Job ID = 4289034 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:18:17 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 ) 2019-12-10T04:21:26 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 : 9,932,507 reads read : 9,932,507 reads written : 9,932,507 spots read : 10,148,172 reads read : 10,148,172 reads written : 10,148,172 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: 00:03:29 20080679 reads; of these: 20080679 (100.00%) were unpaired; of these: 817411 (4.07%) aligned 0 times 14127201 (70.35%) aligned exactly 1 time 5136067 (25.58%) aligned >1 times 95.93% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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 8 files... [bam_rmdupse_core] 9787031 / 19263268 = 0.5081 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:39:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.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 13:39:10: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:39:10: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:39:18: 1000000 INFO @ Tue, 10 Dec 2019 13:39:25: 2000000 INFO @ Tue, 10 Dec 2019 13:39:32: 3000000 INFO @ Tue, 10 Dec 2019 13:39:40: 4000000 INFO @ Tue, 10 Dec 2019 13:39:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.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 13:39:40: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:39:40: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:39:48: 5000000 INFO @ Tue, 10 Dec 2019 13:39:49: 1000000 INFO @ Tue, 10 Dec 2019 13:39:57: 6000000 INFO @ Tue, 10 Dec 2019 13:39:58: 2000000 INFO @ Tue, 10 Dec 2019 13:40:06: 7000000 INFO @ Tue, 10 Dec 2019 13:40:07: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.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 13:40:10: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:40:10: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:40:15: 8000000 INFO @ Tue, 10 Dec 2019 13:40:16: 4000000 INFO @ Tue, 10 Dec 2019 13:40:20: 1000000 INFO @ Tue, 10 Dec 2019 13:40:24: 9000000 INFO @ Tue, 10 Dec 2019 13:40:25: 5000000 INFO @ Tue, 10 Dec 2019 13:40:28: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:40:28: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:40:28: #1 total tags in treatment: 9476237 INFO @ Tue, 10 Dec 2019 13:40:28: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:40:28: #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 13:40:29: #1 tags after filtering in treatment: 9476237 INFO @ Tue, 10 Dec 2019 13:40:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:40:29: #1 finished! INFO @ Tue, 10 Dec 2019 13:40:29: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:40:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:40:29: 2000000 INFO @ Tue, 10 Dec 2019 13:40:29: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:40:29: 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 13:40:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.05_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/SRX3463337/SRX3463337.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:40:33: 6000000 INFO @ Tue, 10 Dec 2019 13:40:38: 3000000 INFO @ Tue, 10 Dec 2019 13:40:40: 7000000 INFO @ Tue, 10 Dec 2019 13:40:48: 4000000 INFO @ Tue, 10 Dec 2019 13:40:48: 8000000 INFO @ Tue, 10 Dec 2019 13:40:55: 9000000 INFO @ Tue, 10 Dec 2019 13:40:57: 5000000 INFO @ Tue, 10 Dec 2019 13:40:59: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:40:59: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:40:59: #1 total tags in treatment: 9476237 INFO @ Tue, 10 Dec 2019 13:40:59: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:40:59: #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 13:40:59: #1 tags after filtering in treatment: 9476237 INFO @ Tue, 10 Dec 2019 13:40:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:40:59: #1 finished! INFO @ Tue, 10 Dec 2019 13:40:59: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:41:00: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:41:00: 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 13:41:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.10_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/SRX3463337/SRX3463337.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:41:06: 6000000 INFO @ Tue, 10 Dec 2019 13:41:15: 7000000 INFO @ Tue, 10 Dec 2019 13:41:24: 8000000 INFO @ Tue, 10 Dec 2019 13:41:33: 9000000 INFO @ Tue, 10 Dec 2019 13:41:37: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:41:37: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:41:37: #1 total tags in treatment: 9476237 INFO @ Tue, 10 Dec 2019 13:41:37: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:41:37: #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 13:41:37: #1 tags after filtering in treatment: 9476237 INFO @ Tue, 10 Dec 2019 13:41:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:41:37: #1 finished! INFO @ Tue, 10 Dec 2019 13:41:37: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:41:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:41:38: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:41:38: 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 13:41:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.20_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/SRX3463337/SRX3463337.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3463337/SRX3463337.20_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。