Job ID = 2011742 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:23:13 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 ) 2019-07-05T17:23:57 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 : 18,612,607 reads read : 37,225,214 reads written : 37,225,214 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: 00:13:04 18612607 reads; of these: 18612607 (100.00%) were paired; of these: 2088242 (11.22%) aligned concordantly 0 times 14152587 (76.04%) aligned concordantly exactly 1 time 2371778 (12.74%) aligned concordantly >1 times ---- 2088242 pairs aligned concordantly 0 times; of these: 527889 (25.28%) aligned discordantly 1 time ---- 1560353 pairs aligned 0 times concordantly or discordantly; of these: 3120706 mates make up the pairs; of these: 2427162 (77.78%) aligned 0 times 352994 (11.31%) aligned exactly 1 time 340550 (10.91%) aligned >1 times 93.48% overall alignment rate Time searching: 00:13:04 Overall time: 00:13:04 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] 1158586 / 17047230 = 0.0680 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 02:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.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 02:52:43: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:52:43: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.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 02:52:44: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:52:44: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:52:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.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 02:52:45: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:52:45: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:52:49: 1000000 INFO @ Sat, 06 Jul 2019 02:52:52: 1000000 INFO @ Sat, 06 Jul 2019 02:52:52: 1000000 INFO @ Sat, 06 Jul 2019 02:52:56: 2000000 INFO @ Sat, 06 Jul 2019 02:52:59: 2000000 INFO @ Sat, 06 Jul 2019 02:53:00: 2000000 INFO @ Sat, 06 Jul 2019 02:53:02: 3000000 INFO @ Sat, 06 Jul 2019 02:53:05: 3000000 INFO @ Sat, 06 Jul 2019 02:53:08: 4000000 INFO @ Sat, 06 Jul 2019 02:53:09: 3000000 INFO @ Sat, 06 Jul 2019 02:53:12: 4000000 INFO @ Sat, 06 Jul 2019 02:53:14: 5000000 INFO @ Sat, 06 Jul 2019 02:53:17: 4000000 INFO @ Sat, 06 Jul 2019 02:53:18: 5000000 INFO @ Sat, 06 Jul 2019 02:53:21: 6000000 INFO @ Sat, 06 Jul 2019 02:53:25: 6000000 INFO @ Sat, 06 Jul 2019 02:53:25: 5000000 INFO @ Sat, 06 Jul 2019 02:53:27: 7000000 INFO @ Sat, 06 Jul 2019 02:53:31: 7000000 INFO @ Sat, 06 Jul 2019 02:53:33: 8000000 INFO @ Sat, 06 Jul 2019 02:53:33: 6000000 INFO @ Sat, 06 Jul 2019 02:53:38: 8000000 INFO @ Sat, 06 Jul 2019 02:53:39: 9000000 INFO @ Sat, 06 Jul 2019 02:53:41: 7000000 INFO @ Sat, 06 Jul 2019 02:53:44: 9000000 INFO @ Sat, 06 Jul 2019 02:53:45: 10000000 INFO @ Sat, 06 Jul 2019 02:53:49: 8000000 INFO @ Sat, 06 Jul 2019 02:53:50: 10000000 INFO @ Sat, 06 Jul 2019 02:53:51: 11000000 INFO @ Sat, 06 Jul 2019 02:53:56: 11000000 INFO @ Sat, 06 Jul 2019 02:53:57: 12000000 INFO @ Sat, 06 Jul 2019 02:53:57: 9000000 INFO @ Sat, 06 Jul 2019 02:54:03: 12000000 INFO @ Sat, 06 Jul 2019 02:54:03: 13000000 INFO @ Sat, 06 Jul 2019 02:54:05: 10000000 INFO @ Sat, 06 Jul 2019 02:54:09: 14000000 INFO @ Sat, 06 Jul 2019 02:54:10: 13000000 INFO @ Sat, 06 Jul 2019 02:54:13: 11000000 INFO @ Sat, 06 Jul 2019 02:54:15: 15000000 INFO @ Sat, 06 Jul 2019 02:54:16: 14000000 INFO @ Sat, 06 Jul 2019 02:54:21: 12000000 INFO @ Sat, 06 Jul 2019 02:54:22: 16000000 INFO @ Sat, 06 Jul 2019 02:54:22: 15000000 INFO @ Sat, 06 Jul 2019 02:54:28: 17000000 INFO @ Sat, 06 Jul 2019 02:54:29: 16000000 INFO @ Sat, 06 Jul 2019 02:54:29: 13000000 INFO @ Sat, 06 Jul 2019 02:54:34: 18000000 INFO @ Sat, 06 Jul 2019 02:54:35: 17000000 INFO @ Sat, 06 Jul 2019 02:54:37: 14000000 INFO @ Sat, 06 Jul 2019 02:54:40: 19000000 INFO @ Sat, 06 Jul 2019 02:54:42: 18000000 INFO @ Sat, 06 Jul 2019 02:54:45: 15000000 INFO @ Sat, 06 Jul 2019 02:54:47: 20000000 INFO @ Sat, 06 Jul 2019 02:54:48: 19000000 INFO @ Sat, 06 Jul 2019 02:54:53: 21000000 INFO @ Sat, 06 Jul 2019 02:54:53: 16000000 INFO @ Sat, 06 Jul 2019 02:54:55: 20000000 INFO @ Sat, 06 Jul 2019 02:54:59: 22000000 INFO @ Sat, 06 Jul 2019 02:55:01: 17000000 INFO @ Sat, 06 Jul 2019 02:55:01: 21000000 INFO @ Sat, 06 Jul 2019 02:55:05: 23000000 INFO @ Sat, 06 Jul 2019 02:55:08: 22000000 INFO @ Sat, 06 Jul 2019 02:55:09: 18000000 INFO @ Sat, 06 Jul 2019 02:55:11: 24000000 INFO @ Sat, 06 Jul 2019 02:55:14: 23000000 INFO @ Sat, 06 Jul 2019 02:55:17: 25000000 INFO @ Sat, 06 Jul 2019 02:55:17: 19000000 INFO @ Sat, 06 Jul 2019 02:55:20: 24000000 INFO @ Sat, 06 Jul 2019 02:55:23: 26000000 INFO @ Sat, 06 Jul 2019 02:55:25: 20000000 INFO @ Sat, 06 Jul 2019 02:55:27: 25000000 INFO @ Sat, 06 Jul 2019 02:55:29: 27000000 INFO @ Sat, 06 Jul 2019 02:55:33: 21000000 INFO @ Sat, 06 Jul 2019 02:55:33: 26000000 INFO @ Sat, 06 Jul 2019 02:55:35: 28000000 INFO @ Sat, 06 Jul 2019 02:55:39: 27000000 INFO @ Sat, 06 Jul 2019 02:55:40: 22000000 INFO @ Sat, 06 Jul 2019 02:55:41: 29000000 INFO @ Sat, 06 Jul 2019 02:55:46: 28000000 INFO @ Sat, 06 Jul 2019 02:55:47: 30000000 INFO @ Sat, 06 Jul 2019 02:55:48: 23000000 INFO @ Sat, 06 Jul 2019 02:55:52: 29000000 INFO @ Sat, 06 Jul 2019 02:55:53: 31000000 INFO @ Sat, 06 Jul 2019 02:55:56: 24000000 INFO @ Sat, 06 Jul 2019 02:55:58: 30000000 INFO @ Sat, 06 Jul 2019 02:55:59: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:56:02: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:56:02: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:56:02: #1 total tags in treatment: 15387717 INFO @ Sat, 06 Jul 2019 02:56:02: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:56:02: #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 02:56:02: #1 tags after filtering in treatment: 9625108 INFO @ Sat, 06 Jul 2019 02:56:02: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 02:56:02: #1 finished! INFO @ Sat, 06 Jul 2019 02:56:02: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:56:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:56:03: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:56:03: 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, 06 Jul 2019 02:56:03: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:56:04: 25000000 INFO @ Sat, 06 Jul 2019 02:56:05: 31000000 INFO @ Sat, 06 Jul 2019 02:56:11: 32000000 INFO @ Sat, 06 Jul 2019 02:56:11: 26000000 INFO @ Sat, 06 Jul 2019 02:56:14: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:56:14: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:56:14: #1 total tags in treatment: 15387717 INFO @ Sat, 06 Jul 2019 02:56:14: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:56:14: #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 02:56:14: #1 tags after filtering in treatment: 9625108 INFO @ Sat, 06 Jul 2019 02:56:14: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 02:56:14: #1 finished! INFO @ Sat, 06 Jul 2019 02:56:14: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:56:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:56:15: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:56:15: 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 02:56:15: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:56:19: 27000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.20_peaks.narrowPeakcut: /home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.05_peaks.narrowPeak: No such file or directory : No such file or directory pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:56:26: 28000000 INFO @ Sat, 06 Jul 2019 02:56:34: 29000000 INFO @ Sat, 06 Jul 2019 02:56:41: 30000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 02:56:49: 31000000 INFO @ Sat, 06 Jul 2019 02:56:56: 32000000 INFO @ Sat, 06 Jul 2019 02:57:00: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:57:00: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:57:00: #1 total tags in treatment: 15387717 INFO @ Sat, 06 Jul 2019 02:57:00: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:57:00: #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 02:57:00: #1 tags after filtering in treatment: 9625108 INFO @ Sat, 06 Jul 2019 02:57:00: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 02:57:00: #1 finished! INFO @ Sat, 06 Jul 2019 02:57:00: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:57:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:57:01: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:57:01: 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 02:57:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.10_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/SRX4915182/SRX4915182.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915182/SRX4915182.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling