Job ID = 4289318 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:07:55 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 ) 2019-12-10T05:07:55 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 : 25,436,749 reads read : 25,436,749 reads written : 25,436,749 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: 00:04:42 25436749 reads; of these: 25436749 (100.00%) were unpaired; of these: 1205846 (4.74%) aligned 0 times 21944752 (86.27%) aligned exactly 1 time 2286151 (8.99%) aligned >1 times 95.26% overall alignment rate Time searching: 00:04:42 Overall time: 00:04:42 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 12 files... [bam_rmdupse_core] 12436958 / 24230903 = 0.5133 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:22:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.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 14:22:38: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:22:38: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:22:51: 1000000 INFO @ Tue, 10 Dec 2019 14:23:03: 2000000 INFO @ Tue, 10 Dec 2019 14:23:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.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 14:23:08: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:23:08: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:23:14: 3000000 INFO @ Tue, 10 Dec 2019 14:23:18: 1000000 INFO @ Tue, 10 Dec 2019 14:23:26: 4000000 INFO @ Tue, 10 Dec 2019 14:23:29: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:23:37: 5000000 INFO @ Tue, 10 Dec 2019 14:23:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.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 14:23:38: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:23:38: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:23:39: 3000000 INFO @ Tue, 10 Dec 2019 14:23:48: 1000000 INFO @ Tue, 10 Dec 2019 14:23:48: 4000000 INFO @ Tue, 10 Dec 2019 14:23:49: 6000000 INFO @ Tue, 10 Dec 2019 14:23:58: 2000000 INFO @ Tue, 10 Dec 2019 14:23:58: 5000000 INFO @ Tue, 10 Dec 2019 14:24:00: 7000000 INFO @ Tue, 10 Dec 2019 14:24:08: 6000000 INFO @ Tue, 10 Dec 2019 14:24:09: 3000000 INFO @ Tue, 10 Dec 2019 14:24:12: 8000000 INFO @ Tue, 10 Dec 2019 14:24:19: 7000000 INFO @ Tue, 10 Dec 2019 14:24:20: 4000000 INFO @ Tue, 10 Dec 2019 14:24:24: 9000000 INFO @ Tue, 10 Dec 2019 14:24:29: 8000000 INFO @ Tue, 10 Dec 2019 14:24:33: 5000000 INFO @ Tue, 10 Dec 2019 14:24:35: 10000000 INFO @ Tue, 10 Dec 2019 14:24:41: 9000000 INFO @ Tue, 10 Dec 2019 14:24:44: 6000000 INFO @ Tue, 10 Dec 2019 14:24:45: 11000000 INFO @ Tue, 10 Dec 2019 14:24:53: 10000000 INFO @ Tue, 10 Dec 2019 14:24:53: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:24:53: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:24:53: #1 total tags in treatment: 11793945 INFO @ Tue, 10 Dec 2019 14:24:53: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:24:53: #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 14:24:53: #1 tags after filtering in treatment: 11793945 INFO @ Tue, 10 Dec 2019 14:24:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:24:53: #1 finished! INFO @ Tue, 10 Dec 2019 14:24:53: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:24:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:24:54: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:24:54: 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 14:24:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.05_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/SRX6678236/SRX6678236.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:24:55: 7000000 INFO @ Tue, 10 Dec 2019 14:25:04: 11000000 INFO @ Tue, 10 Dec 2019 14:25:05: 8000000 INFO @ Tue, 10 Dec 2019 14:25:11: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:25:11: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:25:11: #1 total tags in treatment: 11793945 INFO @ Tue, 10 Dec 2019 14:25:11: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:25:11: #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 14:25:12: #1 tags after filtering in treatment: 11793945 INFO @ Tue, 10 Dec 2019 14:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:25:12: #1 finished! INFO @ Tue, 10 Dec 2019 14:25:12: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:25:13: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:25:13: 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 @ Tue, 10 Dec 2019 14:25:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.10_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/SRX6678236/SRX6678236.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:25:15: 9000000 INFO @ Tue, 10 Dec 2019 14:25:25: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:25:36: 11000000 INFO @ Tue, 10 Dec 2019 14:25:43: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:25:43: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:25:43: #1 total tags in treatment: 11793945 INFO @ Tue, 10 Dec 2019 14:25:43: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:25:43: #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 14:25:44: #1 tags after filtering in treatment: 11793945 INFO @ Tue, 10 Dec 2019 14:25:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:25:44: #1 finished! INFO @ Tue, 10 Dec 2019 14:25:44: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:25:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:25:45: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:25:45: 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 14:25:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.20_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/SRX6678236/SRX6678236.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678236/SRX6678236.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。