Job ID = 4289243 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:59:42 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 ) 2019-12-10T04:59:42 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 ) 2019-12-10T04:59:42 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 ) 2019-12-10T04:59:42 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 ) 2019-12-10T04:59:42 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 ) 2019-12-10T04:59:42 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 ) 2019-12-10T05:06:43 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 ) 2019-12-10T05:10:55 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 ) 2019-12-10T05:10:55 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 ) 2019-12-10T05:10:55 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 : 83,261,993 reads read : 166,523,986 reads written : 83,261,993 reads 0-length : 83,261,993 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: 00:14:15 83261993 reads; of these: 83261993 (100.00%) were unpaired; of these: 2769613 (3.33%) aligned 0 times 65587361 (78.77%) aligned exactly 1 time 14905019 (17.90%) aligned >1 times 96.67% overall alignment rate Time searching: 00:14:15 Overall time: 00:14:15 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] 61241754 / 80492380 = 0.7608 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.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 14:47:40: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:47:40: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:47:48: 1000000 INFO @ Tue, 10 Dec 2019 14:47:56: 2000000 INFO @ Tue, 10 Dec 2019 14:48:04: 3000000 INFO @ Tue, 10 Dec 2019 14:48:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.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 14:48:10: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:48:10: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:48:12: 4000000 INFO @ Tue, 10 Dec 2019 14:48:20: 1000000 INFO @ Tue, 10 Dec 2019 14:48:20: 5000000 INFO @ Tue, 10 Dec 2019 14:48:28: 6000000 INFO @ Tue, 10 Dec 2019 14:48:31: 2000000 INFO @ Tue, 10 Dec 2019 14:48:37: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:48:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.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 14:48:40: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:48:40: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:48:41: 3000000 INFO @ Tue, 10 Dec 2019 14:48:45: 8000000 INFO @ Tue, 10 Dec 2019 14:48:49: 1000000 INFO @ Tue, 10 Dec 2019 14:48:52: 4000000 INFO @ Tue, 10 Dec 2019 14:48:53: 9000000 INFO @ Tue, 10 Dec 2019 14:48:59: 2000000 INFO @ Tue, 10 Dec 2019 14:49:01: 10000000 INFO @ Tue, 10 Dec 2019 14:49:02: 5000000 INFO @ Tue, 10 Dec 2019 14:49:08: 3000000 INFO @ Tue, 10 Dec 2019 14:49:10: 11000000 INFO @ Tue, 10 Dec 2019 14:49:12: 6000000 INFO @ Tue, 10 Dec 2019 14:49:18: 4000000 INFO @ Tue, 10 Dec 2019 14:49:18: 12000000 INFO @ Tue, 10 Dec 2019 14:49:22: 7000000 INFO @ Tue, 10 Dec 2019 14:49:27: 13000000 INFO @ Tue, 10 Dec 2019 14:49:27: 5000000 INFO @ Tue, 10 Dec 2019 14:49:32: 8000000 INFO @ Tue, 10 Dec 2019 14:49:35: 14000000 INFO @ Tue, 10 Dec 2019 14:49:36: 6000000 INFO @ Tue, 10 Dec 2019 14:49:41: 9000000 INFO @ Tue, 10 Dec 2019 14:49:44: 15000000 INFO @ Tue, 10 Dec 2019 14:49:44: 7000000 INFO @ Tue, 10 Dec 2019 14:49:51: 10000000 INFO @ Tue, 10 Dec 2019 14:49:52: 16000000 INFO @ Tue, 10 Dec 2019 14:49:53: 8000000 INFO @ Tue, 10 Dec 2019 14:50:01: 17000000 INFO @ Tue, 10 Dec 2019 14:50:01: 11000000 INFO @ Tue, 10 Dec 2019 14:50:01: 9000000 INFO @ Tue, 10 Dec 2019 14:50:09: 18000000 INFO @ Tue, 10 Dec 2019 14:50:10: 10000000 INFO @ Tue, 10 Dec 2019 14:50:12: 12000000 INFO @ Tue, 10 Dec 2019 14:50:18: 19000000 INFO @ Tue, 10 Dec 2019 14:50:18: 11000000 INFO @ Tue, 10 Dec 2019 14:50:20: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:50:20: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:50:20: #1 total tags in treatment: 19250626 INFO @ Tue, 10 Dec 2019 14:50:20: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:50:20: #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 14:50:20: #1 tags after filtering in treatment: 19250626 INFO @ Tue, 10 Dec 2019 14:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:50:20: #1 finished! INFO @ Tue, 10 Dec 2019 14:50:20: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:50:21: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:50:21: 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 14:50:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.05_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/SRX6635427/SRX6635427.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:50:22: 13000000 INFO @ Tue, 10 Dec 2019 14:50:27: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:50:30: 14000000 INFO @ Tue, 10 Dec 2019 14:50:35: 13000000 INFO @ Tue, 10 Dec 2019 14:50:39: 15000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 14:50:44: 14000000 INFO @ Tue, 10 Dec 2019 14:50:46: 16000000 INFO @ Tue, 10 Dec 2019 14:50:52: 15000000 INFO @ Tue, 10 Dec 2019 14:50:54: 17000000 INFO @ Tue, 10 Dec 2019 14:51:00: 16000000 INFO @ Tue, 10 Dec 2019 14:51:01: 18000000 INFO @ Tue, 10 Dec 2019 14:51:08: 19000000 INFO @ Tue, 10 Dec 2019 14:51:09: 17000000 INFO @ Tue, 10 Dec 2019 14:51:10: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:51:10: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:51:10: #1 total tags in treatment: 19250626 INFO @ Tue, 10 Dec 2019 14:51:10: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:51:10: #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 14:51:10: #1 tags after filtering in treatment: 19250626 INFO @ Tue, 10 Dec 2019 14:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:51:10: #1 finished! INFO @ Tue, 10 Dec 2019 14:51:10: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:51:12: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:51:12: 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 14:51:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.10_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/SRX6635427/SRX6635427.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:51:17: 18000000 INFO @ Tue, 10 Dec 2019 14:51:25: 19000000 INFO @ Tue, 10 Dec 2019 14:51:27: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:51:27: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:51:27: #1 total tags in treatment: 19250626 INFO @ Tue, 10 Dec 2019 14:51:27: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:51:27: #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 14:51:28: #1 tags after filtering in treatment: 19250626 INFO @ Tue, 10 Dec 2019 14:51:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:51:28: #1 finished! INFO @ Tue, 10 Dec 2019 14:51:28: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:51:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:51:29: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:51:29: 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 14:51:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.20_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/SRX6635427/SRX6635427.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635427/SRX6635427.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling