Job ID = 4289245 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:59:42 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 ) 2019-12-10T05:10:55 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 ) 2019-12-10T05:24:20 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 : 106,724,299 reads read : 213,448,598 reads written : 106,724,299 reads 0-length : 106,724,299 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: 00:19:16 106724299 reads; of these: 106724299 (100.00%) were unpaired; of these: 4367765 (4.09%) aligned 0 times 82434918 (77.24%) aligned exactly 1 time 19921616 (18.67%) aligned >1 times 95.91% overall alignment rate Time searching: 00:19:16 Overall time: 00:19:16 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 44 files... [bam_rmdupse_core] 82024244 / 102356534 = 0.8014 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 15:03:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.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 15:03:34: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:03:34: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:03:43: 1000000 INFO @ Tue, 10 Dec 2019 15:03:53: 2000000 INFO @ Tue, 10 Dec 2019 15:04:02: 3000000 INFO @ Tue, 10 Dec 2019 15:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.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 15:04:04: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:04:04: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:04:12: 4000000 INFO @ Tue, 10 Dec 2019 15:04:14: 1000000 INFO @ Tue, 10 Dec 2019 15:04:22: 5000000 INFO @ Tue, 10 Dec 2019 15:04:23: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 15:04:32: 6000000 INFO @ Tue, 10 Dec 2019 15:04:33: 3000000 INFO @ Tue, 10 Dec 2019 15:04:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.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 15:04:34: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:04:34: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:04:42: 7000000 INFO @ Tue, 10 Dec 2019 15:04:43: 4000000 INFO @ Tue, 10 Dec 2019 15:04:43: 1000000 INFO @ Tue, 10 Dec 2019 15:04:52: 2000000 INFO @ Tue, 10 Dec 2019 15:04:52: 5000000 INFO @ Tue, 10 Dec 2019 15:04:53: 8000000 INFO @ Tue, 10 Dec 2019 15:05:01: 3000000 INFO @ Tue, 10 Dec 2019 15:05:02: 6000000 INFO @ Tue, 10 Dec 2019 15:05:03: 9000000 INFO @ Tue, 10 Dec 2019 15:05:10: 4000000 INFO @ Tue, 10 Dec 2019 15:05:11: 7000000 INFO @ Tue, 10 Dec 2019 15:05:13: 10000000 INFO @ Tue, 10 Dec 2019 15:05:19: 5000000 INFO @ Tue, 10 Dec 2019 15:05:20: 8000000 INFO @ Tue, 10 Dec 2019 15:05:23: 11000000 INFO @ Tue, 10 Dec 2019 15:05:28: 6000000 INFO @ Tue, 10 Dec 2019 15:05:30: 9000000 INFO @ Tue, 10 Dec 2019 15:05:34: 12000000 INFO @ Tue, 10 Dec 2019 15:05:37: 7000000 INFO @ Tue, 10 Dec 2019 15:05:39: 10000000 INFO @ Tue, 10 Dec 2019 15:05:44: 13000000 INFO @ Tue, 10 Dec 2019 15:05:46: 8000000 INFO @ Tue, 10 Dec 2019 15:05:48: 11000000 INFO @ Tue, 10 Dec 2019 15:05:54: 14000000 INFO @ Tue, 10 Dec 2019 15:05:55: 9000000 INFO @ Tue, 10 Dec 2019 15:05:57: 12000000 INFO @ Tue, 10 Dec 2019 15:06:04: 10000000 INFO @ Tue, 10 Dec 2019 15:06:04: 15000000 INFO @ Tue, 10 Dec 2019 15:06:07: 13000000 INFO @ Tue, 10 Dec 2019 15:06:13: 11000000 INFO @ Tue, 10 Dec 2019 15:06:14: 16000000 INFO @ Tue, 10 Dec 2019 15:06:16: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 15:06:22: 12000000 INFO @ Tue, 10 Dec 2019 15:06:23: 17000000 INFO @ Tue, 10 Dec 2019 15:06:25: 15000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 15:06:31: 13000000 INFO @ Tue, 10 Dec 2019 15:06:32: 18000000 INFO @ Tue, 10 Dec 2019 15:06:35: 16000000 INFO @ Tue, 10 Dec 2019 15:06:41: 14000000 INFO @ Tue, 10 Dec 2019 15:06:42: 19000000 INFO @ Tue, 10 Dec 2019 15:06:44: 17000000 INFO @ Tue, 10 Dec 2019 15:06:50: 15000000 INFO @ Tue, 10 Dec 2019 15:06:51: 20000000 INFO @ Tue, 10 Dec 2019 15:06:53: 18000000 INFO @ Tue, 10 Dec 2019 15:06:54: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 15:06:54: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 15:06:54: #1 total tags in treatment: 20332290 INFO @ Tue, 10 Dec 2019 15:06:54: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:06:54: #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 15:06:55: #1 tags after filtering in treatment: 20332290 INFO @ Tue, 10 Dec 2019 15:06:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 15:06:55: #1 finished! INFO @ Tue, 10 Dec 2019 15:06:55: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:06:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:06:56: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:06:56: 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 15:06:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.05_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/SRX6635428/SRX6635428.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:06:59: 16000000 INFO @ Tue, 10 Dec 2019 15:07:03: 19000000 INFO @ Tue, 10 Dec 2019 15:07:08: 17000000 INFO @ Tue, 10 Dec 2019 15:07:12: 20000000 INFO @ Tue, 10 Dec 2019 15:07:15: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 15:07:15: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 15:07:15: #1 total tags in treatment: 20332290 INFO @ Tue, 10 Dec 2019 15:07:15: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:07:15: #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 15:07:15: #1 tags after filtering in treatment: 20332290 INFO @ Tue, 10 Dec 2019 15:07:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 15:07:15: #1 finished! INFO @ Tue, 10 Dec 2019 15:07:15: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:07:17: 18000000 INFO @ Tue, 10 Dec 2019 15:07:17: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:07:17: 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 15:07:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.10_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/SRX6635428/SRX6635428.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:07:26: 19000000 INFO @ Tue, 10 Dec 2019 15:07:34: 20000000 INFO @ Tue, 10 Dec 2019 15:07:37: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 15:07:37: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 15:07:37: #1 total tags in treatment: 20332290 INFO @ Tue, 10 Dec 2019 15:07:37: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:07:37: #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 15:07:38: #1 tags after filtering in treatment: 20332290 INFO @ Tue, 10 Dec 2019 15:07:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 15:07:38: #1 finished! INFO @ Tue, 10 Dec 2019 15:07:38: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:07:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:07:39: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:07:39: 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 15:07:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.20_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/SRX6635428/SRX6635428.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635428/SRX6635428.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling