Job ID = 1305986 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T12:27:11 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 ) 2019-06-03T12:27:11 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 ) 2019-06-03T12:28:44 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 ) 2019-06-03T12:30:42 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 ) 2019-06-03T12:32:50 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 ) 2019-06-03T12:40:12 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 ) 2019-06-03T12:45:49 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 ) 2019-06-03T12:48:36 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 : 50,358,398 reads read : 50,358,398 reads written : 50,358,398 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:18:38 50358398 reads; of these: 50358398 (100.00%) were unpaired; of these: 961419 (1.91%) aligned 0 times 41800854 (83.01%) aligned exactly 1 time 7596125 (15.08%) aligned >1 times 98.09% overall alignment rate Time searching: 00:18:38 Overall time: 00:18:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 14890991 / 49396979 = 0.3015 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 @ Mon, 03 Jun 2019 22:24:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 22:24:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 22:24:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 22:24:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:44: 1000000 INFO @ Mon, 03 Jun 2019 22:24:45: 1000000 INFO @ Mon, 03 Jun 2019 22:24:46: 1000000 INFO @ Mon, 03 Jun 2019 22:24:52: 2000000 INFO @ Mon, 03 Jun 2019 22:24:53: 2000000 INFO @ Mon, 03 Jun 2019 22:24:56: 2000000 INFO @ Mon, 03 Jun 2019 22:24:59: 3000000 INFO @ Mon, 03 Jun 2019 22:25:01: 3000000 INFO @ Mon, 03 Jun 2019 22:25:06: 3000000 INFO @ Mon, 03 Jun 2019 22:25:07: 4000000 INFO @ Mon, 03 Jun 2019 22:25:09: 4000000 INFO @ Mon, 03 Jun 2019 22:25:15: 5000000 INFO @ Mon, 03 Jun 2019 22:25:15: 4000000 INFO @ Mon, 03 Jun 2019 22:25:16: 5000000 INFO @ Mon, 03 Jun 2019 22:25:22: 6000000 INFO @ Mon, 03 Jun 2019 22:25:24: 5000000 INFO @ Mon, 03 Jun 2019 22:25:24: 6000000 INFO @ Mon, 03 Jun 2019 22:25:29: 7000000 INFO @ Mon, 03 Jun 2019 22:25:32: 7000000 INFO @ Mon, 03 Jun 2019 22:25:33: 6000000 INFO @ Mon, 03 Jun 2019 22:25:36: 8000000 INFO @ Mon, 03 Jun 2019 22:25:39: 8000000 INFO @ Mon, 03 Jun 2019 22:25:42: 7000000 INFO @ Mon, 03 Jun 2019 22:25:43: 9000000 INFO @ Mon, 03 Jun 2019 22:25:47: 9000000 INFO @ Mon, 03 Jun 2019 22:25:51: 10000000 INFO @ Mon, 03 Jun 2019 22:25:52: 8000000 INFO @ Mon, 03 Jun 2019 22:25:54: 10000000 INFO @ Mon, 03 Jun 2019 22:25:58: 11000000 INFO @ Mon, 03 Jun 2019 22:26:01: 9000000 INFO @ Mon, 03 Jun 2019 22:26:01: 11000000 INFO @ Mon, 03 Jun 2019 22:26:05: 12000000 INFO @ Mon, 03 Jun 2019 22:26:09: 12000000 INFO @ Mon, 03 Jun 2019 22:26:10: 10000000 INFO @ Mon, 03 Jun 2019 22:26:12: 13000000 INFO @ Mon, 03 Jun 2019 22:26:16: 13000000 INFO @ Mon, 03 Jun 2019 22:26:19: 11000000 INFO @ Mon, 03 Jun 2019 22:26:19: 14000000 INFO @ Mon, 03 Jun 2019 22:26:24: 14000000 INFO @ Mon, 03 Jun 2019 22:26:26: 15000000 INFO @ Mon, 03 Jun 2019 22:26:28: 12000000 INFO @ Mon, 03 Jun 2019 22:26:31: 15000000 INFO @ Mon, 03 Jun 2019 22:26:33: 16000000 INFO @ Mon, 03 Jun 2019 22:26:37: 13000000 INFO @ Mon, 03 Jun 2019 22:26:39: 16000000 INFO @ Mon, 03 Jun 2019 22:26:40: 17000000 INFO @ Mon, 03 Jun 2019 22:26:46: 14000000 INFO @ Mon, 03 Jun 2019 22:26:46: 17000000 INFO @ Mon, 03 Jun 2019 22:26:48: 18000000 INFO @ Mon, 03 Jun 2019 22:26:54: 18000000 INFO @ Mon, 03 Jun 2019 22:26:55: 19000000 INFO @ Mon, 03 Jun 2019 22:26:55: 15000000 INFO @ Mon, 03 Jun 2019 22:27:01: 19000000 INFO @ Mon, 03 Jun 2019 22:27:02: 20000000 INFO @ Mon, 03 Jun 2019 22:27:05: 16000000 INFO @ Mon, 03 Jun 2019 22:27:09: 20000000 INFO @ Mon, 03 Jun 2019 22:27:09: 21000000 INFO @ Mon, 03 Jun 2019 22:27:14: 17000000 INFO @ Mon, 03 Jun 2019 22:27:16: 22000000 INFO @ Mon, 03 Jun 2019 22:27:16: 21000000 INFO @ Mon, 03 Jun 2019 22:27:23: 18000000 INFO @ Mon, 03 Jun 2019 22:27:23: 23000000 INFO @ Mon, 03 Jun 2019 22:27:24: 22000000 INFO @ Mon, 03 Jun 2019 22:27:30: 24000000 INFO @ Mon, 03 Jun 2019 22:27:31: 23000000 INFO @ Mon, 03 Jun 2019 22:27:32: 19000000 INFO @ Mon, 03 Jun 2019 22:27:37: 25000000 INFO @ Mon, 03 Jun 2019 22:27:39: 24000000 INFO @ Mon, 03 Jun 2019 22:27:41: 20000000 INFO @ Mon, 03 Jun 2019 22:27:45: 26000000 INFO @ Mon, 03 Jun 2019 22:27:46: 25000000 INFO @ Mon, 03 Jun 2019 22:27:50: 21000000 INFO @ Mon, 03 Jun 2019 22:27:52: 27000000 INFO @ Mon, 03 Jun 2019 22:27:53: 26000000 INFO @ Mon, 03 Jun 2019 22:27:59: 28000000 INFO @ Mon, 03 Jun 2019 22:27:59: 22000000 INFO @ Mon, 03 Jun 2019 22:28:01: 27000000 INFO @ Mon, 03 Jun 2019 22:28:06: 29000000 INFO @ Mon, 03 Jun 2019 22:28:08: 23000000 INFO @ Mon, 03 Jun 2019 22:28:09: 28000000 INFO @ Mon, 03 Jun 2019 22:28:13: 30000000 INFO @ Mon, 03 Jun 2019 22:28:16: 29000000 INFO @ Mon, 03 Jun 2019 22:28:17: 24000000 INFO @ Mon, 03 Jun 2019 22:28:21: 31000000 INFO @ Mon, 03 Jun 2019 22:28:24: 30000000 INFO @ Mon, 03 Jun 2019 22:28:26: 25000000 INFO @ Mon, 03 Jun 2019 22:28:28: 32000000 INFO @ Mon, 03 Jun 2019 22:28:32: 31000000 INFO @ Mon, 03 Jun 2019 22:28:35: 33000000 INFO @ Mon, 03 Jun 2019 22:28:36: 26000000 INFO @ Mon, 03 Jun 2019 22:28:39: 32000000 INFO @ Mon, 03 Jun 2019 22:28:42: 34000000 INFO @ Mon, 03 Jun 2019 22:28:45: 27000000 INFO @ Mon, 03 Jun 2019 22:28:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:28:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:28:46: #1 total tags in treatment: 34505988 INFO @ Mon, 03 Jun 2019 22:28:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:28:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:28:47: 33000000 INFO @ Mon, 03 Jun 2019 22:28:47: #1 tags after filtering in treatment: 34505988 INFO @ Mon, 03 Jun 2019 22:28:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:28:47: #1 finished! INFO @ Mon, 03 Jun 2019 22:28:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:28:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:28:50: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:28:50: 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 @ Mon, 03 Jun 2019 22:28:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.20_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/dm3/SRX495315/SRX495315.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:28:54: 28000000 INFO @ Mon, 03 Jun 2019 22:28:54: 34000000 INFO @ Mon, 03 Jun 2019 22:28:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:28:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:28:58: #1 total tags in treatment: 34505988 INFO @ Mon, 03 Jun 2019 22:28:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:28:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:28:59: #1 tags after filtering in treatment: 34505988 INFO @ Mon, 03 Jun 2019 22:28:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:28:59: #1 finished! INFO @ Mon, 03 Jun 2019 22:28:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:28:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:29:02: 29000000 INFO @ Mon, 03 Jun 2019 22:29:02: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:29:02: 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 @ Mon, 03 Jun 2019 22:29:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.10_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/dm3/SRX495315/SRX495315.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:29:10: 30000000 INFO @ Mon, 03 Jun 2019 22:29:18: 31000000 INFO @ Mon, 03 Jun 2019 22:29:26: 32000000 INFO @ Mon, 03 Jun 2019 22:29:34: 33000000 INFO @ Mon, 03 Jun 2019 22:29:42: 34000000 INFO @ Mon, 03 Jun 2019 22:29:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:29:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:29:47: #1 total tags in treatment: 34505988 INFO @ Mon, 03 Jun 2019 22:29:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:29:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:29:48: #1 tags after filtering in treatment: 34505988 INFO @ Mon, 03 Jun 2019 22:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:29:48: #1 finished! INFO @ Mon, 03 Jun 2019 22:29:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:29:51: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:29:51: 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 @ Mon, 03 Jun 2019 22:29:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.05_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/dm3/SRX495315/SRX495315.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495315/SRX495315.05_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。