Job ID = 2010544 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:05:02 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 ) 2019-07-05T14:17:22 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 ) 2019-07-05T14:17:22 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 ) 2019-07-05T14:21:20 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 ) 2019-07-05T14:21:20 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 ) 2019-07-05T14:21:42 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 ) 2019-07-05T14:23:30 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 ) 2019-07-05T14:25:01 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 ) 2019-07-05T14:25:45 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 ) spots read : 28,417,939 reads read : 56,835,878 reads written : 56,835,878 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: 00:26:12 28417939 reads; of these: 28417939 (100.00%) were paired; of these: 3613325 (12.71%) aligned concordantly 0 times 17272813 (60.78%) aligned concordantly exactly 1 time 7531801 (26.50%) aligned concordantly >1 times ---- 3613325 pairs aligned concordantly 0 times; of these: 439765 (12.17%) aligned discordantly 1 time ---- 3173560 pairs aligned 0 times concordantly or discordantly; of these: 6347120 mates make up the pairs; of these: 5685197 (89.57%) aligned 0 times 259833 (4.09%) aligned exactly 1 time 402090 (6.33%) aligned >1 times 90.00% overall alignment rate Time searching: 00:26:12 Overall time: 00:26:12 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_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] 4936922 / 25212804 = 0.1958 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 00:11:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.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 00:11:38: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:11:38: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:11:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.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 00:11:39: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:11:39: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:11:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.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 00:11:40: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:11:40: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:11:46: 1000000 INFO @ Sat, 06 Jul 2019 00:11:47: 1000000 INFO @ Sat, 06 Jul 2019 00:11:48: 1000000 INFO @ Sat, 06 Jul 2019 00:11:54: 2000000 INFO @ Sat, 06 Jul 2019 00:11:55: 2000000 INFO @ Sat, 06 Jul 2019 00:11:57: 2000000 INFO @ Sat, 06 Jul 2019 00:12:03: 3000000 INFO @ Sat, 06 Jul 2019 00:12:04: 3000000 INFO @ Sat, 06 Jul 2019 00:12:05: 3000000 INFO @ Sat, 06 Jul 2019 00:12:11: 4000000 INFO @ Sat, 06 Jul 2019 00:12:12: 4000000 INFO @ Sat, 06 Jul 2019 00:12:14: 4000000 INFO @ Sat, 06 Jul 2019 00:12:20: 5000000 INFO @ Sat, 06 Jul 2019 00:12:21: 5000000 INFO @ Sat, 06 Jul 2019 00:12:22: 5000000 INFO @ Sat, 06 Jul 2019 00:12:28: 6000000 INFO @ Sat, 06 Jul 2019 00:12:29: 6000000 INFO @ Sat, 06 Jul 2019 00:12:31: 6000000 INFO @ Sat, 06 Jul 2019 00:12:37: 7000000 INFO @ Sat, 06 Jul 2019 00:12:38: 7000000 INFO @ Sat, 06 Jul 2019 00:12:39: 7000000 INFO @ Sat, 06 Jul 2019 00:12:46: 8000000 INFO @ Sat, 06 Jul 2019 00:12:46: 8000000 INFO @ Sat, 06 Jul 2019 00:12:48: 8000000 INFO @ Sat, 06 Jul 2019 00:12:55: 9000000 INFO @ Sat, 06 Jul 2019 00:12:56: 9000000 INFO @ Sat, 06 Jul 2019 00:12:57: 9000000 INFO @ Sat, 06 Jul 2019 00:13:03: 10000000 INFO @ Sat, 06 Jul 2019 00:13:05: 10000000 INFO @ Sat, 06 Jul 2019 00:13:05: 10000000 INFO @ Sat, 06 Jul 2019 00:13:11: 11000000 INFO @ Sat, 06 Jul 2019 00:13:14: 11000000 INFO @ Sat, 06 Jul 2019 00:13:15: 11000000 INFO @ Sat, 06 Jul 2019 00:13:20: 12000000 INFO @ Sat, 06 Jul 2019 00:13:22: 12000000 INFO @ Sat, 06 Jul 2019 00:13:25: 12000000 INFO @ Sat, 06 Jul 2019 00:13:28: 13000000 INFO @ Sat, 06 Jul 2019 00:13:30: 13000000 INFO @ Sat, 06 Jul 2019 00:13:35: 13000000 INFO @ Sat, 06 Jul 2019 00:13:37: 14000000 INFO @ Sat, 06 Jul 2019 00:13:38: 14000000 INFO @ Sat, 06 Jul 2019 00:13:45: 15000000 INFO @ Sat, 06 Jul 2019 00:13:45: 14000000 INFO @ Sat, 06 Jul 2019 00:13:46: 15000000 INFO @ Sat, 06 Jul 2019 00:13:53: 16000000 INFO @ Sat, 06 Jul 2019 00:13:54: 16000000 INFO @ Sat, 06 Jul 2019 00:13:55: 15000000 INFO @ Sat, 06 Jul 2019 00:14:02: 17000000 INFO @ Sat, 06 Jul 2019 00:14:02: 17000000 INFO @ Sat, 06 Jul 2019 00:14:05: 16000000 INFO @ Sat, 06 Jul 2019 00:14:10: 18000000 INFO @ Sat, 06 Jul 2019 00:14:11: 18000000 INFO @ Sat, 06 Jul 2019 00:14:15: 17000000 INFO @ Sat, 06 Jul 2019 00:14:18: 19000000 INFO @ Sat, 06 Jul 2019 00:14:19: 19000000 INFO @ Sat, 06 Jul 2019 00:14:25: 18000000 INFO @ Sat, 06 Jul 2019 00:14:27: 20000000 INFO @ Sat, 06 Jul 2019 00:14:27: 20000000 INFO @ Sat, 06 Jul 2019 00:14:35: 19000000 INFO @ Sat, 06 Jul 2019 00:14:35: 21000000 INFO @ Sat, 06 Jul 2019 00:14:35: 21000000 INFO @ Sat, 06 Jul 2019 00:14:44: 22000000 INFO @ Sat, 06 Jul 2019 00:14:44: 22000000 INFO @ Sat, 06 Jul 2019 00:14:45: 20000000 INFO @ Sat, 06 Jul 2019 00:14:52: 23000000 INFO @ Sat, 06 Jul 2019 00:14:52: 23000000 INFO @ Sat, 06 Jul 2019 00:14:54: 21000000 INFO @ Sat, 06 Jul 2019 00:15:00: 24000000 INFO @ Sat, 06 Jul 2019 00:15:01: 24000000 INFO @ Sat, 06 Jul 2019 00:15:04: 22000000 INFO @ Sat, 06 Jul 2019 00:15:08: 25000000 INFO @ Sat, 06 Jul 2019 00:15:09: 25000000 INFO @ Sat, 06 Jul 2019 00:15:14: 23000000 INFO @ Sat, 06 Jul 2019 00:15:16: 26000000 INFO @ Sat, 06 Jul 2019 00:15:17: 26000000 INFO @ Sat, 06 Jul 2019 00:15:24: 24000000 INFO @ Sat, 06 Jul 2019 00:15:24: 27000000 INFO @ Sat, 06 Jul 2019 00:15:25: 27000000 INFO @ Sat, 06 Jul 2019 00:15:31: 28000000 INFO @ Sat, 06 Jul 2019 00:15:33: 28000000 INFO @ Sat, 06 Jul 2019 00:15:33: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:15:39: 29000000 INFO @ Sat, 06 Jul 2019 00:15:40: 29000000 INFO @ Sat, 06 Jul 2019 00:15:43: 26000000 INFO @ Sat, 06 Jul 2019 00:15:47: 30000000 INFO @ Sat, 06 Jul 2019 00:15:48: 30000000 INFO @ Sat, 06 Jul 2019 00:15:53: 27000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:15:55: 31000000 INFO @ Sat, 06 Jul 2019 00:15:56: 31000000 INFO @ Sat, 06 Jul 2019 00:16:02: 28000000 INFO @ Sat, 06 Jul 2019 00:16:02: 32000000 INFO @ Sat, 06 Jul 2019 00:16:04: 32000000 INFO @ Sat, 06 Jul 2019 00:16:10: 33000000 INFO @ Sat, 06 Jul 2019 00:16:11: 29000000 INFO @ Sat, 06 Jul 2019 00:16:12: 33000000 INFO @ Sat, 06 Jul 2019 00:16:18: 34000000 INFO @ Sat, 06 Jul 2019 00:16:20: 30000000 INFO @ Sat, 06 Jul 2019 00:16:20: 34000000 INFO @ Sat, 06 Jul 2019 00:16:26: 35000000 INFO @ Sat, 06 Jul 2019 00:16:28: 35000000 INFO @ Sat, 06 Jul 2019 00:16:30: 31000000 INFO @ Sat, 06 Jul 2019 00:16:34: 36000000 INFO @ Sat, 06 Jul 2019 00:16:36: 36000000 INFO @ Sat, 06 Jul 2019 00:16:39: 32000000 INFO @ Sat, 06 Jul 2019 00:16:42: 37000000 INFO @ Sat, 06 Jul 2019 00:16:44: 37000000 INFO @ Sat, 06 Jul 2019 00:16:49: 33000000 INFO @ Sat, 06 Jul 2019 00:16:50: 38000000 INFO @ Sat, 06 Jul 2019 00:16:52: 38000000 INFO @ Sat, 06 Jul 2019 00:16:58: 39000000 INFO @ Sat, 06 Jul 2019 00:16:58: 34000000 INFO @ Sat, 06 Jul 2019 00:17:00: 39000000 INFO @ Sat, 06 Jul 2019 00:17:06: 40000000 INFO @ Sat, 06 Jul 2019 00:17:07: 35000000 INFO @ Sat, 06 Jul 2019 00:17:08: 40000000 INFO @ Sat, 06 Jul 2019 00:17:14: 41000000 INFO @ Sat, 06 Jul 2019 00:17:16: 41000000 INFO @ Sat, 06 Jul 2019 00:17:17: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:17:17: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:17:17: #1 total tags in treatment: 19892077 INFO @ Sat, 06 Jul 2019 00:17:17: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:17:17: #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 00:17:17: 36000000 INFO @ Sat, 06 Jul 2019 00:17:17: #1 tags after filtering in treatment: 9448866 INFO @ Sat, 06 Jul 2019 00:17:17: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 06 Jul 2019 00:17:17: #1 finished! INFO @ Sat, 06 Jul 2019 00:17:17: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:17:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:17:18: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:17:18: 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 00:17:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.20_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/SRX381246/SRX381246.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:17:18: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:17:18: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:17:18: #1 total tags in treatment: 19892077 INFO @ Sat, 06 Jul 2019 00:17:18: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:17:18: #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 00:17:19: #1 tags after filtering in treatment: 9448866 INFO @ Sat, 06 Jul 2019 00:17:19: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 06 Jul 2019 00:17:19: #1 finished! INFO @ Sat, 06 Jul 2019 00:17:19: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:17:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:17:20: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:17:20: 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 00:17:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.10_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/SRX381246/SRX381246.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:17:26: 37000000 INFO @ Sat, 06 Jul 2019 00:17:35: 38000000 INFO @ Sat, 06 Jul 2019 00:17:45: 39000000 INFO @ Sat, 06 Jul 2019 00:17:54: 40000000 INFO @ Sat, 06 Jul 2019 00:18:03: 41000000 INFO @ Sat, 06 Jul 2019 00:18:05: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:18:05: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:18:05: #1 total tags in treatment: 19892077 INFO @ Sat, 06 Jul 2019 00:18:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:18:05: #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 00:18:06: #1 tags after filtering in treatment: 9448866 INFO @ Sat, 06 Jul 2019 00:18:06: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 06 Jul 2019 00:18:06: #1 finished! INFO @ Sat, 06 Jul 2019 00:18:06: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:18:07: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:18:07: 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 00:18:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.05_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/SRX381246/SRX381246.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381246/SRX381246.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling