Job ID = 2011680 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:12:28 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 ) 2019-07-05T17:22:49 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 ) 2019-07-05T17:22:49 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 ) 2019-07-05T17:34:45 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 ) 2019-07-05T17:35:27 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 ) 2019-07-05T17:40:15 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 : 23,109,105 reads read : 46,218,210 reads written : 46,218,210 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: 00:34:58 23109105 reads; of these: 23109105 (100.00%) were paired; of these: 4147472 (17.95%) aligned concordantly 0 times 15990836 (69.20%) aligned concordantly exactly 1 time 2970797 (12.86%) aligned concordantly >1 times ---- 4147472 pairs aligned concordantly 0 times; of these: 2090156 (50.40%) aligned discordantly 1 time ---- 2057316 pairs aligned 0 times concordantly or discordantly; of these: 4114632 mates make up the pairs; of these: 2916026 (70.87%) aligned 0 times 355501 (8.64%) aligned exactly 1 time 843105 (20.49%) aligned >1 times 93.69% overall alignment rate Time searching: 00:34:58 Overall time: 00:34:58 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 28 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 1215332 / 20931816 = 0.0581 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 03:42:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.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 03:42:11: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:42:11: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:42:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.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 03:42:12: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:42:12: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.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 03:42:13: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:42:13: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:42:22: 1000000 INFO @ Sat, 06 Jul 2019 03:42:23: 1000000 INFO @ Sat, 06 Jul 2019 03:42:23: 1000000 INFO @ Sat, 06 Jul 2019 03:42:33: 2000000 INFO @ Sat, 06 Jul 2019 03:42:33: 2000000 INFO @ Sat, 06 Jul 2019 03:42:34: 2000000 INFO @ Sat, 06 Jul 2019 03:42:42: 3000000 INFO @ Sat, 06 Jul 2019 03:42:44: 3000000 INFO @ Sat, 06 Jul 2019 03:42:44: 3000000 INFO @ Sat, 06 Jul 2019 03:42:53: 4000000 INFO @ Sat, 06 Jul 2019 03:42:54: 4000000 INFO @ Sat, 06 Jul 2019 03:42:55: 4000000 INFO @ Sat, 06 Jul 2019 03:43:04: 5000000 INFO @ Sat, 06 Jul 2019 03:43:04: 5000000 INFO @ Sat, 06 Jul 2019 03:43:05: 5000000 INFO @ Sat, 06 Jul 2019 03:43:13: 6000000 INFO @ Sat, 06 Jul 2019 03:43:14: 6000000 INFO @ Sat, 06 Jul 2019 03:43:16: 6000000 INFO @ Sat, 06 Jul 2019 03:43:22: 7000000 INFO @ Sat, 06 Jul 2019 03:43:25: 7000000 INFO @ Sat, 06 Jul 2019 03:43:26: 7000000 INFO @ Sat, 06 Jul 2019 03:43:31: 8000000 INFO @ Sat, 06 Jul 2019 03:43:36: 8000000 INFO @ Sat, 06 Jul 2019 03:43:37: 8000000 INFO @ Sat, 06 Jul 2019 03:43:41: 9000000 INFO @ Sat, 06 Jul 2019 03:43:47: 9000000 INFO @ Sat, 06 Jul 2019 03:43:48: 9000000 INFO @ Sat, 06 Jul 2019 03:43:50: 10000000 INFO @ Sat, 06 Jul 2019 03:43:57: 10000000 INFO @ Sat, 06 Jul 2019 03:43:58: 10000000 INFO @ Sat, 06 Jul 2019 03:43:59: 11000000 INFO @ Sat, 06 Jul 2019 03:44:07: 11000000 INFO @ Sat, 06 Jul 2019 03:44:08: 12000000 INFO @ Sat, 06 Jul 2019 03:44:09: 11000000 INFO @ Sat, 06 Jul 2019 03:44:17: 13000000 INFO @ Sat, 06 Jul 2019 03:44:18: 12000000 INFO @ Sat, 06 Jul 2019 03:44:19: 12000000 INFO @ Sat, 06 Jul 2019 03:44:27: 14000000 INFO @ Sat, 06 Jul 2019 03:44:28: 13000000 INFO @ Sat, 06 Jul 2019 03:44:30: 13000000 INFO @ Sat, 06 Jul 2019 03:44:36: 15000000 INFO @ Sat, 06 Jul 2019 03:44:39: 14000000 INFO @ Sat, 06 Jul 2019 03:44:40: 14000000 INFO @ Sat, 06 Jul 2019 03:44:45: 16000000 INFO @ Sat, 06 Jul 2019 03:44:50: 15000000 INFO @ Sat, 06 Jul 2019 03:44:51: 15000000 INFO @ Sat, 06 Jul 2019 03:44:54: 17000000 INFO @ Sat, 06 Jul 2019 03:45:00: 16000000 INFO @ Sat, 06 Jul 2019 03:45:02: 16000000 INFO @ Sat, 06 Jul 2019 03:45:03: 18000000 INFO @ Sat, 06 Jul 2019 03:45:11: 17000000 INFO @ Sat, 06 Jul 2019 03:45:12: 17000000 INFO @ Sat, 06 Jul 2019 03:45:12: 19000000 INFO @ Sat, 06 Jul 2019 03:45:21: 18000000 INFO @ Sat, 06 Jul 2019 03:45:22: 20000000 INFO @ Sat, 06 Jul 2019 03:45:23: 18000000 INFO @ Sat, 06 Jul 2019 03:45:31: 21000000 INFO @ Sat, 06 Jul 2019 03:45:31: 19000000 INFO @ Sat, 06 Jul 2019 03:45:33: 19000000 INFO @ Sat, 06 Jul 2019 03:45:41: 20000000 INFO @ Sat, 06 Jul 2019 03:45:41: 22000000 INFO @ Sat, 06 Jul 2019 03:45:43: 20000000 INFO @ Sat, 06 Jul 2019 03:45:50: 21000000 INFO @ Sat, 06 Jul 2019 03:45:52: 23000000 INFO @ Sat, 06 Jul 2019 03:45:54: 21000000 INFO @ Sat, 06 Jul 2019 03:45:59: 22000000 INFO @ Sat, 06 Jul 2019 03:46:02: 24000000 INFO @ Sat, 06 Jul 2019 03:46:04: 22000000 INFO @ Sat, 06 Jul 2019 03:46:08: 23000000 INFO @ Sat, 06 Jul 2019 03:46:12: 25000000 INFO @ Sat, 06 Jul 2019 03:46:15: 23000000 INFO @ Sat, 06 Jul 2019 03:46:17: 24000000 INFO @ Sat, 06 Jul 2019 03:46:23: 26000000 INFO @ Sat, 06 Jul 2019 03:46:25: 24000000 INFO @ Sat, 06 Jul 2019 03:46:26: 25000000 INFO @ Sat, 06 Jul 2019 03:46:33: 27000000 INFO @ Sat, 06 Jul 2019 03:46:35: 26000000 INFO @ Sat, 06 Jul 2019 03:46:36: 25000000 INFO @ Sat, 06 Jul 2019 03:46:44: 28000000 INFO @ Sat, 06 Jul 2019 03:46:45: 27000000 INFO @ Sat, 06 Jul 2019 03:46:46: 26000000 INFO @ Sat, 06 Jul 2019 03:46:54: 28000000 INFO @ Sat, 06 Jul 2019 03:46:54: 29000000 INFO @ Sat, 06 Jul 2019 03:46:57: 27000000 INFO @ Sat, 06 Jul 2019 03:47:03: 29000000 INFO @ Sat, 06 Jul 2019 03:47:05: 30000000 INFO @ Sat, 06 Jul 2019 03:47:07: 28000000 INFO @ Sat, 06 Jul 2019 03:47:12: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:47:15: 31000000 INFO @ Sat, 06 Jul 2019 03:47:18: 29000000 INFO @ Sat, 06 Jul 2019 03:47:21: 31000000 INFO @ Sat, 06 Jul 2019 03:47:25: 32000000 INFO @ Sat, 06 Jul 2019 03:47:28: 30000000 INFO @ Sat, 06 Jul 2019 03:47:30: 32000000 INFO @ Sat, 06 Jul 2019 03:47:36: 33000000 INFO @ Sat, 06 Jul 2019 03:47:39: 31000000 INFO @ Sat, 06 Jul 2019 03:47:39: 33000000 INFO @ Sat, 06 Jul 2019 03:47:46: 34000000 INFO @ Sat, 06 Jul 2019 03:47:48: 34000000 INFO @ Sat, 06 Jul 2019 03:47:48: 32000000 INFO @ Sat, 06 Jul 2019 03:47:57: 35000000 INFO @ Sat, 06 Jul 2019 03:47:58: 33000000 INFO @ Sat, 06 Jul 2019 03:47:59: 35000000 INFO @ Sat, 06 Jul 2019 03:48:07: 34000000 INFO @ Sat, 06 Jul 2019 03:48:08: 36000000 INFO @ Sat, 06 Jul 2019 03:48:10: 36000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:48:16: 35000000 INFO @ Sat, 06 Jul 2019 03:48:18: 37000000 INFO @ Sat, 06 Jul 2019 03:48:20: 37000000 INFO @ Sat, 06 Jul 2019 03:48:26: 36000000 INFO @ Sat, 06 Jul 2019 03:48:28: 38000000 INFO @ Sat, 06 Jul 2019 03:48:31: 38000000 INFO @ Sat, 06 Jul 2019 03:48:35: 37000000 INFO @ Sat, 06 Jul 2019 03:48:39: 39000000 INFO @ Sat, 06 Jul 2019 03:48:41: 39000000 INFO @ Sat, 06 Jul 2019 03:48:44: 38000000 INFO @ Sat, 06 Jul 2019 03:48:50: 40000000 INFO @ Sat, 06 Jul 2019 03:48:50: 40000000 INFO @ Sat, 06 Jul 2019 03:48:53: 39000000 INFO @ Sat, 06 Jul 2019 03:48:59: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:48:59: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:48:59: #1 total tags in treatment: 17817412 INFO @ Sat, 06 Jul 2019 03:48:59: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:48:59: #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 03:48:59: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:48:59: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:48:59: #1 total tags in treatment: 17817412 INFO @ Sat, 06 Jul 2019 03:48:59: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:48:59: #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 03:49:00: #1 tags after filtering in treatment: 11280575 INFO @ Sat, 06 Jul 2019 03:49:00: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 03:49:00: #1 finished! INFO @ Sat, 06 Jul 2019 03:49:00: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:49:00: #1 tags after filtering in treatment: 11280575 INFO @ Sat, 06 Jul 2019 03:49:00: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 03:49:00: #1 finished! INFO @ Sat, 06 Jul 2019 03:49:00: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:49:00: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:49:00: 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 03:49:00: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:49:00: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:49:00: 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 03:49:00: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:49:02: 40000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.20_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms)pass1 - making usageList (0 chroms): 2 millis : 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.10_model.r’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.20_model.r’: No such file or directory: No such file or directory rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.10_*.xls’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.20_*.xls’: No such file or directory: No such file or directory rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.10_peaks.narrowPeak’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.20_peaks.narrowPeak’: No such file or directory: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:49:09: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:49:09: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:49:09: #1 total tags in treatment: 17817412 INFO @ Sat, 06 Jul 2019 03:49:09: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:49:09: #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 03:49:10: #1 tags after filtering in treatment: 11280575 INFO @ Sat, 06 Jul 2019 03:49:10: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 03:49:10: #1 finished! INFO @ Sat, 06 Jul 2019 03:49:10: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:49:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:49:11: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:49:11: 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 03:49:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.05_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/SRX4560561/SRX4560561.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560561/SRX4560561.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling