Job ID = 4289352 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:16:22 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 ) 2019-12-10T05:18:25 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 ) 2019-12-10T05:18:25 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 : 25,207,707 reads read : 25,207,707 reads written : 25,207,707 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: 00:04:31 25207707 reads; of these: 25207707 (100.00%) were unpaired; of these: 1288357 (5.11%) aligned 0 times 21821789 (86.57%) aligned exactly 1 time 2097561 (8.32%) aligned >1 times 94.89% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 12453283 / 23919350 = 0.5206 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:34:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.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 14:34:18: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:34:18: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:34:25: 1000000 INFO @ Tue, 10 Dec 2019 14:34:31: 2000000 INFO @ Tue, 10 Dec 2019 14:34:37: 3000000 INFO @ Tue, 10 Dec 2019 14:34:44: 4000000 INFO @ Tue, 10 Dec 2019 14:34:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.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 14:34:48: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:34:48: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:34:51: 5000000 INFO @ Tue, 10 Dec 2019 14:34:57: 1000000 INFO @ Tue, 10 Dec 2019 14:34:57: 6000000 INFO @ Tue, 10 Dec 2019 14:35:04: 7000000 INFO @ Tue, 10 Dec 2019 14:35:05: 2000000 INFO @ Tue, 10 Dec 2019 14:35:11: 8000000 INFO @ Tue, 10 Dec 2019 14:35:13: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:35:17: 9000000 INFO @ Tue, 10 Dec 2019 14:35:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.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 14:35:18: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:35:18: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:35:21: 4000000 INFO @ Tue, 10 Dec 2019 14:35:24: 10000000 INFO @ Tue, 10 Dec 2019 14:35:25: 1000000 INFO @ Tue, 10 Dec 2019 14:35:29: 5000000 INFO @ Tue, 10 Dec 2019 14:35:30: 11000000 INFO @ Tue, 10 Dec 2019 14:35:32: 2000000 INFO @ Tue, 10 Dec 2019 14:35:33: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:35:33: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:35:33: #1 total tags in treatment: 11466067 INFO @ Tue, 10 Dec 2019 14:35:33: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:35:33: #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 14:35:33: #1 tags after filtering in treatment: 11466067 INFO @ Tue, 10 Dec 2019 14:35:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:35:33: #1 finished! INFO @ Tue, 10 Dec 2019 14:35:33: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:35:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:35:34: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:35:34: 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 14:35:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.05_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/SRX6678248/SRX6678248.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:35:37: 6000000 INFO @ Tue, 10 Dec 2019 14:35:39: 3000000 INFO @ Tue, 10 Dec 2019 14:35:45: 7000000 INFO @ Tue, 10 Dec 2019 14:35:46: 4000000 INFO @ Tue, 10 Dec 2019 14:35:53: 8000000 INFO @ Tue, 10 Dec 2019 14:35:54: 5000000 INFO @ Tue, 10 Dec 2019 14:36:01: 6000000 INFO @ Tue, 10 Dec 2019 14:36:01: 9000000 INFO @ Tue, 10 Dec 2019 14:36:07: 7000000 INFO @ Tue, 10 Dec 2019 14:36:09: 10000000 INFO @ Tue, 10 Dec 2019 14:36:14: 8000000 INFO @ Tue, 10 Dec 2019 14:36:18: 11000000 INFO @ Tue, 10 Dec 2019 14:36:21: 9000000 INFO @ Tue, 10 Dec 2019 14:36:21: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:36:21: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:36:21: #1 total tags in treatment: 11466067 INFO @ Tue, 10 Dec 2019 14:36:21: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:36:21: #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 14:36:21: #1 tags after filtering in treatment: 11466067 INFO @ Tue, 10 Dec 2019 14:36:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:36:21: #1 finished! INFO @ Tue, 10 Dec 2019 14:36:21: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:36:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:36:22: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:36:22: 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 14:36:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.10_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/SRX6678248/SRX6678248.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:36:28: 10000000 INFO @ Tue, 10 Dec 2019 14:36:35: 11000000 INFO @ Tue, 10 Dec 2019 14:36:38: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:36:38: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:36:38: #1 total tags in treatment: 11466067 INFO @ Tue, 10 Dec 2019 14:36:38: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:36:38: #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 14:36:38: #1 tags after filtering in treatment: 11466067 INFO @ Tue, 10 Dec 2019 14:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:36:38: #1 finished! INFO @ Tue, 10 Dec 2019 14:36:38: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:36:39: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:36:39: 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 14:36:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.20_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/SRX6678248/SRX6678248.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678248/SRX6678248.20_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。