Job ID = 2010310 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T13:03:13 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 ) 2019-07-05T13:03:13 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 ) 2019-07-05T13:03:13 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 ) 2019-07-05T13:03:13 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 ) 2019-07-05T13:05:49 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 ) 2019-07-05T13:05:49 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 ) 2019-07-05T13:06:03 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 ) 2019-07-05T13:10:14 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 ) 2019-07-05T13:10:44 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 ) 2019-07-05T13:10:44 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 ) spots read : 56,965,590 reads read : 113,931,180 reads written : 56,965,590 reads 0-length : 56,965,590 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:41 56965590 reads; of these: 56965590 (100.00%) were unpaired; of these: 1684500 (2.96%) aligned 0 times 44678077 (78.43%) aligned exactly 1 time 10603013 (18.61%) aligned >1 times 97.04% overall alignment rate Time searching: 00:10:42 Overall time: 00:10:42 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 24 files... [bam_rmdupse_core] 37262334 / 55281090 = 0.6741 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 @ Fri, 05 Jul 2019 22:49:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.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 @ Fri, 05 Jul 2019 22:49:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:49:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.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 @ Fri, 05 Jul 2019 22:49:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:49:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:49:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.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 @ Fri, 05 Jul 2019 22:49:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:49:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:49:45: 1000000 INFO @ Fri, 05 Jul 2019 22:49:46: 1000000 INFO @ Fri, 05 Jul 2019 22:49:47: 1000000 INFO @ Fri, 05 Jul 2019 22:49:54: 2000000 INFO @ Fri, 05 Jul 2019 22:49:55: 2000000 INFO @ Fri, 05 Jul 2019 22:49:57: 2000000 INFO @ Fri, 05 Jul 2019 22:50:03: 3000000 INFO @ Fri, 05 Jul 2019 22:50:03: 3000000 INFO @ Fri, 05 Jul 2019 22:50:07: 3000000 INFO @ Fri, 05 Jul 2019 22:50:11: 4000000 INFO @ Fri, 05 Jul 2019 22:50:12: 4000000 INFO @ Fri, 05 Jul 2019 22:50:17: 4000000 INFO @ Fri, 05 Jul 2019 22:50:20: 5000000 INFO @ Fri, 05 Jul 2019 22:50:20: 5000000 INFO @ Fri, 05 Jul 2019 22:50:28: 5000000 INFO @ Fri, 05 Jul 2019 22:50:28: 6000000 INFO @ Fri, 05 Jul 2019 22:50:29: 6000000 INFO @ Fri, 05 Jul 2019 22:50:36: 7000000 INFO @ Fri, 05 Jul 2019 22:50:37: 7000000 INFO @ Fri, 05 Jul 2019 22:50:38: 6000000 INFO @ Fri, 05 Jul 2019 22:50:45: 8000000 INFO @ Fri, 05 Jul 2019 22:50:45: 8000000 INFO @ Fri, 05 Jul 2019 22:50:49: 7000000 INFO @ Fri, 05 Jul 2019 22:50:53: 9000000 INFO @ Fri, 05 Jul 2019 22:50:54: 9000000 INFO @ Fri, 05 Jul 2019 22:50:59: 8000000 INFO @ Fri, 05 Jul 2019 22:51:02: 10000000 INFO @ Fri, 05 Jul 2019 22:51:02: 10000000 INFO @ Fri, 05 Jul 2019 22:51:09: 9000000 INFO @ Fri, 05 Jul 2019 22:51:10: 11000000 INFO @ Fri, 05 Jul 2019 22:51:11: 11000000 INFO @ Fri, 05 Jul 2019 22:51:17: 10000000 INFO @ Fri, 05 Jul 2019 22:51:19: 12000000 INFO @ Fri, 05 Jul 2019 22:51:21: 12000000 INFO @ Fri, 05 Jul 2019 22:51:24: 11000000 INFO @ Fri, 05 Jul 2019 22:51:29: 13000000 INFO @ Fri, 05 Jul 2019 22:51:30: 13000000 INFO @ Fri, 05 Jul 2019 22:51:32: 12000000 INFO @ Fri, 05 Jul 2019 22:51:38: 14000000 INFO @ Fri, 05 Jul 2019 22:51:38: 14000000 INFO @ Fri, 05 Jul 2019 22:51:40: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 22:51:46: 15000000 INFO @ Fri, 05 Jul 2019 22:51:46: 15000000 INFO @ Fri, 05 Jul 2019 22:51:48: 14000000 INFO @ Fri, 05 Jul 2019 22:51:54: 16000000 INFO @ Fri, 05 Jul 2019 22:51:55: 16000000 INFO @ Fri, 05 Jul 2019 22:51:55: 15000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 22:52:03: 17000000 INFO @ Fri, 05 Jul 2019 22:52:03: 16000000 INFO @ Fri, 05 Jul 2019 22:52:03: 17000000 INFO @ Fri, 05 Jul 2019 22:52:10: 17000000 INFO @ Fri, 05 Jul 2019 22:52:11: 18000000 INFO @ Fri, 05 Jul 2019 22:52:11: 18000000 INFO @ Fri, 05 Jul 2019 22:52:11: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 22:52:11: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 22:52:11: #1 total tags in treatment: 18018756 INFO @ Fri, 05 Jul 2019 22:52:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:52:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 22:52:11: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 22:52:11: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 22:52:11: #1 total tags in treatment: 18018756 INFO @ Fri, 05 Jul 2019 22:52:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:52:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 22:52:11: #1 tags after filtering in treatment: 18018756 INFO @ Fri, 05 Jul 2019 22:52:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:52:11: #1 finished! INFO @ Fri, 05 Jul 2019 22:52:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:52:12: #1 tags after filtering in treatment: 18018756 INFO @ Fri, 05 Jul 2019 22:52:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:52:12: #1 finished! INFO @ Fri, 05 Jul 2019 22:52:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:52:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:52:13: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:52:13: 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 @ Fri, 05 Jul 2019 22:52:13: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 22:52:13: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:52:13: 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 @ Fri, 05 Jul 2019 22:52:13: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 22:52:17: 18000000 INFO @ Fri, 05 Jul 2019 22:52:18: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 22:52:18: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 22:52:18: #1 total tags in treatment: 18018756 INFO @ Fri, 05 Jul 2019 22:52:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:52:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 22:52:18: #1 tags after filtering in treatment: 18018756 INFO @ Fri, 05 Jul 2019 22:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:52:18: #1 finished! INFO @ Fri, 05 Jul 2019 22:52:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:52:19: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:52:19: 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 @ Fri, 05 Jul 2019 22:52:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.20_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.10_peaks.narrowPeakcut: /home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.05_peaks.narrowPeak: No such file or directory : No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.20_*.xls’: No such file or directory pass1 - making usageList (0 chroms): 1 millis rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.20_peaks.narrowPeak’: No such file or directory needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.10_peaks.narrowPeak’: No such file or directory rm: CompletedMACS2peakCalling cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3334035/SRX3334035.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling