Job ID = 4289219 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 ) spots read : 74,109,595 reads read : 148,219,190 reads written : 74,109,595 reads 0-length : 74,109,595 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: 00:13:09 74109595 reads; of these: 74109595 (100.00%) were unpaired; of these: 5397885 (7.28%) aligned 0 times 56706924 (76.52%) aligned exactly 1 time 12004786 (16.20%) aligned >1 times 92.72% overall alignment rate Time searching: 00:13:09 Overall time: 00:13:09 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 28 files... [bam_rmdupse_core] 48527636 / 68711710 = 0.7062 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:39:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.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 14:39:29: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:39:29: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:39:37: 1000000 INFO @ Tue, 10 Dec 2019 14:39:46: 2000000 INFO @ Tue, 10 Dec 2019 14:39:54: 3000000 INFO @ Tue, 10 Dec 2019 14:39:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.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 14:39:59: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:39:59: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:40:02: 4000000 INFO @ Tue, 10 Dec 2019 14:40:08: 1000000 INFO @ Tue, 10 Dec 2019 14:40:09: 5000000 INFO @ Tue, 10 Dec 2019 14:40:16: 6000000 INFO @ Tue, 10 Dec 2019 14:40:17: 2000000 INFO @ Tue, 10 Dec 2019 14:40:23: 7000000 INFO @ Tue, 10 Dec 2019 14:40:25: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.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 14:40:29: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:40:29: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:40:30: 8000000 INFO @ Tue, 10 Dec 2019 14:40:33: 4000000 INFO @ Tue, 10 Dec 2019 14:40:38: 1000000 INFO @ Tue, 10 Dec 2019 14:40:38: 9000000 INFO @ Tue, 10 Dec 2019 14:40:42: 5000000 INFO @ Tue, 10 Dec 2019 14:40:46: 2000000 INFO @ Tue, 10 Dec 2019 14:40:47: 10000000 INFO @ Tue, 10 Dec 2019 14:40:51: 6000000 INFO @ Tue, 10 Dec 2019 14:40:54: 3000000 INFO @ Tue, 10 Dec 2019 14:40:55: 11000000 INFO @ Tue, 10 Dec 2019 14:41:00: 7000000 INFO @ Tue, 10 Dec 2019 14:41:02: 12000000 INFO @ Tue, 10 Dec 2019 14:41:02: 4000000 INFO @ Tue, 10 Dec 2019 14:41:08: 8000000 INFO @ Tue, 10 Dec 2019 14:41:10: 13000000 INFO @ Tue, 10 Dec 2019 14:41:10: 5000000 INFO @ Tue, 10 Dec 2019 14:41:17: 14000000 INFO @ Tue, 10 Dec 2019 14:41:17: 9000000 INFO @ Tue, 10 Dec 2019 14:41:18: 6000000 INFO @ Tue, 10 Dec 2019 14:41:25: 15000000 INFO @ Tue, 10 Dec 2019 14:41:26: 10000000 INFO @ Tue, 10 Dec 2019 14:41:26: 7000000 INFO @ Tue, 10 Dec 2019 14:41:32: 16000000 INFO @ Tue, 10 Dec 2019 14:41:35: 8000000 INFO @ Tue, 10 Dec 2019 14:41:35: 11000000 INFO @ Tue, 10 Dec 2019 14:41:39: 17000000 INFO @ Tue, 10 Dec 2019 14:41:42: 9000000 INFO @ Tue, 10 Dec 2019 14:41:44: 12000000 INFO @ Tue, 10 Dec 2019 14:41:46: 18000000 INFO @ Tue, 10 Dec 2019 14:41:51: 10000000 INFO @ Tue, 10 Dec 2019 14:41:52: 13000000 INFO @ Tue, 10 Dec 2019 14:41:54: 19000000 INFO @ Tue, 10 Dec 2019 14:41:59: 11000000 INFO @ Tue, 10 Dec 2019 14:42:01: 20000000 INFO @ Tue, 10 Dec 2019 14:42:01: 14000000 INFO @ Tue, 10 Dec 2019 14:42:03: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:42:03: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:42:03: #1 total tags in treatment: 20184074 INFO @ Tue, 10 Dec 2019 14:42:03: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:42:03: #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 14:42:03: #1 tags after filtering in treatment: 20184074 INFO @ Tue, 10 Dec 2019 14:42:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:42:03: #1 finished! INFO @ Tue, 10 Dec 2019 14:42:03: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:42:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:42:05: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:42:05: 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 14:42:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.05_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/SRX6635424/SRX6635424.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:42:07: 12000000 INFO @ Tue, 10 Dec 2019 14:42:10: 15000000 INFO @ Tue, 10 Dec 2019 14:42:15: 13000000 INFO @ Tue, 10 Dec 2019 14:42:19: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:42:23: 14000000 INFO @ Tue, 10 Dec 2019 14:42:29: 17000000 INFO @ Tue, 10 Dec 2019 14:42:31: 15000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 14:42:38: 18000000 INFO @ Tue, 10 Dec 2019 14:42:39: 16000000 INFO @ Tue, 10 Dec 2019 14:42:47: 19000000 INFO @ Tue, 10 Dec 2019 14:42:48: 17000000 INFO @ Tue, 10 Dec 2019 14:42:56: 20000000 INFO @ Tue, 10 Dec 2019 14:42:57: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:42:57: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:42:57: #1 total tags in treatment: 20184074 INFO @ Tue, 10 Dec 2019 14:42:57: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:42:57: #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 14:42:57: 18000000 INFO @ Tue, 10 Dec 2019 14:42:58: #1 tags after filtering in treatment: 20184074 INFO @ Tue, 10 Dec 2019 14:42:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:42:58: #1 finished! INFO @ Tue, 10 Dec 2019 14:42:58: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:42:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:42:59: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:42:59: 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 14:42:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.10_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/SRX6635424/SRX6635424.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:43:06: 19000000 INFO @ Tue, 10 Dec 2019 14:43:15: 20000000 INFO @ Tue, 10 Dec 2019 14:43:17: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:43:17: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:43:17: #1 total tags in treatment: 20184074 INFO @ Tue, 10 Dec 2019 14:43:17: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:43:17: #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 14:43:18: #1 tags after filtering in treatment: 20184074 INFO @ Tue, 10 Dec 2019 14:43:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:43:18: #1 finished! INFO @ Tue, 10 Dec 2019 14:43:18: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:43:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:43:19: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:43:19: 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 14:43:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.20_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/SRX6635424/SRX6635424.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635424/SRX6635424.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling