Job ID = 2640927 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 ) 2019-08-24T10:58:58 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 ) 2019-08-24T11:04:20 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 : 39,674,761 reads read : 39,674,761 reads written : 39,674,761 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: 00:06:55 39674761 reads; of these: 39674761 (100.00%) were unpaired; of these: 4356889 (10.98%) aligned 0 times 29950480 (75.49%) aligned exactly 1 time 5367392 (13.53%) aligned >1 times 89.02% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:56 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] 19645069 / 35317872 = 0.5562 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:32:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.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 20:32:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:32:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:32:44: 1000000 INFO @ Sat, 24 Aug 2019 20:32:54: 2000000 INFO @ Sat, 24 Aug 2019 20:33:03: 3000000 INFO @ Sat, 24 Aug 2019 20:33:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.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 20:33:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:33:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:33:12: 4000000 INFO @ Sat, 24 Aug 2019 20:33:14: 1000000 INFO @ Sat, 24 Aug 2019 20:33:22: 5000000 INFO @ Sat, 24 Aug 2019 20:33:24: 2000000 INFO @ Sat, 24 Aug 2019 20:33:31: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:33:33: 3000000 INFO @ Sat, 24 Aug 2019 20:33:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.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 20:33:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:33:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:33:41: 7000000 INFO @ Sat, 24 Aug 2019 20:33:44: 4000000 INFO @ Sat, 24 Aug 2019 20:33:45: 1000000 INFO @ Sat, 24 Aug 2019 20:33:50: 8000000 INFO @ Sat, 24 Aug 2019 20:33:54: 5000000 INFO @ Sat, 24 Aug 2019 20:33:56: 2000000 INFO @ Sat, 24 Aug 2019 20:33:59: 9000000 INFO @ Sat, 24 Aug 2019 20:34:05: 6000000 INFO @ Sat, 24 Aug 2019 20:34:06: 3000000 INFO @ Sat, 24 Aug 2019 20:34:08: 10000000 INFO @ Sat, 24 Aug 2019 20:34:15: 7000000 INFO @ Sat, 24 Aug 2019 20:34:16: 4000000 INFO @ Sat, 24 Aug 2019 20:34:18: 11000000 INFO @ Sat, 24 Aug 2019 20:34:26: 8000000 INFO @ Sat, 24 Aug 2019 20:34:27: 5000000 INFO @ Sat, 24 Aug 2019 20:34:27: 12000000 INFO @ Sat, 24 Aug 2019 20:34:36: 13000000 INFO @ Sat, 24 Aug 2019 20:34:36: 9000000 INFO @ Sat, 24 Aug 2019 20:34:37: 6000000 INFO @ Sat, 24 Aug 2019 20:34:45: 14000000 INFO @ Sat, 24 Aug 2019 20:34:47: 10000000 INFO @ Sat, 24 Aug 2019 20:34:48: 7000000 INFO @ Sat, 24 Aug 2019 20:34:55: 15000000 INFO @ Sat, 24 Aug 2019 20:34:57: 11000000 INFO @ Sat, 24 Aug 2019 20:34:58: 8000000 INFO @ Sat, 24 Aug 2019 20:35:01: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:35:01: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:35:01: #1 total tags in treatment: 15672803 INFO @ Sat, 24 Aug 2019 20:35:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:35:01: #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 20:35:01: #1 tags after filtering in treatment: 15672803 INFO @ Sat, 24 Aug 2019 20:35:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:35:01: #1 finished! INFO @ Sat, 24 Aug 2019 20:35:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:35:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:35:02: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:35:02: 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 20:35:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.05_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/SRX4703450/SRX4703450.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:35:07: 12000000 INFO @ Sat, 24 Aug 2019 20:35:08: 9000000 INFO @ Sat, 24 Aug 2019 20:35:17: 13000000 INFO @ Sat, 24 Aug 2019 20:35:18: 10000000 INFO @ Sat, 24 Aug 2019 20:35:27: 14000000 INFO @ Sat, 24 Aug 2019 20:35:28: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 20:35:37: 15000000 INFO @ Sat, 24 Aug 2019 20:35:38: 12000000 INFO @ Sat, 24 Aug 2019 20:35:44: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:35:44: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:35:44: #1 total tags in treatment: 15672803 INFO @ Sat, 24 Aug 2019 20:35:44: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:35:44: #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 20:35:44: #1 tags after filtering in treatment: 15672803 INFO @ Sat, 24 Aug 2019 20:35:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:35:44: #1 finished! INFO @ Sat, 24 Aug 2019 20:35:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:35:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:35:46: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:35:46: 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 20:35:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.10_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/SRX4703450/SRX4703450.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:35:47: 13000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 20:35:57: 14000000 INFO @ Sat, 24 Aug 2019 20:36:06: 15000000 INFO @ Sat, 24 Aug 2019 20:36:12: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:36:12: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:36:12: #1 total tags in treatment: 15672803 INFO @ Sat, 24 Aug 2019 20:36:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:36:12: #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 20:36:12: #1 tags after filtering in treatment: 15672803 INFO @ Sat, 24 Aug 2019 20:36:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:36:12: #1 finished! INFO @ Sat, 24 Aug 2019 20:36:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:36:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:36:13: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:36:13: 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 20:36:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.20_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/SRX4703450/SRX4703450.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703450/SRX4703450.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling