Job ID = 4289417 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:28:30 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 ) 2019-12-10T05:28:30 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 ) 1900-01-00T05:28:30 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 ) 2019-12-10T05:28:30 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 : 17,878,718 reads read : 17,878,718 reads written : 17,878,718 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:06 17878718 reads; of these: 17878718 (100.00%) were unpaired; of these: 1259630 (7.05%) aligned 0 times 15181129 (84.91%) aligned exactly 1 time 1437959 (8.04%) aligned >1 times 92.95% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 8261872 / 16619088 = 0.4971 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:43:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.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 14:43:05: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:43:05: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:43:14: 1000000 INFO @ Tue, 10 Dec 2019 14:43:26: 2000000 INFO @ Tue, 10 Dec 2019 14:43:34: 3000000 INFO @ Tue, 10 Dec 2019 14:43:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.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 14:43:36: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:43:36: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:43:44: 4000000 INFO @ Tue, 10 Dec 2019 14:43:45: 1000000 INFO @ Tue, 10 Dec 2019 14:43:52: 5000000 INFO @ Tue, 10 Dec 2019 14:43:53: 2000000 INFO @ Tue, 10 Dec 2019 14:44:01: 6000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:44:03: 3000000 INFO @ Tue, 10 Dec 2019 14:44:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.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 14:44:05: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:44:05: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:44:10: 7000000 INFO @ Tue, 10 Dec 2019 14:44:12: 4000000 INFO @ Tue, 10 Dec 2019 14:44:15: 1000000 INFO @ Tue, 10 Dec 2019 14:44:20: 8000000 INFO @ Tue, 10 Dec 2019 14:44:22: 5000000 INFO @ Tue, 10 Dec 2019 14:44:23: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:44:23: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:44:23: #1 total tags in treatment: 8357216 INFO @ Tue, 10 Dec 2019 14:44:23: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:44:23: #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 14:44:24: #1 tags after filtering in treatment: 8357216 INFO @ Tue, 10 Dec 2019 14:44:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:44:24: #1 finished! INFO @ Tue, 10 Dec 2019 14:44:24: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:44:25: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:44:25: 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 14:44:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.05_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/SRX6678259/SRX6678259.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:44:25: 2000000 INFO @ Tue, 10 Dec 2019 14:44:32: 6000000 INFO @ Tue, 10 Dec 2019 14:44:33: 3000000 INFO @ Tue, 10 Dec 2019 14:44:41: 7000000 INFO @ Tue, 10 Dec 2019 14:44:42: 4000000 INFO @ Tue, 10 Dec 2019 14:44:49: 8000000 INFO @ Tue, 10 Dec 2019 14:44:50: 5000000 INFO @ Tue, 10 Dec 2019 14:44:52: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:44:52: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:44:52: #1 total tags in treatment: 8357216 INFO @ Tue, 10 Dec 2019 14:44:52: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:44:52: #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 14:44:52: #1 tags after filtering in treatment: 8357216 INFO @ Tue, 10 Dec 2019 14:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:44:52: #1 finished! INFO @ Tue, 10 Dec 2019 14:44:52: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:44:53: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:44:53: 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 14:44:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.10_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/SRX6678259/SRX6678259.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:44:59: 6000000 INFO @ Tue, 10 Dec 2019 14:45:07: 7000000 INFO @ Tue, 10 Dec 2019 14:45:14: 8000000 INFO @ Tue, 10 Dec 2019 14:45:17: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:45:17: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:45:17: #1 total tags in treatment: 8357216 INFO @ Tue, 10 Dec 2019 14:45:17: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:45:17: #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 14:45:17: #1 tags after filtering in treatment: 8357216 INFO @ Tue, 10 Dec 2019 14:45:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:45:17: #1 finished! INFO @ Tue, 10 Dec 2019 14:45:17: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:45:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:45:18: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:45:18: 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 14:45:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.20_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/SRX6678259/SRX6678259.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678259/SRX6678259.20_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。