Job ID = 4289291 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:59:27 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 ) 2019-12-10T05:07:55 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 ) 2019-12-10T05:07:55 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 ) 2019-12-10T05:07:55 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 : 36,026,900 reads read : 72,053,800 reads written : 36,026,900 reads 0-length : 36,026,900 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: 00:08:23 36026900 reads; of these: 36026900 (100.00%) were unpaired; of these: 722324 (2.00%) aligned 0 times 31247436 (86.73%) aligned exactly 1 time 4057140 (11.26%) aligned >1 times 98.00% overall alignment rate Time searching: 00:08:23 Overall time: 00:08:23 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 16 files... [bam_rmdupse_core] 19079525 / 35304576 = 0.5404 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:26:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.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 14:26:27: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:26:27: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:26:34: 1000000 INFO @ Tue, 10 Dec 2019 14:26:43: 2000000 INFO @ Tue, 10 Dec 2019 14:26:51: 3000000 INFO @ Tue, 10 Dec 2019 14:26:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.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 14:26:56: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:26:56: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:26:59: 4000000 INFO @ Tue, 10 Dec 2019 14:27:04: 1000000 INFO @ Tue, 10 Dec 2019 14:27:07: 5000000 INFO @ Tue, 10 Dec 2019 14:27:11: 2000000 INFO @ Tue, 10 Dec 2019 14:27:15: 6000000 INFO @ Tue, 10 Dec 2019 14:27:19: 3000000 INFO @ Tue, 10 Dec 2019 14:27:23: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:27:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.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 14:27:26: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:27:26: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:27:26: 4000000 INFO @ Tue, 10 Dec 2019 14:27:30: 8000000 INFO @ Tue, 10 Dec 2019 14:27:34: 1000000 INFO @ Tue, 10 Dec 2019 14:27:34: 5000000 INFO @ Tue, 10 Dec 2019 14:27:38: 9000000 INFO @ Tue, 10 Dec 2019 14:27:42: 2000000 INFO @ Tue, 10 Dec 2019 14:27:44: 6000000 INFO @ Tue, 10 Dec 2019 14:27:45: 10000000 INFO @ Tue, 10 Dec 2019 14:27:49: 3000000 INFO @ Tue, 10 Dec 2019 14:27:52: 7000000 INFO @ Tue, 10 Dec 2019 14:27:54: 11000000 INFO @ Tue, 10 Dec 2019 14:27:57: 4000000 INFO @ Tue, 10 Dec 2019 14:28:00: 8000000 INFO @ Tue, 10 Dec 2019 14:28:03: 12000000 INFO @ Tue, 10 Dec 2019 14:28:07: 5000000 INFO @ Tue, 10 Dec 2019 14:28:08: 9000000 INFO @ Tue, 10 Dec 2019 14:28:10: 13000000 INFO @ Tue, 10 Dec 2019 14:28:15: 6000000 INFO @ Tue, 10 Dec 2019 14:28:17: 10000000 INFO @ Tue, 10 Dec 2019 14:28:19: 14000000 INFO @ Tue, 10 Dec 2019 14:28:23: 7000000 INFO @ Tue, 10 Dec 2019 14:28:26: 11000000 INFO @ Tue, 10 Dec 2019 14:28:27: 15000000 INFO @ Tue, 10 Dec 2019 14:28:31: 8000000 INFO @ Tue, 10 Dec 2019 14:28:34: 12000000 INFO @ Tue, 10 Dec 2019 14:28:35: 16000000 INFO @ Tue, 10 Dec 2019 14:28:37: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:28:37: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:28:37: #1 total tags in treatment: 16225051 INFO @ Tue, 10 Dec 2019 14:28:37: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:28:37: #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 14:28:37: #1 tags after filtering in treatment: 16225051 INFO @ Tue, 10 Dec 2019 14:28:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:28:37: #1 finished! INFO @ Tue, 10 Dec 2019 14:28:37: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:28:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:28:38: 9000000 INFO @ Tue, 10 Dec 2019 14:28:38: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:28:38: 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 14:28:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.05_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/SRX6635440/SRX6635440.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:28:42: 13000000 INFO @ Tue, 10 Dec 2019 14:28:46: 10000000 INFO @ Tue, 10 Dec 2019 14:28:50: 14000000 INFO @ Tue, 10 Dec 2019 14:28:53: 11000000 INFO @ Tue, 10 Dec 2019 14:28:59: 15000000 INFO @ Tue, 10 Dec 2019 14:29:00: 12000000 INFO @ Tue, 10 Dec 2019 14:29:07: 16000000 INFO @ Tue, 10 Dec 2019 14:29:08: 13000000 INFO @ Tue, 10 Dec 2019 14:29:09: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:29:09: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:29:09: #1 total tags in treatment: 16225051 INFO @ Tue, 10 Dec 2019 14:29:09: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:29:09: #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 14:29:09: #1 tags after filtering in treatment: 16225051 INFO @ Tue, 10 Dec 2019 14:29:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:29:09: #1 finished! INFO @ Tue, 10 Dec 2019 14:29:09: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:29:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:29:11: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:29:11: 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 14:29:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.10_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/SRX6635440/SRX6635440.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:29:15: 14000000 INFO @ Tue, 10 Dec 2019 14:29:23: 15000000 INFO @ Tue, 10 Dec 2019 14:29:30: 16000000 INFO @ Tue, 10 Dec 2019 14:29:32: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:29:32: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:29:32: #1 total tags in treatment: 16225051 INFO @ Tue, 10 Dec 2019 14:29:32: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:29:32: #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 14:29:32: #1 tags after filtering in treatment: 16225051 INFO @ Tue, 10 Dec 2019 14:29:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:29:32: #1 finished! INFO @ Tue, 10 Dec 2019 14:29:32: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:29:32: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:29:34: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:29:34: 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 14:29:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.20_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/SRX6635440/SRX6635440.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635440/SRX6635440.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。