Job ID = 4289126 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:33:44 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 ) 2019-12-10T04:40:25 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 28,578,433 reads read : 57,156,866 reads written : 28,578,433 reads 0-length : 28,578,433 spots read : 27,157,645 reads read : 54,315,290 reads written : 27,157,645 reads 0-length : 27,157,645 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: 00:06:01 55736078 reads; of these: 55736078 (100.00%) were unpaired; of these: 41409437 (74.30%) aligned 0 times 8806360 (15.80%) aligned exactly 1 time 5520281 (9.90%) aligned >1 times 25.70% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 7123177 / 14326641 = 0.4972 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:02:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.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 14:02:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:02:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:02:43: 1000000 INFO @ Tue, 10 Dec 2019 14:02:56: 2000000 INFO @ Tue, 10 Dec 2019 14:03:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.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 14:03:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:03:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:03:09: 3000000 INFO @ Tue, 10 Dec 2019 14:03:15: 1000000 INFO @ Tue, 10 Dec 2019 14:03:23: 4000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:03:28: 2000000 INFO @ Tue, 10 Dec 2019 14:03:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.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 14:03:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:03:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:03:37: 5000000 INFO @ Tue, 10 Dec 2019 14:03:40: 1000000 INFO @ Tue, 10 Dec 2019 14:03:43: 3000000 INFO @ Tue, 10 Dec 2019 14:03:49: 2000000 INFO @ Tue, 10 Dec 2019 14:03:51: 6000000 INFO @ Tue, 10 Dec 2019 14:03:57: 4000000 INFO @ Tue, 10 Dec 2019 14:03:58: 3000000 INFO @ Tue, 10 Dec 2019 14:04:05: 7000000 INFO @ Tue, 10 Dec 2019 14:04:06: 4000000 INFO @ Tue, 10 Dec 2019 14:04:07: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 14:04:07: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 14:04:07: #1 total tags in treatment: 7203464 INFO @ Tue, 10 Dec 2019 14:04:07: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:04:07: #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 14:04:07: #1 tags after filtering in treatment: 7203464 INFO @ Tue, 10 Dec 2019 14:04:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:04:07: #1 finished! INFO @ Tue, 10 Dec 2019 14:04:07: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:04:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:04:08: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:04:08: 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 14:04:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.05_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/SRX5486253/SRX5486253.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:04:10: 5000000 INFO @ Tue, 10 Dec 2019 14:04:14: 5000000 INFO @ Tue, 10 Dec 2019 14:04:22: 6000000 INFO @ Tue, 10 Dec 2019 14:04:22: 6000000 INFO @ Tue, 10 Dec 2019 14:04:31: 7000000 INFO @ Tue, 10 Dec 2019 14:04:32: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 14:04:32: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 14:04:32: #1 total tags in treatment: 7203464 INFO @ Tue, 10 Dec 2019 14:04:32: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:04:32: #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 14:04:32: #1 tags after filtering in treatment: 7203464 INFO @ Tue, 10 Dec 2019 14:04:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:04:32: #1 finished! INFO @ Tue, 10 Dec 2019 14:04:32: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:04:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:04:33: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:04:33: 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 14:04:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.20_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/SRX5486253/SRX5486253.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:04:34: 7000000 INFO @ Tue, 10 Dec 2019 14:04:36: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 14:04:36: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 14:04:36: #1 total tags in treatment: 7203464 INFO @ Tue, 10 Dec 2019 14:04:36: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:04:36: #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 14:04:36: #1 tags after filtering in treatment: 7203464 INFO @ Tue, 10 Dec 2019 14:04:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:04:36: #1 finished! INFO @ Tue, 10 Dec 2019 14:04:36: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:04:37: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:04:37: 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 14:04:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.10_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/SRX5486253/SRX5486253.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486253/SRX5486253.10_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。