Job ID = 2010763 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T15:26:50 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 ) 2019-07-05T15:26:52 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 ) 2019-07-05T15:31:59 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 ) 2019-07-05T15:31:59 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 ) 2019-07-05T15:32:34 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 ) 2019-07-05T15:39:04 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 : 105,283,808 reads read : 105,283,808 reads written : 105,283,808 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: 00:18:57 105283808 reads; of these: 105283808 (100.00%) were unpaired; of these: 4273254 (4.06%) aligned 0 times 89310158 (84.83%) aligned exactly 1 time 11700396 (11.11%) aligned >1 times 95.94% overall alignment rate Time searching: 00:18:57 Overall time: 00:18:57 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 44 files... [bam_rmdupse_core] 78414833 / 101010554 = 0.7763 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 06 Jul 2019 02:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.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, 06 Jul 2019 02:05:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:05:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.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, 06 Jul 2019 02:05:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:05:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:05:51: 1000000 INFO @ Sat, 06 Jul 2019 02:05:51: 1000000 INFO @ Sat, 06 Jul 2019 02:05:59: 2000000 INFO @ Sat, 06 Jul 2019 02:05:59: 2000000 INFO @ Sat, 06 Jul 2019 02:06:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.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, 06 Jul 2019 02:06:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:06:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:06:07: 3000000 INFO @ Sat, 06 Jul 2019 02:06:07: 3000000 INFO @ Sat, 06 Jul 2019 02:06:14: 4000000 INFO @ Sat, 06 Jul 2019 02:06:15: 1000000 INFO @ Sat, 06 Jul 2019 02:06:15: 4000000 INFO @ Sat, 06 Jul 2019 02:06:22: 5000000 INFO @ Sat, 06 Jul 2019 02:06:23: 2000000 INFO @ Sat, 06 Jul 2019 02:06:23: 5000000 INFO @ Sat, 06 Jul 2019 02:06:30: 6000000 INFO @ Sat, 06 Jul 2019 02:06:31: 3000000 INFO @ Sat, 06 Jul 2019 02:06:31: 6000000 INFO @ Sat, 06 Jul 2019 02:06:38: 7000000 INFO @ Sat, 06 Jul 2019 02:06:39: 4000000 INFO @ Sat, 06 Jul 2019 02:06:39: 7000000 INFO @ Sat, 06 Jul 2019 02:06:46: 8000000 INFO @ Sat, 06 Jul 2019 02:06:47: 5000000 INFO @ Sat, 06 Jul 2019 02:06:48: 8000000 INFO @ Sat, 06 Jul 2019 02:06:54: 9000000 INFO @ Sat, 06 Jul 2019 02:06:55: 6000000 INFO @ Sat, 06 Jul 2019 02:06:56: 9000000 INFO @ Sat, 06 Jul 2019 02:07:02: 10000000 INFO @ Sat, 06 Jul 2019 02:07:04: 7000000 INFO @ Sat, 06 Jul 2019 02:07:04: 10000000 INFO @ Sat, 06 Jul 2019 02:07:10: 11000000 INFO @ Sat, 06 Jul 2019 02:07:12: 8000000 INFO @ Sat, 06 Jul 2019 02:07:12: 11000000 INFO @ Sat, 06 Jul 2019 02:07:17: 12000000 INFO @ Sat, 06 Jul 2019 02:07:20: 12000000 INFO @ Sat, 06 Jul 2019 02:07:20: 9000000 INFO @ Sat, 06 Jul 2019 02:07:25: 13000000 INFO @ Sat, 06 Jul 2019 02:07:28: 13000000 INFO @ Sat, 06 Jul 2019 02:07:28: 10000000 INFO @ Sat, 06 Jul 2019 02:07:33: 14000000 INFO @ Sat, 06 Jul 2019 02:07:36: 14000000 INFO @ Sat, 06 Jul 2019 02:07:36: 11000000 INFO @ Sat, 06 Jul 2019 02:07:41: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:07:44: 15000000 INFO @ Sat, 06 Jul 2019 02:07:44: 12000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 02:07:49: 16000000 INFO @ Sat, 06 Jul 2019 02:07:52: 16000000 INFO @ Sat, 06 Jul 2019 02:07:52: 13000000 INFO @ Sat, 06 Jul 2019 02:07:57: 17000000 INFO @ Sat, 06 Jul 2019 02:08:00: 14000000 INFO @ Sat, 06 Jul 2019 02:08:00: 17000000 INFO @ Sat, 06 Jul 2019 02:08:05: 18000000 INFO @ Sat, 06 Jul 2019 02:08:09: 15000000 INFO @ Sat, 06 Jul 2019 02:08:09: 18000000 INFO @ Sat, 06 Jul 2019 02:08:13: 19000000 INFO @ Sat, 06 Jul 2019 02:08:17: 19000000 INFO @ Sat, 06 Jul 2019 02:08:17: 16000000 INFO @ Sat, 06 Jul 2019 02:08:21: 20000000 INFO @ Sat, 06 Jul 2019 02:08:25: 20000000 INFO @ Sat, 06 Jul 2019 02:08:25: 17000000 INFO @ Sat, 06 Jul 2019 02:08:29: 21000000 INFO @ Sat, 06 Jul 2019 02:08:33: 21000000 INFO @ Sat, 06 Jul 2019 02:08:33: 18000000 INFO @ Sat, 06 Jul 2019 02:08:37: 22000000 INFO @ Sat, 06 Jul 2019 02:08:41: 22000000 INFO @ Sat, 06 Jul 2019 02:08:41: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:08:41: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:08:41: #1 total tags in treatment: 22595721 INFO @ Sat, 06 Jul 2019 02:08:41: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:08:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:08:42: 19000000 INFO @ Sat, 06 Jul 2019 02:08:42: #1 tags after filtering in treatment: 22595721 INFO @ Sat, 06 Jul 2019 02:08:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:08:42: #1 finished! INFO @ Sat, 06 Jul 2019 02:08:42: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:08:44: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:08:44: 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, 06 Jul 2019 02:08:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.10_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/SRX387221/SRX387221.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:08:46: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:08:46: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:08:46: #1 total tags in treatment: 22595721 INFO @ Sat, 06 Jul 2019 02:08:46: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:08:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:08:46: #1 tags after filtering in treatment: 22595721 INFO @ Sat, 06 Jul 2019 02:08:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:08:46: #1 finished! INFO @ Sat, 06 Jul 2019 02:08:46: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:08:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:08:48: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:08:48: 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, 06 Jul 2019 02:08:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.05_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/SRX387221/SRX387221.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:08:50: 20000000 INFO @ Sat, 06 Jul 2019 02:08:58: 21000000 INFO @ Sat, 06 Jul 2019 02:09:06: 22000000 INFO @ Sat, 06 Jul 2019 02:09:10: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:09:10: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:09:10: #1 total tags in treatment: 22595721 INFO @ Sat, 06 Jul 2019 02:09:10: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:09:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:09:11: #1 tags after filtering in treatment: 22595721 INFO @ Sat, 06 Jul 2019 02:09:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:09:11: #1 finished! INFO @ Sat, 06 Jul 2019 02:09:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:09:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:09:13: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:09:13: 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, 06 Jul 2019 02:09:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.20_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/SRX387221/SRX387221.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387221/SRX387221.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling