Job ID = 4289602 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:56:21 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 ) 2019-12-10T06:30:50 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 ) 2019-12-10T06:30:50 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 : 28,713,876 reads read : 57,427,752 reads written : 28,713,876 reads 0-length : 28,713,876 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: 00:04:58 28713876 reads; of these: 28713876 (100.00%) were unpaired; of these: 2401649 (8.36%) aligned 0 times 20889200 (72.75%) aligned exactly 1 time 5423027 (18.89%) aligned >1 times 91.64% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 14465489 / 26312227 = 0.5498 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 15:43:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.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 15:43:07: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:43:07: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:43:14: 1000000 INFO @ Tue, 10 Dec 2019 15:43:22: 2000000 INFO @ Tue, 10 Dec 2019 15:43:29: 3000000 INFO @ Tue, 10 Dec 2019 15:43:36: 4000000 INFO @ Tue, 10 Dec 2019 15:43:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.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 15:43:37: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:43:37: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:43:44: 5000000 INFO @ Tue, 10 Dec 2019 15:43:46: 1000000 INFO @ Tue, 10 Dec 2019 15:43:51: 6000000 INFO @ Tue, 10 Dec 2019 15:43:54: 2000000 INFO @ Tue, 10 Dec 2019 15:43:59: 7000000 INFO @ Tue, 10 Dec 2019 15:44:03: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 15:44:06: 8000000 INFO @ Tue, 10 Dec 2019 15:44:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.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 15:44:07: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:44:07: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:44:12: 4000000 INFO @ Tue, 10 Dec 2019 15:44:14: 9000000 INFO @ Tue, 10 Dec 2019 15:44:15: 1000000 INFO @ Tue, 10 Dec 2019 15:44:21: 5000000 INFO @ Tue, 10 Dec 2019 15:44:21: 10000000 INFO @ Tue, 10 Dec 2019 15:44:24: 2000000 INFO @ Tue, 10 Dec 2019 15:44:29: 11000000 INFO @ Tue, 10 Dec 2019 15:44:30: 6000000 INFO @ Tue, 10 Dec 2019 15:44:32: 3000000 INFO @ Tue, 10 Dec 2019 15:44:35: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 15:44:35: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 15:44:35: #1 total tags in treatment: 11846738 INFO @ Tue, 10 Dec 2019 15:44:35: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:44:35: #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 15:44:35: #1 tags after filtering in treatment: 11846738 INFO @ Tue, 10 Dec 2019 15:44:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 15:44:35: #1 finished! INFO @ Tue, 10 Dec 2019 15:44:35: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:44:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:44:36: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:44:36: 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 15:44:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.05_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/SRX7106974/SRX7106974.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:44:38: 7000000 INFO @ Tue, 10 Dec 2019 15:44:41: 4000000 INFO @ Tue, 10 Dec 2019 15:44:46: 8000000 INFO @ Tue, 10 Dec 2019 15:44:49: 5000000 INFO @ Tue, 10 Dec 2019 15:44:55: 9000000 INFO @ Tue, 10 Dec 2019 15:44:58: 6000000 INFO @ Tue, 10 Dec 2019 15:45:02: 10000000 INFO @ Tue, 10 Dec 2019 15:45:07: 7000000 INFO @ Tue, 10 Dec 2019 15:45:10: 11000000 INFO @ Tue, 10 Dec 2019 15:45:15: 8000000 INFO @ Tue, 10 Dec 2019 15:45:17: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 15:45:17: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 15:45:17: #1 total tags in treatment: 11846738 INFO @ Tue, 10 Dec 2019 15:45:17: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:45:17: #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 15:45:17: #1 tags after filtering in treatment: 11846738 INFO @ Tue, 10 Dec 2019 15:45:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 15:45:17: #1 finished! INFO @ Tue, 10 Dec 2019 15:45:17: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:45:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:45:18: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:45:18: 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 15:45:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:45:24: 9000000 INFO @ Tue, 10 Dec 2019 15:45:32: 10000000 INFO @ Tue, 10 Dec 2019 15:45:39: 11000000 INFO @ Tue, 10 Dec 2019 15:45:46: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 15:45:46: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 15:45:46: #1 total tags in treatment: 11846738 INFO @ Tue, 10 Dec 2019 15:45:46: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:45:46: #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 15:45:46: #1 tags after filtering in treatment: 11846738 INFO @ Tue, 10 Dec 2019 15:45:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 15:45:46: #1 finished! INFO @ Tue, 10 Dec 2019 15:45:46: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:45:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:45:47: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:45:47: 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 15:45:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.20_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/SRX7106974/SRX7106974.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106974/SRX7106974.20_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。