Job ID = 2640930 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T10:58:58 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 ) 2019-08-24T11:09:01 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 : 35,509,414 reads read : 35,509,414 reads written : 35,509,414 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: 00:10:48 35509414 reads; of these: 35509414 (100.00%) were unpaired; of these: 1047821 (2.95%) aligned 0 times 31503845 (88.72%) aligned exactly 1 time 2957748 (8.33%) aligned >1 times 97.05% overall alignment rate Time searching: 00:10:48 Overall time: 00:10:48 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] 21218033 / 34461593 = 0.6157 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.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 @ Sat, 24 Aug 2019 20:48:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:48:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:48:54: 1000000 INFO @ Sat, 24 Aug 2019 20:49:02: 2000000 INFO @ Sat, 24 Aug 2019 20:49:10: 3000000 INFO @ Sat, 24 Aug 2019 20:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.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 @ Sat, 24 Aug 2019 20:49:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:49:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:49:18: 4000000 INFO @ Sat, 24 Aug 2019 20:49:24: 1000000 INFO @ Sat, 24 Aug 2019 20:49:27: 5000000 INFO @ Sat, 24 Aug 2019 20:49:33: 2000000 INFO @ Sat, 24 Aug 2019 20:49:36: 6000000 INFO @ Sat, 24 Aug 2019 20:49:42: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.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 @ Sat, 24 Aug 2019 20:49:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:49:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:49:46: 7000000 INFO @ Sat, 24 Aug 2019 20:49:51: 4000000 INFO @ Sat, 24 Aug 2019 20:49:55: 8000000 INFO @ Sat, 24 Aug 2019 20:49:56: 1000000 INFO @ Sat, 24 Aug 2019 20:50:01: 5000000 INFO @ Sat, 24 Aug 2019 20:50:05: 9000000 INFO @ Sat, 24 Aug 2019 20:50:07: 2000000 INFO @ Sat, 24 Aug 2019 20:50:11: 6000000 INFO @ Sat, 24 Aug 2019 20:50:14: 10000000 INFO @ Sat, 24 Aug 2019 20:50:17: 3000000 INFO @ Sat, 24 Aug 2019 20:50:21: 7000000 INFO @ Sat, 24 Aug 2019 20:50:24: 11000000 INFO @ Sat, 24 Aug 2019 20:50:27: 4000000 INFO @ Sat, 24 Aug 2019 20:50:31: 8000000 INFO @ Sat, 24 Aug 2019 20:50:34: 12000000 INFO @ Sat, 24 Aug 2019 20:50:36: 5000000 INFO @ Sat, 24 Aug 2019 20:50:41: 9000000 INFO @ Sat, 24 Aug 2019 20:50:44: 13000000 INFO @ Sat, 24 Aug 2019 20:50:46: 6000000 INFO @ Sat, 24 Aug 2019 20:50:47: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:50:47: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:50:47: #1 total tags in treatment: 13243560 INFO @ Sat, 24 Aug 2019 20:50:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:50:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:50:47: #1 tags after filtering in treatment: 13243560 INFO @ Sat, 24 Aug 2019 20:50:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:50:47: #1 finished! INFO @ Sat, 24 Aug 2019 20:50:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:50:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:50:48: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:50:48: 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 @ Sat, 24 Aug 2019 20:50:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:50:51: 10000000 INFO @ Sat, 24 Aug 2019 20:50:56: 7000000 INFO @ Sat, 24 Aug 2019 20:51:00: 11000000 INFO @ Sat, 24 Aug 2019 20:51:06: 8000000 INFO @ Sat, 24 Aug 2019 20:51:10: 12000000 INFO @ Sat, 24 Aug 2019 20:51:16: 9000000 INFO @ Sat, 24 Aug 2019 20:51:19: 13000000 INFO @ Sat, 24 Aug 2019 20:51:21: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:51:21: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:51:21: #1 total tags in treatment: 13243560 INFO @ Sat, 24 Aug 2019 20:51:21: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:51:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:51:21: #1 tags after filtering in treatment: 13243560 INFO @ Sat, 24 Aug 2019 20:51:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:51:21: #1 finished! INFO @ Sat, 24 Aug 2019 20:51:21: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:51:22: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:51:22: 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 @ Sat, 24 Aug 2019 20:51:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.10_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/SRX4703452/SRX4703452.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:51:26: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 20:51:35: 11000000 INFO @ Sat, 24 Aug 2019 20:51:45: 12000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 20:51:55: 13000000 INFO @ Sat, 24 Aug 2019 20:51:58: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:51:58: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:51:58: #1 total tags in treatment: 13243560 INFO @ Sat, 24 Aug 2019 20:51:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:51:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:51:59: #1 tags after filtering in treatment: 13243560 INFO @ Sat, 24 Aug 2019 20:51:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:51:59: #1 finished! INFO @ Sat, 24 Aug 2019 20:51:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:51:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:52:00: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:52:00: 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 @ Sat, 24 Aug 2019 20:52:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.20_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/SRX4703452/SRX4703452.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703452/SRX4703452.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling