Job ID = 4289485 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:34:38 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 ) 2019-12-10T05:34:38 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 ) 2019-12-10T05:37:39 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 : 30,305,301 reads read : 30,305,301 reads written : 30,305,301 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: 00:05:08 30305301 reads; of these: 30305301 (100.00%) were unpaired; of these: 2016118 (6.65%) aligned 0 times 25650724 (84.64%) aligned exactly 1 time 2638459 (8.71%) aligned >1 times 93.35% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 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] 17688584 / 28289183 = 0.6253 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:54:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.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 14:54:51: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:54:51: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:54:59: 1000000 INFO @ Tue, 10 Dec 2019 14:55:07: 2000000 INFO @ Tue, 10 Dec 2019 14:55:16: 3000000 INFO @ Tue, 10 Dec 2019 14:55:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.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 14:55:20: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:55:20: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:55:24: 4000000 INFO @ Tue, 10 Dec 2019 14:55:28: 1000000 INFO @ Tue, 10 Dec 2019 14:55:34: 5000000 INFO @ Tue, 10 Dec 2019 14:55:35: 2000000 INFO @ Tue, 10 Dec 2019 14:55:43: 6000000 INFO @ Tue, 10 Dec 2019 14:55:44: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:55:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.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 14:55:51: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:55:51: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:55:51: 4000000 INFO @ Tue, 10 Dec 2019 14:55:52: 7000000 INFO @ Tue, 10 Dec 2019 14:55:59: 5000000 INFO @ Tue, 10 Dec 2019 14:56:01: 1000000 INFO @ Tue, 10 Dec 2019 14:56:03: 8000000 INFO @ Tue, 10 Dec 2019 14:56:07: 6000000 INFO @ Tue, 10 Dec 2019 14:56:11: 2000000 INFO @ Tue, 10 Dec 2019 14:56:12: 9000000 INFO @ Tue, 10 Dec 2019 14:56:15: 7000000 INFO @ Tue, 10 Dec 2019 14:56:22: 3000000 INFO @ Tue, 10 Dec 2019 14:56:23: 10000000 INFO @ Tue, 10 Dec 2019 14:56:23: 8000000 INFO @ Tue, 10 Dec 2019 14:56:29: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:56:29: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:56:29: #1 total tags in treatment: 10600599 INFO @ Tue, 10 Dec 2019 14:56:29: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:56:29: #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 14:56:29: #1 tags after filtering in treatment: 10600599 INFO @ Tue, 10 Dec 2019 14:56:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:56:29: #1 finished! INFO @ Tue, 10 Dec 2019 14:56:29: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:56:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:56:30: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:56:30: 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 14:56:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.05_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/SRX6678272/SRX6678272.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:56:31: 9000000 INFO @ Tue, 10 Dec 2019 14:56:32: 4000000 INFO @ Tue, 10 Dec 2019 14:56:39: 10000000 INFO @ Tue, 10 Dec 2019 14:56:42: 5000000 INFO @ Tue, 10 Dec 2019 14:56:44: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:56:44: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:56:44: #1 total tags in treatment: 10600599 INFO @ Tue, 10 Dec 2019 14:56:44: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:56:44: #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 14:56:44: #1 tags after filtering in treatment: 10600599 INFO @ Tue, 10 Dec 2019 14:56:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:56:44: #1 finished! INFO @ Tue, 10 Dec 2019 14:56:44: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:56:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:56:45: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:56:45: 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 14:56:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.10_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/SRX6678272/SRX6678272.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:56:52: 6000000 INFO @ Tue, 10 Dec 2019 14:57:00: 7000000 INFO @ Tue, 10 Dec 2019 14:57:08: 8000000 INFO @ Tue, 10 Dec 2019 14:57:16: 9000000 INFO @ Tue, 10 Dec 2019 14:57:25: 10000000 INFO @ Tue, 10 Dec 2019 14:57:30: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:57:30: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:57:30: #1 total tags in treatment: 10600599 INFO @ Tue, 10 Dec 2019 14:57:30: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:57:30: #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 14:57:30: #1 tags after filtering in treatment: 10600599 INFO @ Tue, 10 Dec 2019 14:57:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:57:30: #1 finished! INFO @ Tue, 10 Dec 2019 14:57:30: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:57:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:57:31: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:57:31: 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 14:57:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.20_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/SRX6678272/SRX6678272.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678272/SRX6678272.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。