12:30: 1000000 INFO @ Tue, 10 Dec 2019 14:12:36: 3000000 INFO @ Tue, 10 Dec 2019 14:12:38: 5000000 INFO @ Tue, 10 Dec 2019 14:12:50: 2000000 INFO @ Tue, 10 Dec 2019 14:12:55: 4000000 INFO @ Tue, 10 Dec 2019 14:12:58: 6000000 INFO @ Tue, 10 Dec 2019 14:13:09: 3000000 INFO @ Tue, 10 Dec 2019 14:13:14: 5000000 INFO @ Tue, 10 Dec 2019 14:13:17: 7000000 INFO @ Tue, 10 Dec 2019 14:13:26: #1 tag size is determined as 125 bps INFO @ Tue, 10 Dec 2019 14:13:26: #1 tag size = 125 INFO @ Tue, 10 Dec 2019 14:13:26: #1 total tags in treatment: 7502108 INFO @ Tue, 10 Dec 2019 14:13:26: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:13:26: #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 14:13:26: #1 tags after filtering in treatment: 7502108 INFO @ Tue, 10 Dec 2019 14:13:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:13:26: #1 finished! INFO @ Tue, 10 Dec 2019 14:13:26: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:13:27: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:13:27: 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 14:13:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.05_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/SRX6635410/SRX6635410.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:13:28: 4000000 INFO @ Tue, 10 Dec 2019 14:13:32: 6000000 INFO @ Tue, 10 Dec 2019 14:13:44: 5000000 INFO @ Tue, 10 Dec 2019 14:13:50: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:13:59: #1 tag size is determined as 125 bps INFO @ Tue, 10 Dec 2019 14:13:59: #1 tag size = 125 INFO @ Tue, 10 Dec 2019 14:13:59: #1 total tags in treatment: 7502108 INFO @ Tue, 10 Dec 2019 14:13:59: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:13:59: #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 14:13:59: #1 tags after filtering in treatment: 7502108 INFO @ Tue, 10 Dec 2019 14:13:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:13:59: #1 finished! INFO @ Tue, 10 Dec 2019 14:13:59: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:13:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:13:59: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:13:59: 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 14:13:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.10_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/SRX6635410/SRX6635410.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:14:01: 6000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 14:14:17: 7000000 INFO @ Tue, 10 Dec 2019 14:14:24: #1 tag size is determined as 125 bps INFO @ Tue, 10 Dec 2019 14:14:24: #1 tag size = 125 INFO @ Tue, 10 Dec 2019 14:14:24: #1 total tags in treatment: 7502108 INFO @ Tue, 10 Dec 2019 14:14:24: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:14:24: #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 14:14:24: #1 tags after filtering in treatment: 7502108 INFO @ Tue, 10 Dec 2019 14:14:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:14:24: #1 finished! INFO @ Tue, 10 Dec 2019 14:14:24: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:14:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:14:25: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:14:25: 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 14:14:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.20_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/SRX6635410/SRX6635410.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635410/SRX6635410.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling