Job ID = 4289218 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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 ) 2019-12-10T05:12:44 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 ) 2019-12-10T05:15:28 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 : 88,067,954 reads read : 176,135,908 reads written : 88,067,954 reads 0-length : 88,067,954 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: 00:16:06 88067954 reads; of these: 88067954 (100.00%) were unpaired; of these: 3538399 (4.02%) aligned 0 times 69886016 (79.35%) aligned exactly 1 time 14643539 (16.63%) aligned >1 times 95.98% overall alignment rate Time searching: 00:16:06 Overall time: 00:16:06 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] 63172558 / 84529555 = 0.7473 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:46:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.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 14:46:47: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:46:47: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:46:54: 1000000 INFO @ Tue, 10 Dec 2019 14:47:02: 2000000 INFO @ Tue, 10 Dec 2019 14:47:10: 3000000 INFO @ Tue, 10 Dec 2019 14:47:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.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 14:47:16: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:47:16: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:47:17: 4000000 INFO @ Tue, 10 Dec 2019 14:47:25: 5000000 INFO @ Tue, 10 Dec 2019 14:47:25: 1000000 INFO @ Tue, 10 Dec 2019 14:47:33: 6000000 INFO @ Tue, 10 Dec 2019 14:47:34: 2000000 INFO @ Tue, 10 Dec 2019 14:47:40: 7000000 INFO @ Tue, 10 Dec 2019 14:47:43: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.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 14:47:46: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:47:46: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:47:48: 8000000 INFO @ Tue, 10 Dec 2019 14:47:53: 4000000 INFO @ Tue, 10 Dec 2019 14:47:54: 1000000 INFO @ Tue, 10 Dec 2019 14:47:56: 9000000 INFO @ Tue, 10 Dec 2019 14:48:02: 5000000 INFO @ Tue, 10 Dec 2019 14:48:02: 2000000 INFO @ Tue, 10 Dec 2019 14:48:03: 10000000 INFO @ Tue, 10 Dec 2019 14:48:10: 3000000 INFO @ Tue, 10 Dec 2019 14:48:11: 6000000 INFO @ Tue, 10 Dec 2019 14:48:11: 11000000 INFO @ Tue, 10 Dec 2019 14:48:18: 4000000 INFO @ Tue, 10 Dec 2019 14:48:19: 12000000 INFO @ Tue, 10 Dec 2019 14:48:19: 7000000 INFO @ Tue, 10 Dec 2019 14:48:26: 5000000 INFO @ Tue, 10 Dec 2019 14:48:27: 13000000 INFO @ Tue, 10 Dec 2019 14:48:28: 8000000 INFO @ Tue, 10 Dec 2019 14:48:34: 6000000 INFO @ Tue, 10 Dec 2019 14:48:35: 14000000 INFO @ Tue, 10 Dec 2019 14:48:37: 9000000 INFO @ Tue, 10 Dec 2019 14:48:41: 7000000 INFO @ Tue, 10 Dec 2019 14:48:42: 15000000 INFO @ Tue, 10 Dec 2019 14:48:46: 10000000 INFO @ Tue, 10 Dec 2019 14:48:49: 8000000 INFO @ Tue, 10 Dec 2019 14:48:50: 16000000 INFO @ Tue, 10 Dec 2019 14:48:55: 11000000 INFO @ Tue, 10 Dec 2019 14:48:57: 9000000 INFO @ Tue, 10 Dec 2019 14:48:58: 17000000 INFO @ Tue, 10 Dec 2019 14:49:04: 12000000 INFO @ Tue, 10 Dec 2019 14:49:05: 10000000 INFO @ Tue, 10 Dec 2019 14:49:06: 18000000 INFO @ Tue, 10 Dec 2019 14:49:13: 13000000 INFO @ Tue, 10 Dec 2019 14:49:13: 11000000 INFO @ Tue, 10 Dec 2019 14:49:14: 19000000 INFO @ Tue, 10 Dec 2019 14:49:21: 12000000 INFO @ Tue, 10 Dec 2019 14:49:22: 14000000 INFO @ Tue, 10 Dec 2019 14:49:22: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:49:29: 13000000 INFO @ Tue, 10 Dec 2019 14:49:30: 21000000 INFO @ Tue, 10 Dec 2019 14:49:30: 15000000 INFO @ Tue, 10 Dec 2019 14:49:32: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:49:32: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:49:32: #1 total tags in treatment: 21356997 INFO @ Tue, 10 Dec 2019 14:49:32: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:49:32: #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 14:49:33: #1 tags after filtering in treatment: 21356997 INFO @ Tue, 10 Dec 2019 14:49:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:49:33: #1 finished! INFO @ Tue, 10 Dec 2019 14:49:33: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:49:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:49:34: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:49:34: 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 14:49:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.05_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/SRX6635423/SRX6635423.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:49:36: 14000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 14:49:39: 16000000 INFO @ Tue, 10 Dec 2019 14:49:44: 15000000 INFO @ Tue, 10 Dec 2019 14:49:48: 17000000 INFO @ Tue, 10 Dec 2019 14:49:52: 16000000 INFO @ Tue, 10 Dec 2019 14:49:57: 18000000 INFO @ Tue, 10 Dec 2019 14:49:59: 17000000 INFO @ Tue, 10 Dec 2019 14:50:06: 19000000 INFO @ Tue, 10 Dec 2019 14:50:07: 18000000 INFO @ Tue, 10 Dec 2019 14:50:14: 20000000 INFO @ Tue, 10 Dec 2019 14:50:15: 19000000 INFO @ Tue, 10 Dec 2019 14:50:22: 20000000 INFO @ Tue, 10 Dec 2019 14:50:23: 21000000 INFO @ Tue, 10 Dec 2019 14:50:26: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:50:26: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:50:26: #1 total tags in treatment: 21356997 INFO @ Tue, 10 Dec 2019 14:50:26: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:50:26: #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 14:50:27: #1 tags after filtering in treatment: 21356997 INFO @ Tue, 10 Dec 2019 14:50:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:50:27: #1 finished! INFO @ Tue, 10 Dec 2019 14:50:27: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:50:28: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:50:28: 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 14:50:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.10_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/SRX6635423/SRX6635423.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:50:30: 21000000 INFO @ Tue, 10 Dec 2019 14:50:32: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:50:32: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:50:32: #1 total tags in treatment: 21356997 INFO @ Tue, 10 Dec 2019 14:50:32: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:50:32: #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 14:50:33: #1 tags after filtering in treatment: 21356997 INFO @ Tue, 10 Dec 2019 14:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:50:33: #1 finished! INFO @ Tue, 10 Dec 2019 14:50:33: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:50:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:50:34: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:50:34: 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 14:50:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.20_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/SRX6635423/SRX6635423.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635423/SRX6635423.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling