Job ID = 2641147 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T12:51:02 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 ) 2019-08-24T12:51:02 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 ) spots read : 34,061,705 reads read : 68,123,410 reads written : 68,123,410 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: 00:25:38 34061705 reads; of these: 34061705 (100.00%) were paired; of these: 5969206 (17.52%) aligned concordantly 0 times 23427695 (68.78%) aligned concordantly exactly 1 time 4664804 (13.70%) aligned concordantly >1 times ---- 5969206 pairs aligned concordantly 0 times; of these: 1367593 (22.91%) aligned discordantly 1 time ---- 4601613 pairs aligned 0 times concordantly or discordantly; of these: 9203226 mates make up the pairs; of these: 6332592 (68.81%) aligned 0 times 1442393 (15.67%) aligned exactly 1 time 1428241 (15.52%) aligned >1 times 90.70% overall alignment rate Time searching: 00:25:38 Overall time: 00:25:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 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] 10033424 / 28235957 = 0.3553 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:35:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.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, 24 Aug 2019 22:35:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:35:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:35:59: 1000000 INFO @ Sat, 24 Aug 2019 22:36:09: 2000000 INFO @ Sat, 24 Aug 2019 22:36:18: 3000000 INFO @ Sat, 24 Aug 2019 22:36:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.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, 24 Aug 2019 22:36:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:36:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:36:28: 4000000 INFO @ Sat, 24 Aug 2019 22:36:30: 1000000 INFO @ Sat, 24 Aug 2019 22:36:38: 5000000 INFO @ Sat, 24 Aug 2019 22:36:40: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:36:48: 6000000 INFO @ Sat, 24 Aug 2019 22:36:49: 3000000 INFO @ Sat, 24 Aug 2019 22:36:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.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, 24 Aug 2019 22:36:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:36:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:36:58: 7000000 INFO @ Sat, 24 Aug 2019 22:36:59: 1000000 INFO @ Sat, 24 Aug 2019 22:36:59: 4000000 INFO @ Sat, 24 Aug 2019 22:37:08: 8000000 INFO @ Sat, 24 Aug 2019 22:37:09: 2000000 INFO @ Sat, 24 Aug 2019 22:37:09: 5000000 INFO @ Sat, 24 Aug 2019 22:37:18: 9000000 INFO @ Sat, 24 Aug 2019 22:37:18: 3000000 INFO @ Sat, 24 Aug 2019 22:37:19: 6000000 INFO @ Sat, 24 Aug 2019 22:37:28: 4000000 INFO @ Sat, 24 Aug 2019 22:37:28: 10000000 INFO @ Sat, 24 Aug 2019 22:37:29: 7000000 INFO @ Sat, 24 Aug 2019 22:37:37: 5000000 INFO @ Sat, 24 Aug 2019 22:37:38: 11000000 INFO @ Sat, 24 Aug 2019 22:37:39: 8000000 INFO @ Sat, 24 Aug 2019 22:37:46: 6000000 INFO @ Sat, 24 Aug 2019 22:37:47: 12000000 INFO @ Sat, 24 Aug 2019 22:37:49: 9000000 INFO @ Sat, 24 Aug 2019 22:37:56: 7000000 INFO @ Sat, 24 Aug 2019 22:37:57: 13000000 INFO @ Sat, 24 Aug 2019 22:37:59: 10000000 INFO @ Sat, 24 Aug 2019 22:38:05: 8000000 INFO @ Sat, 24 Aug 2019 22:38:07: 14000000 INFO @ Sat, 24 Aug 2019 22:38:09: 11000000 INFO @ Sat, 24 Aug 2019 22:38:15: 9000000 INFO @ Sat, 24 Aug 2019 22:38:17: 15000000 INFO @ Sat, 24 Aug 2019 22:38:18: 12000000 INFO @ Sat, 24 Aug 2019 22:38:24: 10000000 INFO @ Sat, 24 Aug 2019 22:38:26: 16000000 INFO @ Sat, 24 Aug 2019 22:38:28: 13000000 INFO @ Sat, 24 Aug 2019 22:38:33: 11000000 INFO @ Sat, 24 Aug 2019 22:38:36: 17000000 INFO @ Sat, 24 Aug 2019 22:38:38: 14000000 INFO @ Sat, 24 Aug 2019 22:38:43: 12000000 INFO @ Sat, 24 Aug 2019 22:38:46: 18000000 INFO @ Sat, 24 Aug 2019 22:38:47: 15000000 INFO @ Sat, 24 Aug 2019 22:38:52: 13000000 INFO @ Sat, 24 Aug 2019 22:38:55: 19000000 INFO @ Sat, 24 Aug 2019 22:38:57: 16000000 INFO @ Sat, 24 Aug 2019 22:39:01: 14000000 INFO @ Sat, 24 Aug 2019 22:39:05: 20000000 INFO @ Sat, 24 Aug 2019 22:39:07: 17000000 INFO @ Sat, 24 Aug 2019 22:39:10: 15000000 INFO @ Sat, 24 Aug 2019 22:39:15: 21000000 INFO @ Sat, 24 Aug 2019 22:39:17: 18000000 INFO @ Sat, 24 Aug 2019 22:39:19: 16000000 INFO @ Sat, 24 Aug 2019 22:39:25: 22000000 INFO @ Sat, 24 Aug 2019 22:39:26: 19000000 INFO @ Sat, 24 Aug 2019 22:39:29: 17000000 INFO @ Sat, 24 Aug 2019 22:39:34: 23000000 INFO @ Sat, 24 Aug 2019 22:39:36: 20000000 INFO @ Sat, 24 Aug 2019 22:39:38: 18000000 INFO @ Sat, 24 Aug 2019 22:39:44: 24000000 INFO @ Sat, 24 Aug 2019 22:39:46: 21000000 INFO @ Sat, 24 Aug 2019 22:39:47: 19000000 INFO @ Sat, 24 Aug 2019 22:39:54: 25000000 INFO @ Sat, 24 Aug 2019 22:39:55: 22000000 INFO @ Sat, 24 Aug 2019 22:39:56: 20000000 INFO @ Sat, 24 Aug 2019 22:40:03: 26000000 INFO @ Sat, 24 Aug 2019 22:40:05: 23000000 INFO @ Sat, 24 Aug 2019 22:40:05: 21000000 INFO @ Sat, 24 Aug 2019 22:40:13: 27000000 INFO @ Sat, 24 Aug 2019 22:40:15: 22000000 INFO @ Sat, 24 Aug 2019 22:40:15: 24000000 INFO @ Sat, 24 Aug 2019 22:40:22: 28000000 INFO @ Sat, 24 Aug 2019 22:40:24: 23000000 INFO @ Sat, 24 Aug 2019 22:40:25: 25000000 INFO @ Sat, 24 Aug 2019 22:40:32: 29000000 INFO @ Sat, 24 Aug 2019 22:40:33: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:40:34: 26000000 INFO @ Sat, 24 Aug 2019 22:40:41: 30000000 INFO @ Sat, 24 Aug 2019 22:40:42: 25000000 INFO @ Sat, 24 Aug 2019 22:40:43: 27000000 INFO @ Sat, 24 Aug 2019 22:40:51: 31000000 INFO @ Sat, 24 Aug 2019 22:40:51: 26000000 INFO @ Sat, 24 Aug 2019 22:40:53: 28000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:41:00: 27000000 INFO @ Sat, 24 Aug 2019 22:41:00: 32000000 INFO @ Sat, 24 Aug 2019 22:41:02: 29000000 INFO @ Sat, 24 Aug 2019 22:41:09: 28000000 INFO @ Sat, 24 Aug 2019 22:41:10: 33000000 INFO @ Sat, 24 Aug 2019 22:41:12: 30000000 INFO @ Sat, 24 Aug 2019 22:41:18: 29000000 INFO @ Sat, 24 Aug 2019 22:41:20: 34000000 INFO @ Sat, 24 Aug 2019 22:41:22: 31000000 INFO @ Sat, 24 Aug 2019 22:41:27: 30000000 INFO @ Sat, 24 Aug 2019 22:41:29: 35000000 INFO @ Sat, 24 Aug 2019 22:41:31: 32000000 INFO @ Sat, 24 Aug 2019 22:41:37: 31000000 INFO @ Sat, 24 Aug 2019 22:41:38: 36000000 INFO @ Sat, 24 Aug 2019 22:41:41: 33000000 INFO @ Sat, 24 Aug 2019 22:41:46: 32000000 INFO @ Sat, 24 Aug 2019 22:41:48: 37000000 INFO @ Sat, 24 Aug 2019 22:41:50: 34000000 INFO @ Sat, 24 Aug 2019 22:41:55: 33000000 INFO @ Sat, 24 Aug 2019 22:41:57: 38000000 INFO @ Sat, 24 Aug 2019 22:42:00: 35000000 INFO @ Sat, 24 Aug 2019 22:42:04: 34000000 INFO @ Sat, 24 Aug 2019 22:42:07: 39000000 INFO @ Sat, 24 Aug 2019 22:42:09: 36000000 INFO @ Sat, 24 Aug 2019 22:42:13: 35000000 INFO @ Sat, 24 Aug 2019 22:42:16: 40000000 INFO @ Sat, 24 Aug 2019 22:42:18: 37000000 INFO @ Sat, 24 Aug 2019 22:42:22: 36000000 INFO @ Sat, 24 Aug 2019 22:42:25: 41000000 INFO @ Sat, 24 Aug 2019 22:42:28: 38000000 INFO @ Sat, 24 Aug 2019 22:42:31: 37000000 INFO @ Sat, 24 Aug 2019 22:42:32: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:42:32: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:42:32: #1 total tags in treatment: 18079384 INFO @ Sat, 24 Aug 2019 22:42:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:42:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:42:33: #1 tags after filtering in treatment: 6898962 INFO @ Sat, 24 Aug 2019 22:42:33: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 24 Aug 2019 22:42:33: #1 finished! INFO @ Sat, 24 Aug 2019 22:42:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:42:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:42:33: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:42:33: 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, 24 Aug 2019 22:42:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.05_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/SRX5811102/SRX5811102.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:42:37: 39000000 INFO @ Sat, 24 Aug 2019 22:42:40: 38000000 INFO @ Sat, 24 Aug 2019 22:42:46: 40000000 INFO @ Sat, 24 Aug 2019 22:42:48: 39000000 INFO @ Sat, 24 Aug 2019 22:42:56: 41000000 INFO @ Sat, 24 Aug 2019 22:42:57: 40000000 INFO @ Sat, 24 Aug 2019 22:43:02: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:43:02: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:43:02: #1 total tags in treatment: 18079384 INFO @ Sat, 24 Aug 2019 22:43:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:43:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:43:03: #1 tags after filtering in treatment: 6898962 INFO @ Sat, 24 Aug 2019 22:43:03: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 24 Aug 2019 22:43:03: #1 finished! INFO @ Sat, 24 Aug 2019 22:43:03: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:43:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:43:03: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:43:03: 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, 24 Aug 2019 22:43:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.10_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/SRX5811102/SRX5811102.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:43:06: 41000000 INFO @ Sat, 24 Aug 2019 22:43:12: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:43:12: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:43:12: #1 total tags in treatment: 18079384 INFO @ Sat, 24 Aug 2019 22:43:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:43:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:43:13: #1 tags after filtering in treatment: 6898962 INFO @ Sat, 24 Aug 2019 22:43:13: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 24 Aug 2019 22:43:13: #1 finished! INFO @ Sat, 24 Aug 2019 22:43:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:43:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:43:13: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:43:13: 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, 24 Aug 2019 22:43:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.20_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/SRX5811102/SRX5811102.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811102/SRX5811102.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling