Job ID = 4289159 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,376,526 reads read : 60,753,052 reads written : 30,376,526 reads 0-length : 30,376,526 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 ) 2019-12-10T04:59:27 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 ) spots read : 29,015,746 reads read : 58,031,492 reads written : 29,015,746 reads 0-length : 29,015,746 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: 00:09:12 59392272 reads; of these: 59392272 (100.00%) were unpaired; of these: 21802887 (36.71%) aligned 0 times 27060618 (45.56%) aligned exactly 1 time 10528767 (17.73%) aligned >1 times 63.29% overall alignment rate Time searching: 00:09:12 Overall time: 00:09:12 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] 22366750 / 37589385 = 0.5950 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:19:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.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 14:19:28: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:19:28: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:19:35: 1000000 INFO @ Tue, 10 Dec 2019 14:19:43: 2000000 INFO @ Tue, 10 Dec 2019 14:19:51: 3000000 INFO @ Tue, 10 Dec 2019 14:19:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.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 14:19:58: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:19:58: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:19:59: 4000000 INFO @ Tue, 10 Dec 2019 14:20:07: 5000000 INFO @ Tue, 10 Dec 2019 14:20:09: 1000000 INFO @ Tue, 10 Dec 2019 14:20:16: 6000000 INFO @ Tue, 10 Dec 2019 14:20:19: 2000000 INFO @ Tue, 10 Dec 2019 14:20:24: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.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 14:20:28: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:20:28: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:20:30: 3000000 INFO @ Tue, 10 Dec 2019 14:20:34: 8000000 INFO @ Tue, 10 Dec 2019 14:20:37: 1000000 INFO @ Tue, 10 Dec 2019 14:20:40: 4000000 INFO @ Tue, 10 Dec 2019 14:20:43: 9000000 INFO @ Tue, 10 Dec 2019 14:20:46: 2000000 INFO @ Tue, 10 Dec 2019 14:20:51: 5000000 INFO @ Tue, 10 Dec 2019 14:20:52: 10000000 INFO @ Tue, 10 Dec 2019 14:20:55: 3000000 INFO @ Tue, 10 Dec 2019 14:21:02: 6000000 INFO @ Tue, 10 Dec 2019 14:21:02: 11000000 INFO @ Tue, 10 Dec 2019 14:21:04: 4000000 INFO @ Tue, 10 Dec 2019 14:21:11: 12000000 INFO @ Tue, 10 Dec 2019 14:21:12: 7000000 INFO @ Tue, 10 Dec 2019 14:21:13: 5000000 INFO @ Tue, 10 Dec 2019 14:21:20: 13000000 INFO @ Tue, 10 Dec 2019 14:21:22: 6000000 INFO @ Tue, 10 Dec 2019 14:21:23: 8000000 INFO @ Tue, 10 Dec 2019 14:21:29: 14000000 INFO @ Tue, 10 Dec 2019 14:21:32: 7000000 INFO @ Tue, 10 Dec 2019 14:21:34: 9000000 INFO @ Tue, 10 Dec 2019 14:21:38: 15000000 INFO @ Tue, 10 Dec 2019 14:21:40: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 14:21:40: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 14:21:40: #1 total tags in treatment: 15222635 INFO @ Tue, 10 Dec 2019 14:21:40: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:21:40: #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 14:21:41: #1 tags after filtering in treatment: 15222635 INFO @ Tue, 10 Dec 2019 14:21:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:21:41: #1 finished! INFO @ Tue, 10 Dec 2019 14:21:41: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:21:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:21:41: 8000000 INFO @ Tue, 10 Dec 2019 14:21:42: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:21:42: 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 14:21:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.05_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/SRX6616773/SRX6616773.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:21:45: 10000000 INFO @ Tue, 10 Dec 2019 14:21:50: 9000000 INFO @ Tue, 10 Dec 2019 14:21:55: 11000000 INFO @ Tue, 10 Dec 2019 14:21:59: 10000000 INFO @ Tue, 10 Dec 2019 14:22:06: 12000000 INFO @ Tue, 10 Dec 2019 14:22:08: 11000000 INFO @ Tue, 10 Dec 2019 14:22:16: 13000000 INFO @ Tue, 10 Dec 2019 14:22:17: 12000000 INFO @ Tue, 10 Dec 2019 14:22:26: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:22:27: 14000000 INFO @ Tue, 10 Dec 2019 14:22:35: 14000000 INFO @ Tue, 10 Dec 2019 14:22:37: 15000000 INFO @ Tue, 10 Dec 2019 14:22:39: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 14:22:39: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 14:22:39: #1 total tags in treatment: 15222635 INFO @ Tue, 10 Dec 2019 14:22:39: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:22:39: #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 14:22:39: #1 tags after filtering in treatment: 15222635 INFO @ Tue, 10 Dec 2019 14:22:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:22:39: #1 finished! INFO @ Tue, 10 Dec 2019 14:22:39: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:22:39: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 14:22:41: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:22:41: 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 14:22:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.10_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/SRX6616773/SRX6616773.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:22:43: 15000000 INFO @ Tue, 10 Dec 2019 14:22:45: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 14:22:45: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 14:22:45: #1 total tags in treatment: 15222635 INFO @ Tue, 10 Dec 2019 14:22:45: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:22:45: #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 14:22:46: #1 tags after filtering in treatment: 15222635 INFO @ Tue, 10 Dec 2019 14:22:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:22:46: #1 finished! INFO @ Tue, 10 Dec 2019 14:22:46: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:22:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:22:47: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:22:47: 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 14:22:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.20_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/SRX6616773/SRX6616773.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6616773/SRX6616773.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling