Job ID = 4289217 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:58:02 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 ) 2019-12-10T04:58:02 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 ) 2019-12-10T04:58:02 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 ) 2019-12-10T04:58:02 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 ) 2019-12-10T04:59:27 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 ) 2019-12-10T04:59:42 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 ) 2019-12-10T05:02:54 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 : 88,126,399 reads read : 176,252,798 reads written : 88,126,399 reads 0-length : 88,126,399 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: 00:14:38 88126399 reads; of these: 88126399 (100.00%) were unpaired; of these: 3261112 (3.70%) aligned 0 times 63920934 (72.53%) aligned exactly 1 time 20944353 (23.77%) aligned >1 times 96.30% overall alignment rate Time searching: 00:14:38 Overall time: 00:14:38 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] 64177316 / 84865287 = 0.7562 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:42:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.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 14:42:36: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:42:36: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:42:43: 1000000 INFO @ Tue, 10 Dec 2019 14:42:49: 2000000 INFO @ Tue, 10 Dec 2019 14:42:56: 3000000 INFO @ Tue, 10 Dec 2019 14:43:02: 4000000 INFO @ Tue, 10 Dec 2019 14:43:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.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 14:43:05: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:43:05: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:43:09: 5000000 INFO @ Tue, 10 Dec 2019 14:43:13: 1000000 INFO @ Tue, 10 Dec 2019 14:43:16: 6000000 INFO @ Tue, 10 Dec 2019 14:43:20: 2000000 INFO @ Tue, 10 Dec 2019 14:43:23: 7000000 INFO @ Tue, 10 Dec 2019 14:43:27: 3000000 INFO @ Tue, 10 Dec 2019 14:43:30: 8000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:43:33: 4000000 INFO @ Tue, 10 Dec 2019 14:43:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.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 14:43:35: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:43:35: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:43:36: 9000000 INFO @ Tue, 10 Dec 2019 14:43:40: 5000000 INFO @ Tue, 10 Dec 2019 14:43:43: 10000000 INFO @ Tue, 10 Dec 2019 14:43:45: 1000000 INFO @ Tue, 10 Dec 2019 14:43:46: 6000000 INFO @ Tue, 10 Dec 2019 14:43:49: 11000000 INFO @ Tue, 10 Dec 2019 14:43:53: 7000000 INFO @ Tue, 10 Dec 2019 14:43:55: 2000000 INFO @ Tue, 10 Dec 2019 14:43:56: 12000000 INFO @ Tue, 10 Dec 2019 14:43:59: 8000000 INFO @ Tue, 10 Dec 2019 14:44:02: 13000000 INFO @ Tue, 10 Dec 2019 14:44:05: 3000000 INFO @ Tue, 10 Dec 2019 14:44:06: 9000000 INFO @ Tue, 10 Dec 2019 14:44:08: 14000000 INFO @ Tue, 10 Dec 2019 14:44:12: 10000000 INFO @ Tue, 10 Dec 2019 14:44:15: 15000000 INFO @ Tue, 10 Dec 2019 14:44:16: 4000000 INFO @ Tue, 10 Dec 2019 14:44:19: 11000000 INFO @ Tue, 10 Dec 2019 14:44:21: 16000000 INFO @ Tue, 10 Dec 2019 14:44:25: 12000000 INFO @ Tue, 10 Dec 2019 14:44:26: 5000000 INFO @ Tue, 10 Dec 2019 14:44:28: 17000000 INFO @ Tue, 10 Dec 2019 14:44:32: 13000000 INFO @ Tue, 10 Dec 2019 14:44:34: 18000000 INFO @ Tue, 10 Dec 2019 14:44:36: 6000000 INFO @ Tue, 10 Dec 2019 14:44:38: 14000000 INFO @ Tue, 10 Dec 2019 14:44:40: 19000000 INFO @ Tue, 10 Dec 2019 14:44:45: 15000000 INFO @ Tue, 10 Dec 2019 14:44:46: 7000000 INFO @ Tue, 10 Dec 2019 14:44:47: 20000000 INFO @ Tue, 10 Dec 2019 14:44:51: 16000000 INFO @ Tue, 10 Dec 2019 14:44:52: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:44:52: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:44:52: #1 total tags in treatment: 20687971 INFO @ Tue, 10 Dec 2019 14:44:52: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:44:52: #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 14:44:52: #1 tags after filtering in treatment: 20687971 INFO @ Tue, 10 Dec 2019 14:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:44:52: #1 finished! INFO @ Tue, 10 Dec 2019 14:44:52: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:44:54: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:44:54: 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 14:44:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:44:55: 8000000 INFO @ Tue, 10 Dec 2019 14:44:57: 17000000 INFO @ Tue, 10 Dec 2019 14:45:04: 18000000 INFO @ Tue, 10 Dec 2019 14:45:05: 9000000 INFO @ Tue, 10 Dec 2019 14:45:10: 19000000 INFO @ Tue, 10 Dec 2019 14:45:15: 10000000 INFO @ Tue, 10 Dec 2019 14:45:16: 20000000 INFO @ Tue, 10 Dec 2019 14:45:21: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:45:21: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:45:21: #1 total tags in treatment: 20687971 INFO @ Tue, 10 Dec 2019 14:45:21: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:45:21: #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 14:45:21: #1 tags after filtering in treatment: 20687971 INFO @ Tue, 10 Dec 2019 14:45:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:45:21: #1 finished! INFO @ Tue, 10 Dec 2019 14:45:21: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:45:23: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:45:23: 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 14:45:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.10_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/SRX6635422/SRX6635422.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:45:25: 11000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 14:45:35: 12000000 INFO @ Tue, 10 Dec 2019 14:45:45: 13000000 INFO @ Tue, 10 Dec 2019 14:45:53: 14000000 INFO @ Tue, 10 Dec 2019 14:46:01: 15000000 INFO @ Tue, 10 Dec 2019 14:46:10: 16000000 INFO @ Tue, 10 Dec 2019 14:46:18: 17000000 INFO @ Tue, 10 Dec 2019 14:46:26: 18000000 INFO @ Tue, 10 Dec 2019 14:46:34: 19000000 INFO @ Tue, 10 Dec 2019 14:46:42: 20000000 INFO @ Tue, 10 Dec 2019 14:46:47: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:46:47: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:46:47: #1 total tags in treatment: 20687971 INFO @ Tue, 10 Dec 2019 14:46:47: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:46:47: #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 14:46:48: #1 tags after filtering in treatment: 20687971 INFO @ Tue, 10 Dec 2019 14:46:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:46:48: #1 finished! INFO @ Tue, 10 Dec 2019 14:46:48: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:46:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:46:49: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:46:49: 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 14:46:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.20_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/SRX6635422/SRX6635422.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635422/SRX6635422.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling