Job ID = 2641053 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T12:05:21 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 ) 2019-08-24T12:05:21 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 ) 2019-08-24T12:15:41 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 : 27,394,376 reads read : 27,394,376 reads written : 27,394,376 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: 00:08:58 27394376 reads; of these: 27394376 (100.00%) were unpaired; of these: 405869 (1.48%) aligned 0 times 24489620 (89.40%) aligned exactly 1 time 2498887 (9.12%) aligned >1 times 98.52% overall alignment rate Time searching: 00:08:58 Overall time: 00:08:58 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] 15034556 / 26988507 = 0.5571 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:36:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.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 @ Sat, 24 Aug 2019 21:36:40: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:36:40: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:36:50: 1000000 INFO @ Sat, 24 Aug 2019 21:36:59: 2000000 INFO @ Sat, 24 Aug 2019 21:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.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 @ Sat, 24 Aug 2019 21:37:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:37:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:37:09: 3000000 INFO @ Sat, 24 Aug 2019 21:37:19: 1000000 INFO @ Sat, 24 Aug 2019 21:37:20: 4000000 INFO @ Sat, 24 Aug 2019 21:37:30: 2000000 INFO @ Sat, 24 Aug 2019 21:37:30: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:37:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.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 @ Sat, 24 Aug 2019 21:37:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:37:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:37:40: 3000000 INFO @ Sat, 24 Aug 2019 21:37:41: 6000000 INFO @ Sat, 24 Aug 2019 21:37:49: 1000000 INFO @ Sat, 24 Aug 2019 21:37:51: 4000000 INFO @ Sat, 24 Aug 2019 21:37:51: 7000000 INFO @ Sat, 24 Aug 2019 21:37:58: 2000000 INFO @ Sat, 24 Aug 2019 21:38:02: 5000000 INFO @ Sat, 24 Aug 2019 21:38:02: 8000000 INFO @ Sat, 24 Aug 2019 21:38:09: 3000000 INFO @ Sat, 24 Aug 2019 21:38:12: 9000000 INFO @ Sat, 24 Aug 2019 21:38:12: 6000000 INFO @ Sat, 24 Aug 2019 21:38:19: 4000000 INFO @ Sat, 24 Aug 2019 21:38:23: 10000000 INFO @ Sat, 24 Aug 2019 21:38:23: 7000000 INFO @ Sat, 24 Aug 2019 21:38:30: 5000000 INFO @ Sat, 24 Aug 2019 21:38:33: 11000000 INFO @ Sat, 24 Aug 2019 21:38:33: 8000000 INFO @ Sat, 24 Aug 2019 21:38:41: 6000000 INFO @ Sat, 24 Aug 2019 21:38:43: #1 tag size is determined as 100 bps INFO @ Sat, 24 Aug 2019 21:38:43: #1 tag size = 100 INFO @ Sat, 24 Aug 2019 21:38:43: #1 total tags in treatment: 11953951 INFO @ Sat, 24 Aug 2019 21:38:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:38:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:38:43: #1 tags after filtering in treatment: 11953951 INFO @ Sat, 24 Aug 2019 21:38:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:38:43: #1 finished! INFO @ Sat, 24 Aug 2019 21:38:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:38:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:38:44: 9000000 INFO @ Sat, 24 Aug 2019 21:38:44: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:38:44: 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 @ Sat, 24 Aug 2019 21:38:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.05_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/SRX5257248/SRX5257248.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:38:51: 7000000 INFO @ Sat, 24 Aug 2019 21:38:54: 10000000 INFO @ Sat, 24 Aug 2019 21:39:02: 8000000 INFO @ Sat, 24 Aug 2019 21:39:04: 11000000 INFO @ Sat, 24 Aug 2019 21:39:12: 9000000 INFO @ Sat, 24 Aug 2019 21:39:14: #1 tag size is determined as 100 bps INFO @ Sat, 24 Aug 2019 21:39:14: #1 tag size = 100 INFO @ Sat, 24 Aug 2019 21:39:14: #1 total tags in treatment: 11953951 INFO @ Sat, 24 Aug 2019 21:39:14: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:39:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:39:14: #1 tags after filtering in treatment: 11953951 INFO @ Sat, 24 Aug 2019 21:39:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:39:14: #1 finished! INFO @ Sat, 24 Aug 2019 21:39:14: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:39:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:39:15: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:39:15: 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 @ Sat, 24 Aug 2019 21:39:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.10_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/SRX5257248/SRX5257248.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:39:22: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:39:31: 11000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:39:41: #1 tag size is determined as 100 bps INFO @ Sat, 24 Aug 2019 21:39:41: #1 tag size = 100 INFO @ Sat, 24 Aug 2019 21:39:41: #1 total tags in treatment: 11953951 INFO @ Sat, 24 Aug 2019 21:39:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:39:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:39:41: #1 tags after filtering in treatment: 11953951 INFO @ Sat, 24 Aug 2019 21:39:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:39:41: #1 finished! INFO @ Sat, 24 Aug 2019 21:39:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:39:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:39:42: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:39:42: 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 @ Sat, 24 Aug 2019 21:39:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.20_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/SRX5257248/SRX5257248.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257248/SRX5257248.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling