Job ID = 2641253 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,339,502 reads read : 14,679,004 reads written : 14,679,004 2019-08-24T13:19:23 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 : 7,330,296 reads read : 14,660,592 reads written : 14,660,592 spots read : 7,590,511 reads read : 15,181,022 reads written : 15,181,022 spots read : 7,465,156 reads read : 14,930,312 reads written : 14,930,312 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: 00:12:41 29725465 reads; of these: 29725465 (100.00%) were paired; of these: 9241910 (31.09%) aligned concordantly 0 times 19473378 (65.51%) aligned concordantly exactly 1 time 1010177 (3.40%) aligned concordantly >1 times ---- 9241910 pairs aligned concordantly 0 times; of these: 77201 (0.84%) aligned discordantly 1 time ---- 9164709 pairs aligned 0 times concordantly or discordantly; of these: 18329418 mates make up the pairs; of these: 14161785 (77.26%) aligned 0 times 3942910 (21.51%) aligned exactly 1 time 224723 (1.23%) aligned >1 times 76.18% overall alignment rate Time searching: 00:12:41 Overall time: 00:12:41 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 12 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] 1395611 / 20557791 = 0.0679 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:54:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.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 22:54:29: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:54:29: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:54:34: 1000000 INFO @ Sat, 24 Aug 2019 22:54:40: 2000000 INFO @ Sat, 24 Aug 2019 22:54:45: 3000000 INFO @ Sat, 24 Aug 2019 22:54:50: 4000000 INFO @ Sat, 24 Aug 2019 22:54:55: 5000000 INFO @ Sat, 24 Aug 2019 22:54:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.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 22:54:58: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:54:58: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:55:01: 6000000 INFO @ Sat, 24 Aug 2019 22:55:04: 1000000 INFO @ Sat, 24 Aug 2019 22:55:06: 7000000 INFO @ Sat, 24 Aug 2019 22:55:10: 2000000 INFO @ Sat, 24 Aug 2019 22:55:11: 8000000 INFO @ Sat, 24 Aug 2019 22:55:16: 3000000 INFO @ Sat, 24 Aug 2019 22:55:16: 9000000 INFO @ Sat, 24 Aug 2019 22:55:21: 4000000 INFO @ Sat, 24 Aug 2019 22:55:22: 10000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:55:27: 11000000 INFO @ Sat, 24 Aug 2019 22:55:27: 5000000 INFO @ Sat, 24 Aug 2019 22:55:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.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 22:55:28: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:55:28: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:55:32: 12000000 INFO @ Sat, 24 Aug 2019 22:55:33: 6000000 INFO @ Sat, 24 Aug 2019 22:55:34: 1000000 INFO @ Sat, 24 Aug 2019 22:55:38: 13000000 INFO @ Sat, 24 Aug 2019 22:55:39: 7000000 INFO @ Sat, 24 Aug 2019 22:55:40: 2000000 INFO @ Sat, 24 Aug 2019 22:55:43: 14000000 INFO @ Sat, 24 Aug 2019 22:55:45: 8000000 INFO @ Sat, 24 Aug 2019 22:55:46: 3000000 INFO @ Sat, 24 Aug 2019 22:55:48: 15000000 INFO @ Sat, 24 Aug 2019 22:55:51: 9000000 INFO @ Sat, 24 Aug 2019 22:55:52: 4000000 INFO @ Sat, 24 Aug 2019 22:55:54: 16000000 INFO @ Sat, 24 Aug 2019 22:55:57: 10000000 INFO @ Sat, 24 Aug 2019 22:55:57: 5000000 INFO @ Sat, 24 Aug 2019 22:55:59: 17000000 INFO @ Sat, 24 Aug 2019 22:56:03: 11000000 INFO @ Sat, 24 Aug 2019 22:56:03: 6000000 INFO @ Sat, 24 Aug 2019 22:56:04: 18000000 INFO @ Sat, 24 Aug 2019 22:56:08: 12000000 INFO @ Sat, 24 Aug 2019 22:56:09: 7000000 INFO @ Sat, 24 Aug 2019 22:56:09: 19000000 INFO @ Sat, 24 Aug 2019 22:56:14: 13000000 INFO @ Sat, 24 Aug 2019 22:56:15: 20000000 INFO @ Sat, 24 Aug 2019 22:56:15: 8000000 INFO @ Sat, 24 Aug 2019 22:56:20: 21000000 INFO @ Sat, 24 Aug 2019 22:56:20: 14000000 INFO @ Sat, 24 Aug 2019 22:56:21: 9000000 INFO @ Sat, 24 Aug 2019 22:56:25: 22000000 INFO @ Sat, 24 Aug 2019 22:56:26: 15000000 INFO @ Sat, 24 Aug 2019 22:56:27: 10000000 INFO @ Sat, 24 Aug 2019 22:56:31: 23000000 INFO @ Sat, 24 Aug 2019 22:56:32: 16000000 INFO @ Sat, 24 Aug 2019 22:56:33: 11000000 INFO @ Sat, 24 Aug 2019 22:56:36: 24000000 INFO @ Sat, 24 Aug 2019 22:56:38: 17000000 INFO @ Sat, 24 Aug 2019 22:56:39: 12000000 INFO @ Sat, 24 Aug 2019 22:56:41: 25000000 INFO @ Sat, 24 Aug 2019 22:56:44: 18000000 INFO @ Sat, 24 Aug 2019 22:56:45: 13000000 INFO @ Sat, 24 Aug 2019 22:56:46: 26000000 INFO @ Sat, 24 Aug 2019 22:56:49: 19000000 INFO @ Sat, 24 Aug 2019 22:56:51: 14000000 INFO @ Sat, 24 Aug 2019 22:56:52: 27000000 INFO @ Sat, 24 Aug 2019 22:56:55: 20000000 INFO @ Sat, 24 Aug 2019 22:56:56: 15000000 INFO @ Sat, 24 Aug 2019 22:56:57: 28000000 INFO @ Sat, 24 Aug 2019 22:57:01: 21000000 INFO @ Sat, 24 Aug 2019 22:57:02: 29000000 INFO @ Sat, 24 Aug 2019 22:57:02: 16000000 INFO @ Sat, 24 Aug 2019 22:57:07: 22000000 INFO @ Sat, 24 Aug 2019 22:57:08: 30000000 INFO @ Sat, 24 Aug 2019 22:57:08: 17000000 INFO @ Sat, 24 Aug 2019 22:57:13: 23000000 INFO @ Sat, 24 Aug 2019 22:57:13: 31000000 INFO @ Sat, 24 Aug 2019 22:57:14: 18000000 INFO @ Sat, 24 Aug 2019 22:57:18: 32000000 INFO @ Sat, 24 Aug 2019 22:57:18: 24000000 INFO @ Sat, 24 Aug 2019 22:57:20: 19000000 INFO @ Sat, 24 Aug 2019 22:57:24: 33000000 INFO @ Sat, 24 Aug 2019 22:57:24: 25000000 INFO @ Sat, 24 Aug 2019 22:57:26: 20000000 INFO @ Sat, 24 Aug 2019 22:57:29: 34000000 INFO @ Sat, 24 Aug 2019 22:57:30: 26000000 INFO @ Sat, 24 Aug 2019 22:57:31: 21000000 INFO @ Sat, 24 Aug 2019 22:57:34: 35000000 INFO @ Sat, 24 Aug 2019 22:57:36: 27000000 INFO @ Sat, 24 Aug 2019 22:57:37: 22000000 INFO @ Sat, 24 Aug 2019 22:57:39: 36000000 INFO @ Sat, 24 Aug 2019 22:57:42: 28000000 INFO @ Sat, 24 Aug 2019 22:57:43: 23000000 INFO @ Sat, 24 Aug 2019 22:57:45: 37000000 INFO @ Sat, 24 Aug 2019 22:57:48: 29000000 INFO @ Sat, 24 Aug 2019 22:57:49: 24000000 INFO @ Sat, 24 Aug 2019 22:57:50: 38000000 INFO @ Sat, 24 Aug 2019 22:57:53: 30000000 INFO @ Sat, 24 Aug 2019 22:57:55: 25000000 INFO @ Sat, 24 Aug 2019 22:57:55: 39000000 INFO @ Sat, 24 Aug 2019 22:57:59: 31000000 INFO @ Sat, 24 Aug 2019 22:58:00: 26000000 INFO @ Sat, 24 Aug 2019 22:58:01: 40000000 INFO @ Sat, 24 Aug 2019 22:58:05: 32000000 INFO @ Sat, 24 Aug 2019 22:58:06: 41000000 INFO @ Sat, 24 Aug 2019 22:58:06: 27000000 INFO @ Sat, 24 Aug 2019 22:58:11: 33000000 INFO @ Sat, 24 Aug 2019 22:58:11: 42000000 INFO @ Sat, 24 Aug 2019 22:58:12: 28000000 INFO @ Sat, 24 Aug 2019 22:58:14: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:58:14: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:58:14: #1 total tags in treatment: 19089815 INFO @ Sat, 24 Aug 2019 22:58:14: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:58:14: #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 22:58:15: #1 tags after filtering in treatment: 9229019 INFO @ Sat, 24 Aug 2019 22:58:15: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 24 Aug 2019 22:58:15: #1 finished! INFO @ Sat, 24 Aug 2019 22:58:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:58:16: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:58:16: 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 22:58:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.05_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/SRX6403229/SRX6403229.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:58:17: 34000000 INFO @ Sat, 24 Aug 2019 22:58:18: 29000000 INFO @ Sat, 24 Aug 2019 22:58:23: 35000000 INFO @ Sat, 24 Aug 2019 22:58:24: 30000000 INFO @ Sat, 24 Aug 2019 22:58:29: 36000000 INFO @ Sat, 24 Aug 2019 22:58:30: 31000000 INFO @ Sat, 24 Aug 2019 22:58:35: 37000000 INFO @ Sat, 24 Aug 2019 22:58:36: 32000000 INFO @ Sat, 24 Aug 2019 22:58:41: 38000000 INFO @ Sat, 24 Aug 2019 22:58:41: 33000000 INFO @ Sat, 24 Aug 2019 22:58:46: 39000000 INFO @ Sat, 24 Aug 2019 22:58:47: 34000000 INFO @ Sat, 24 Aug 2019 22:58:52: 40000000 INFO @ Sat, 24 Aug 2019 22:58:53: 35000000 INFO @ Sat, 24 Aug 2019 22:58:58: 41000000 INFO @ Sat, 24 Aug 2019 22:58:59: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:59:04: 42000000 INFO @ Sat, 24 Aug 2019 22:59:05: 37000000 INFO @ Sat, 24 Aug 2019 22:59:07: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:59:07: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:59:07: #1 total tags in treatment: 19089815 INFO @ Sat, 24 Aug 2019 22:59:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:59:07: #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 22:59:08: #1 tags after filtering in treatment: 9229019 INFO @ Sat, 24 Aug 2019 22:59:08: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 24 Aug 2019 22:59:08: #1 finished! INFO @ Sat, 24 Aug 2019 22:59:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:59:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:59:08: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:59:08: 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 22:59:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.10_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/SRX6403229/SRX6403229.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:59:11: 38000000 INFO @ Sat, 24 Aug 2019 22:59:16: 39000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:59:22: 40000000 INFO @ Sat, 24 Aug 2019 22:59:28: 41000000 INFO @ Sat, 24 Aug 2019 22:59:34: 42000000 INFO @ Sat, 24 Aug 2019 22:59:37: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:59:37: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:59:37: #1 total tags in treatment: 19089815 INFO @ Sat, 24 Aug 2019 22:59:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:59:37: #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 22:59:37: #1 tags after filtering in treatment: 9229019 INFO @ Sat, 24 Aug 2019 22:59:37: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 24 Aug 2019 22:59:37: #1 finished! INFO @ Sat, 24 Aug 2019 22:59:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:59:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:59:38: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:59:38: 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 22:59:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.20_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/SRX6403229/SRX6403229.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403229/SRX6403229.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling