Job ID = 2011687 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:27:22 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 ) 2019-07-05T17:27:22 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 ) spots read : 21,917,942 reads read : 43,835,884 reads written : 43,835,884 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: 00:33:16 21917942 reads; of these: 21917942 (100.00%) were paired; of these: 4617148 (21.07%) aligned concordantly 0 times 14411302 (65.75%) aligned concordantly exactly 1 time 2889492 (13.18%) aligned concordantly >1 times ---- 4617148 pairs aligned concordantly 0 times; of these: 2135084 (46.24%) aligned discordantly 1 time ---- 2482064 pairs aligned 0 times concordantly or discordantly; of these: 4964128 mates make up the pairs; of these: 3626574 (73.06%) aligned 0 times 426102 (8.58%) aligned exactly 1 time 911452 (18.36%) aligned >1 times 91.73% overall alignment rate Time searching: 00:33:16 Overall time: 00:33:16 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] 784804 / 19282283 = 0.0407 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 03:42:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.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 03:42:30: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:42:30: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:42:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.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 03:42:31: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:42:31: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:42:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.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 03:42:32: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:42:32: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:42:40: 1000000 INFO @ Sat, 06 Jul 2019 03:42:42: 1000000 INFO @ Sat, 06 Jul 2019 03:42:44: 1000000 INFO @ Sat, 06 Jul 2019 03:42:49: 2000000 INFO @ Sat, 06 Jul 2019 03:42:53: 2000000 INFO @ Sat, 06 Jul 2019 03:42:56: 2000000 INFO @ Sat, 06 Jul 2019 03:42:58: 3000000 INFO @ Sat, 06 Jul 2019 03:43:04: 3000000 INFO @ Sat, 06 Jul 2019 03:43:08: 4000000 INFO @ Sat, 06 Jul 2019 03:43:08: 3000000 INFO @ Sat, 06 Jul 2019 03:43:15: 4000000 INFO @ Sat, 06 Jul 2019 03:43:17: 5000000 INFO @ Sat, 06 Jul 2019 03:43:19: 4000000 INFO @ Sat, 06 Jul 2019 03:43:25: 5000000 INFO @ Sat, 06 Jul 2019 03:43:26: 6000000 INFO @ Sat, 06 Jul 2019 03:43:31: 5000000 INFO @ Sat, 06 Jul 2019 03:43:35: 7000000 INFO @ Sat, 06 Jul 2019 03:43:36: 6000000 INFO @ Sat, 06 Jul 2019 03:43:43: 6000000 INFO @ Sat, 06 Jul 2019 03:43:45: 8000000 INFO @ Sat, 06 Jul 2019 03:43:47: 7000000 INFO @ Sat, 06 Jul 2019 03:43:54: 7000000 INFO @ Sat, 06 Jul 2019 03:43:55: 9000000 INFO @ Sat, 06 Jul 2019 03:43:58: 8000000 INFO @ Sat, 06 Jul 2019 03:44:06: 8000000 INFO @ Sat, 06 Jul 2019 03:44:06: 10000000 INFO @ Sat, 06 Jul 2019 03:44:08: 9000000 INFO @ Sat, 06 Jul 2019 03:44:18: 9000000 INFO @ Sat, 06 Jul 2019 03:44:19: 10000000 INFO @ Sat, 06 Jul 2019 03:44:20: 11000000 INFO @ Sat, 06 Jul 2019 03:44:29: 12000000 INFO @ Sat, 06 Jul 2019 03:44:29: 10000000 INFO @ Sat, 06 Jul 2019 03:44:30: 11000000 INFO @ Sat, 06 Jul 2019 03:44:38: 13000000 INFO @ Sat, 06 Jul 2019 03:44:41: 11000000 INFO @ Sat, 06 Jul 2019 03:44:41: 12000000 INFO @ Sat, 06 Jul 2019 03:44:47: 14000000 INFO @ Sat, 06 Jul 2019 03:44:51: 13000000 INFO @ Sat, 06 Jul 2019 03:44:52: 12000000 INFO @ Sat, 06 Jul 2019 03:44:57: 15000000 INFO @ Sat, 06 Jul 2019 03:45:02: 14000000 INFO @ Sat, 06 Jul 2019 03:45:04: 13000000 INFO @ Sat, 06 Jul 2019 03:45:06: 16000000 INFO @ Sat, 06 Jul 2019 03:45:13: 15000000 INFO @ Sat, 06 Jul 2019 03:45:15: 14000000 INFO @ Sat, 06 Jul 2019 03:45:16: 17000000 INFO @ Sat, 06 Jul 2019 03:45:24: 16000000 INFO @ Sat, 06 Jul 2019 03:45:25: 18000000 INFO @ Sat, 06 Jul 2019 03:45:27: 15000000 INFO @ Sat, 06 Jul 2019 03:45:34: 19000000 INFO @ Sat, 06 Jul 2019 03:45:35: 17000000 INFO @ Sat, 06 Jul 2019 03:45:38: 16000000 INFO @ Sat, 06 Jul 2019 03:45:44: 20000000 INFO @ Sat, 06 Jul 2019 03:45:45: 18000000 INFO @ Sat, 06 Jul 2019 03:45:50: 17000000 INFO @ Sat, 06 Jul 2019 03:45:53: 21000000 INFO @ Sat, 06 Jul 2019 03:45:56: 19000000 INFO @ Sat, 06 Jul 2019 03:46:02: 18000000 INFO @ Sat, 06 Jul 2019 03:46:02: 22000000 INFO @ Sat, 06 Jul 2019 03:46:07: 20000000 INFO @ Sat, 06 Jul 2019 03:46:12: 23000000 INFO @ Sat, 06 Jul 2019 03:46:14: 19000000 INFO @ Sat, 06 Jul 2019 03:46:18: 21000000 INFO @ Sat, 06 Jul 2019 03:46:21: 24000000 INFO @ Sat, 06 Jul 2019 03:46:25: 20000000 INFO @ Sat, 06 Jul 2019 03:46:28: 22000000 INFO @ Sat, 06 Jul 2019 03:46:30: 25000000 INFO @ Sat, 06 Jul 2019 03:46:37: 21000000 INFO @ Sat, 06 Jul 2019 03:46:39: 23000000 INFO @ Sat, 06 Jul 2019 03:46:39: 26000000 INFO @ Sat, 06 Jul 2019 03:46:48: 22000000 INFO @ Sat, 06 Jul 2019 03:46:49: 27000000 INFO @ Sat, 06 Jul 2019 03:46:50: 24000000 INFO @ Sat, 06 Jul 2019 03:46:58: 28000000 INFO @ Sat, 06 Jul 2019 03:47:00: 23000000 INFO @ Sat, 06 Jul 2019 03:47:00: 25000000 INFO @ Sat, 06 Jul 2019 03:47:07: 29000000 INFO @ Sat, 06 Jul 2019 03:47:11: 26000000 INFO @ Sat, 06 Jul 2019 03:47:11: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:47:16: 30000000 INFO @ Sat, 06 Jul 2019 03:47:22: 27000000 INFO @ Sat, 06 Jul 2019 03:47:23: 25000000 INFO @ Sat, 06 Jul 2019 03:47:26: 31000000 INFO @ Sat, 06 Jul 2019 03:47:32: 28000000 INFO @ Sat, 06 Jul 2019 03:47:34: 26000000 INFO @ Sat, 06 Jul 2019 03:47:35: 32000000 INFO @ Sat, 06 Jul 2019 03:47:43: 29000000 INFO @ Sat, 06 Jul 2019 03:47:44: 33000000 INFO @ Sat, 06 Jul 2019 03:47:45: 27000000 INFO @ Sat, 06 Jul 2019 03:47:53: 34000000 INFO @ Sat, 06 Jul 2019 03:47:54: 30000000 INFO @ Sat, 06 Jul 2019 03:47:57: 28000000 INFO @ Sat, 06 Jul 2019 03:48:03: 35000000 INFO @ Sat, 06 Jul 2019 03:48:04: 31000000 INFO @ Sat, 06 Jul 2019 03:48:08: 29000000 INFO @ Sat, 06 Jul 2019 03:48:12: 36000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:48:15: 32000000 INFO @ Sat, 06 Jul 2019 03:48:19: 30000000 INFO @ Sat, 06 Jul 2019 03:48:21: 37000000 INFO @ Sat, 06 Jul 2019 03:48:26: 33000000 INFO @ Sat, 06 Jul 2019 03:48:30: 38000000 INFO @ Sat, 06 Jul 2019 03:48:31: 31000000 INFO @ Sat, 06 Jul 2019 03:48:36: 34000000 INFO @ Sat, 06 Jul 2019 03:48:36: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:48:36: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:48:36: #1 total tags in treatment: 16568205 INFO @ Sat, 06 Jul 2019 03:48:36: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:48:36: #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 03:48:37: #1 tags after filtering in treatment: 10611491 INFO @ Sat, 06 Jul 2019 03:48:37: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 03:48:37: #1 finished! INFO @ Sat, 06 Jul 2019 03:48:37: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:48:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:48:38: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:48:38: 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, 06 Jul 2019 03:48:38: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:48:42: 32000000 INFO @ Sat, 06 Jul 2019 03:48:47: 35000000 INFO @ Sat, 06 Jul 2019 03:48:53: 33000000 INFO @ Sat, 06 Jul 2019 03:48:57: 36000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.05_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/SRX4560568/SRX4560568.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:49:04: 34000000 INFO @ Sat, 06 Jul 2019 03:49:07: 37000000 INFO @ Sat, 06 Jul 2019 03:49:14: 35000000 INFO @ Sat, 06 Jul 2019 03:49:18: 38000000 INFO @ Sat, 06 Jul 2019 03:49:24: 36000000 INFO @ Sat, 06 Jul 2019 03:49:25: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:49:25: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:49:25: #1 total tags in treatment: 16568205 INFO @ Sat, 06 Jul 2019 03:49:25: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:49:25: #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 03:49:25: #1 tags after filtering in treatment: 10611491 INFO @ Sat, 06 Jul 2019 03:49:25: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 03:49:25: #1 finished! INFO @ Sat, 06 Jul 2019 03:49:25: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:49:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:49:26: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:49:26: 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, 06 Jul 2019 03:49:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.10_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/SRX4560568/SRX4560568.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:49:34: 37000000 INFO @ Sat, 06 Jul 2019 03:49:44: 38000000 INFO @ Sat, 06 Jul 2019 03:49:51: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:49:51: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:49:51: #1 total tags in treatment: 16568205 INFO @ Sat, 06 Jul 2019 03:49:51: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:49:51: #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 03:49:51: #1 tags after filtering in treatment: 10611491 INFO @ Sat, 06 Jul 2019 03:49:51: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 03:49:51: #1 finished! INFO @ Sat, 06 Jul 2019 03:49:51: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:49:52: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:49:52: 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 03:49:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.20_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/SRX4560568/SRX4560568.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560568/SRX4560568.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling