Job ID = 2641215 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T12:48:28 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 ) spots read : 30,065,493 reads read : 60,130,986 reads written : 60,130,986 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: 00:22:03 30065493 reads; of these: 30065493 (100.00%) were paired; of these: 3621940 (12.05%) aligned concordantly 0 times 23027462 (76.59%) aligned concordantly exactly 1 time 3416091 (11.36%) aligned concordantly >1 times ---- 3621940 pairs aligned concordantly 0 times; of these: 783406 (21.63%) aligned discordantly 1 time ---- 2838534 pairs aligned 0 times concordantly or discordantly; of these: 5677068 mates make up the pairs; of these: 4852829 (85.48%) aligned 0 times 474006 (8.35%) aligned exactly 1 time 350233 (6.17%) aligned >1 times 91.93% overall alignment rate Time searching: 00:22:03 Overall time: 00:22:03 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] 4551411 / 26703962 = 0.1704 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:36:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.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 22:36:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:36:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:36:12: 1000000 INFO @ Sat, 24 Aug 2019 22:36:20: 2000000 INFO @ Sat, 24 Aug 2019 22:36:28: 3000000 INFO @ Sat, 24 Aug 2019 22:36:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.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 22:36:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:36:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:36:35: 4000000 INFO @ Sat, 24 Aug 2019 22:36:41: 1000000 INFO @ Sat, 24 Aug 2019 22:36:43: 5000000 INFO @ Sat, 24 Aug 2019 22:36:49: 2000000 INFO @ Sat, 24 Aug 2019 22:36:51: 6000000 INFO @ Sat, 24 Aug 2019 22:36:56: 3000000 INFO @ Sat, 24 Aug 2019 22:36:59: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:37:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.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 22:37:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:37:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:37:04: 4000000 INFO @ Sat, 24 Aug 2019 22:37:06: 8000000 INFO @ Sat, 24 Aug 2019 22:37:11: 1000000 INFO @ Sat, 24 Aug 2019 22:37:11: 5000000 INFO @ Sat, 24 Aug 2019 22:37:13: 9000000 INFO @ Sat, 24 Aug 2019 22:37:19: 2000000 INFO @ Sat, 24 Aug 2019 22:37:19: 6000000 INFO @ Sat, 24 Aug 2019 22:37:20: 10000000 INFO @ Sat, 24 Aug 2019 22:37:26: 3000000 INFO @ Sat, 24 Aug 2019 22:37:26: 7000000 INFO @ Sat, 24 Aug 2019 22:37:27: 11000000 INFO @ Sat, 24 Aug 2019 22:37:33: 8000000 INFO @ Sat, 24 Aug 2019 22:37:34: 12000000 INFO @ Sat, 24 Aug 2019 22:37:34: 4000000 INFO @ Sat, 24 Aug 2019 22:37:39: 9000000 INFO @ Sat, 24 Aug 2019 22:37:41: 13000000 INFO @ Sat, 24 Aug 2019 22:37:41: 5000000 INFO @ Sat, 24 Aug 2019 22:37:45: 10000000 INFO @ Sat, 24 Aug 2019 22:37:48: 14000000 INFO @ Sat, 24 Aug 2019 22:37:49: 6000000 INFO @ Sat, 24 Aug 2019 22:37:51: 11000000 INFO @ Sat, 24 Aug 2019 22:37:55: 15000000 INFO @ Sat, 24 Aug 2019 22:37:56: 7000000 INFO @ Sat, 24 Aug 2019 22:37:58: 12000000 INFO @ Sat, 24 Aug 2019 22:38:01: 16000000 INFO @ Sat, 24 Aug 2019 22:38:03: 8000000 INFO @ Sat, 24 Aug 2019 22:38:04: 13000000 INFO @ Sat, 24 Aug 2019 22:38:08: 17000000 INFO @ Sat, 24 Aug 2019 22:38:10: 14000000 INFO @ Sat, 24 Aug 2019 22:38:10: 9000000 INFO @ Sat, 24 Aug 2019 22:38:15: 18000000 INFO @ Sat, 24 Aug 2019 22:38:16: 15000000 INFO @ Sat, 24 Aug 2019 22:38:17: 10000000 INFO @ Sat, 24 Aug 2019 22:38:22: 16000000 INFO @ Sat, 24 Aug 2019 22:38:22: 19000000 INFO @ Sat, 24 Aug 2019 22:38:24: 11000000 INFO @ Sat, 24 Aug 2019 22:38:29: 17000000 INFO @ Sat, 24 Aug 2019 22:38:29: 20000000 INFO @ Sat, 24 Aug 2019 22:38:31: 12000000 INFO @ Sat, 24 Aug 2019 22:38:35: 18000000 INFO @ Sat, 24 Aug 2019 22:38:36: 21000000 INFO @ Sat, 24 Aug 2019 22:38:38: 13000000 INFO @ Sat, 24 Aug 2019 22:38:41: 19000000 INFO @ Sat, 24 Aug 2019 22:38:43: 22000000 INFO @ Sat, 24 Aug 2019 22:38:45: 14000000 INFO @ Sat, 24 Aug 2019 22:38:47: 20000000 INFO @ Sat, 24 Aug 2019 22:38:50: 23000000 INFO @ Sat, 24 Aug 2019 22:38:52: 15000000 INFO @ Sat, 24 Aug 2019 22:38:53: 21000000 INFO @ Sat, 24 Aug 2019 22:38:57: 24000000 INFO @ Sat, 24 Aug 2019 22:38:59: 16000000 INFO @ Sat, 24 Aug 2019 22:39:00: 22000000 INFO @ Sat, 24 Aug 2019 22:39:04: 25000000 INFO @ Sat, 24 Aug 2019 22:39:06: 23000000 INFO @ Sat, 24 Aug 2019 22:39:06: 17000000 INFO @ Sat, 24 Aug 2019 22:39:11: 26000000 INFO @ Sat, 24 Aug 2019 22:39:12: 24000000 INFO @ Sat, 24 Aug 2019 22:39:13: 18000000 INFO @ Sat, 24 Aug 2019 22:39:18: 27000000 INFO @ Sat, 24 Aug 2019 22:39:18: 25000000 INFO @ Sat, 24 Aug 2019 22:39:20: 19000000 INFO @ Sat, 24 Aug 2019 22:39:24: 26000000 INFO @ Sat, 24 Aug 2019 22:39:25: 28000000 INFO @ Sat, 24 Aug 2019 22:39:27: 20000000 INFO @ Sat, 24 Aug 2019 22:39:30: 27000000 INFO @ Sat, 24 Aug 2019 22:39:32: 29000000 INFO @ Sat, 24 Aug 2019 22:39:33: 21000000 INFO @ Sat, 24 Aug 2019 22:39:36: 28000000 INFO @ Sat, 24 Aug 2019 22:39:38: 30000000 INFO @ Sat, 24 Aug 2019 22:39:40: 22000000 INFO @ Sat, 24 Aug 2019 22:39:42: 29000000 INFO @ Sat, 24 Aug 2019 22:39:45: 31000000 INFO @ Sat, 24 Aug 2019 22:39:47: 23000000 INFO @ Sat, 24 Aug 2019 22:39:48: 30000000 INFO @ Sat, 24 Aug 2019 22:39:51: 32000000 INFO @ Sat, 24 Aug 2019 22:39:54: 24000000 INFO @ Sat, 24 Aug 2019 22:39:54: 31000000 INFO @ Sat, 24 Aug 2019 22:39:58: 33000000 INFO @ Sat, 24 Aug 2019 22:40:00: 32000000 INFO @ Sat, 24 Aug 2019 22:40:01: 25000000 INFO @ Sat, 24 Aug 2019 22:40:04: 34000000 INFO @ Sat, 24 Aug 2019 22:40:06: 33000000 INFO @ Sat, 24 Aug 2019 22:40:08: 26000000 INFO @ Sat, 24 Aug 2019 22:40:11: 35000000 INFO @ Sat, 24 Aug 2019 22:40:12: 34000000 INFO @ Sat, 24 Aug 2019 22:40:15: 27000000 INFO @ Sat, 24 Aug 2019 22:40:17: 36000000 INFO @ Sat, 24 Aug 2019 22:40:18: 35000000 INFO @ Sat, 24 Aug 2019 22:40:22: 28000000 INFO @ Sat, 24 Aug 2019 22:40:24: 37000000 INFO @ Sat, 24 Aug 2019 22:40:24: 36000000 INFO @ Sat, 24 Aug 2019 22:40:28: 29000000 INFO @ Sat, 24 Aug 2019 22:40:30: 37000000 INFO @ Sat, 24 Aug 2019 22:40:31: 38000000 INFO @ Sat, 24 Aug 2019 22:40:35: 30000000 INFO @ Sat, 24 Aug 2019 22:40:36: 38000000 INFO @ Sat, 24 Aug 2019 22:40:37: 39000000 INFO @ Sat, 24 Aug 2019 22:40:41: 31000000 INFO @ Sat, 24 Aug 2019 22:40:42: 39000000 INFO @ Sat, 24 Aug 2019 22:40:44: 40000000 INFO @ Sat, 24 Aug 2019 22:40:48: 40000000 INFO @ Sat, 24 Aug 2019 22:40:48: 32000000 INFO @ Sat, 24 Aug 2019 22:40:50: 41000000 INFO @ Sat, 24 Aug 2019 22:40:54: 41000000 INFO @ Sat, 24 Aug 2019 22:40:54: 33000000 INFO @ Sat, 24 Aug 2019 22:40:57: 42000000 INFO @ Sat, 24 Aug 2019 22:41:00: 42000000 INFO @ Sat, 24 Aug 2019 22:41:01: 34000000 INFO @ Sat, 24 Aug 2019 22:41:03: 43000000 INFO @ Sat, 24 Aug 2019 22:41:06: 43000000 INFO @ Sat, 24 Aug 2019 22:41:08: 35000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:41:10: 44000000 INFO @ Sat, 24 Aug 2019 22:41:11: 44000000 INFO @ Sat, 24 Aug 2019 22:41:14: 36000000 INFO @ Sat, 24 Aug 2019 22:41:16: 45000000 INFO @ Sat, 24 Aug 2019 22:41:17: 45000000 INFO @ Sat, 24 Aug 2019 22:41:21: 37000000 INFO @ Sat, 24 Aug 2019 22:41:23: 46000000 INFO @ Sat, 24 Aug 2019 22:41:23: 46000000 INFO @ Sat, 24 Aug 2019 22:41:24: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:41:24: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:41:24: #1 total tags in treatment: 21907878 INFO @ Sat, 24 Aug 2019 22:41:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:41:24: #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 22:41:25: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:41:25: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:41:25: #1 total tags in treatment: 21907878 INFO @ Sat, 24 Aug 2019 22:41:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:41:25: #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 22:41:25: #1 tags after filtering in treatment: 9206765 INFO @ Sat, 24 Aug 2019 22:41:25: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 24 Aug 2019 22:41:25: #1 finished! INFO @ Sat, 24 Aug 2019 22:41:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:41:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:41:25: #1 tags after filtering in treatment: 9206765 INFO @ Sat, 24 Aug 2019 22:41:25: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 24 Aug 2019 22:41:25: #1 finished! INFO @ Sat, 24 Aug 2019 22:41:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:41:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:41:26: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:41:26: 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 22:41:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.05_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/SRX5811112/SRX5811112.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:41:26: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:41:26: 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 22:41:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.10_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/SRX5811112/SRX5811112.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:41:27: 38000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:41:34: 39000000 INFO @ Sat, 24 Aug 2019 22:41:40: 40000000 INFO @ Sat, 24 Aug 2019 22:41:46: 41000000 INFO @ Sat, 24 Aug 2019 22:41:53: 42000000 INFO @ Sat, 24 Aug 2019 22:41:59: 43000000 INFO @ Sat, 24 Aug 2019 22:42:05: 44000000 INFO @ Sat, 24 Aug 2019 22:42:12: 45000000 INFO @ Sat, 24 Aug 2019 22:42:18: 46000000 INFO @ Sat, 24 Aug 2019 22:42:20: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:42:20: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:42:20: #1 total tags in treatment: 21907878 INFO @ Sat, 24 Aug 2019 22:42:20: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:42:20: #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 22:42:20: #1 tags after filtering in treatment: 9206765 INFO @ Sat, 24 Aug 2019 22:42:20: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 24 Aug 2019 22:42:20: #1 finished! INFO @ Sat, 24 Aug 2019 22:42:20: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:42:21: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:42:21: 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 22:42:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.20_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/SRX5811112/SRX5811112.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811112/SRX5811112.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling