Job ID = 2011858 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:53:55 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 ) 2019-07-05T17:56:45 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 ) 2019-07-05T17:57:46 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 ) 2019-07-05T17:57:46 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 ) 2019-07-05T17:57:46 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 : 29,144,260 reads read : 58,288,520 reads written : 58,288,520 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: 00:22:36 29144260 reads; of these: 29144260 (100.00%) were paired; of these: 1545307 (5.30%) aligned concordantly 0 times 21719343 (74.52%) aligned concordantly exactly 1 time 5879610 (20.17%) aligned concordantly >1 times ---- 1545307 pairs aligned concordantly 0 times; of these: 338149 (21.88%) aligned discordantly 1 time ---- 1207158 pairs aligned 0 times concordantly or discordantly; of these: 2414316 mates make up the pairs; of these: 1770821 (73.35%) aligned 0 times 342487 (14.19%) aligned exactly 1 time 301008 (12.47%) aligned >1 times 96.96% overall alignment rate Time searching: 00:22:36 Overall time: 00:22:36 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] 2524093 / 27652924 = 0.0913 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 03:45:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.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 03:45:38: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:45:38: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:45:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.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 03:45:39: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:45:39: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.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 03:45:40: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:45:40: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:45:48: 1000000 INFO @ Sat, 06 Jul 2019 03:45:49: 1000000 INFO @ Sat, 06 Jul 2019 03:45:50: 1000000 INFO @ Sat, 06 Jul 2019 03:45:57: 2000000 INFO @ Sat, 06 Jul 2019 03:45:58: 2000000 INFO @ Sat, 06 Jul 2019 03:45:59: 2000000 INFO @ Sat, 06 Jul 2019 03:46:08: 3000000 INFO @ Sat, 06 Jul 2019 03:46:09: 3000000 INFO @ Sat, 06 Jul 2019 03:46:10: 3000000 INFO @ Sat, 06 Jul 2019 03:46:19: 4000000 INFO @ Sat, 06 Jul 2019 03:46:19: 4000000 INFO @ Sat, 06 Jul 2019 03:46:20: 4000000 INFO @ Sat, 06 Jul 2019 03:46:27: 5000000 INFO @ Sat, 06 Jul 2019 03:46:29: 5000000 INFO @ Sat, 06 Jul 2019 03:46:29: 5000000 INFO @ Sat, 06 Jul 2019 03:46:35: 6000000 INFO @ Sat, 06 Jul 2019 03:46:36: 6000000 INFO @ Sat, 06 Jul 2019 03:46:39: 6000000 INFO @ Sat, 06 Jul 2019 03:46:43: 7000000 INFO @ Sat, 06 Jul 2019 03:46:44: 7000000 INFO @ Sat, 06 Jul 2019 03:46:48: 7000000 INFO @ Sat, 06 Jul 2019 03:46:50: 8000000 INFO @ Sat, 06 Jul 2019 03:46:52: 8000000 INFO @ Sat, 06 Jul 2019 03:46:58: 8000000 INFO @ Sat, 06 Jul 2019 03:46:58: 9000000 INFO @ Sat, 06 Jul 2019 03:47:00: 9000000 INFO @ Sat, 06 Jul 2019 03:47:07: 10000000 INFO @ Sat, 06 Jul 2019 03:47:07: 9000000 INFO @ Sat, 06 Jul 2019 03:47:08: 10000000 INFO @ Sat, 06 Jul 2019 03:47:14: 11000000 INFO @ Sat, 06 Jul 2019 03:47:16: 11000000 INFO @ Sat, 06 Jul 2019 03:47:16: 10000000 INFO @ Sat, 06 Jul 2019 03:47:22: 12000000 INFO @ Sat, 06 Jul 2019 03:47:24: 12000000 INFO @ Sat, 06 Jul 2019 03:47:26: 11000000 INFO @ Sat, 06 Jul 2019 03:47:30: 13000000 INFO @ Sat, 06 Jul 2019 03:47:31: 13000000 INFO @ Sat, 06 Jul 2019 03:47:35: 12000000 INFO @ Sat, 06 Jul 2019 03:47:37: 14000000 INFO @ Sat, 06 Jul 2019 03:47:39: 14000000 INFO @ Sat, 06 Jul 2019 03:47:44: 13000000 INFO @ Sat, 06 Jul 2019 03:47:45: 15000000 INFO @ Sat, 06 Jul 2019 03:47:46: 15000000 INFO @ Sat, 06 Jul 2019 03:47:52: 16000000 INFO @ Sat, 06 Jul 2019 03:47:54: 16000000 INFO @ Sat, 06 Jul 2019 03:47:54: 14000000 INFO @ Sat, 06 Jul 2019 03:48:00: 17000000 INFO @ Sat, 06 Jul 2019 03:48:02: 17000000 INFO @ Sat, 06 Jul 2019 03:48:03: 15000000 INFO @ Sat, 06 Jul 2019 03:48:08: 18000000 INFO @ Sat, 06 Jul 2019 03:48:09: 18000000 INFO @ Sat, 06 Jul 2019 03:48:13: 16000000 INFO @ Sat, 06 Jul 2019 03:48:15: 19000000 INFO @ Sat, 06 Jul 2019 03:48:16: 19000000 INFO @ Sat, 06 Jul 2019 03:48:22: 20000000 INFO @ Sat, 06 Jul 2019 03:48:22: 17000000 INFO @ Sat, 06 Jul 2019 03:48:23: 20000000 INFO @ Sat, 06 Jul 2019 03:48:29: 21000000 INFO @ Sat, 06 Jul 2019 03:48:30: 21000000 INFO @ Sat, 06 Jul 2019 03:48:31: 18000000 INFO @ Sat, 06 Jul 2019 03:48:36: 22000000 INFO @ Sat, 06 Jul 2019 03:48:37: 22000000 INFO @ Sat, 06 Jul 2019 03:48:41: 19000000 INFO @ Sat, 06 Jul 2019 03:48:43: 23000000 INFO @ Sat, 06 Jul 2019 03:48:44: 23000000 INFO @ Sat, 06 Jul 2019 03:48:50: 24000000 INFO @ Sat, 06 Jul 2019 03:48:50: 20000000 INFO @ Sat, 06 Jul 2019 03:48:51: 24000000 INFO @ Sat, 06 Jul 2019 03:48:57: 25000000 INFO @ Sat, 06 Jul 2019 03:48:58: 25000000 INFO @ Sat, 06 Jul 2019 03:49:00: 21000000 INFO @ Sat, 06 Jul 2019 03:49:04: 26000000 INFO @ Sat, 06 Jul 2019 03:49:05: 26000000 INFO @ Sat, 06 Jul 2019 03:49:09: 22000000 INFO @ Sat, 06 Jul 2019 03:49:11: 27000000 INFO @ Sat, 06 Jul 2019 03:49:13: 27000000 INFO @ Sat, 06 Jul 2019 03:49:18: 28000000 INFO @ Sat, 06 Jul 2019 03:49:19: 23000000 INFO @ Sat, 06 Jul 2019 03:49:20: 28000000 INFO @ Sat, 06 Jul 2019 03:49:25: 29000000 INFO @ Sat, 06 Jul 2019 03:49:27: 29000000 INFO @ Sat, 06 Jul 2019 03:49:28: 24000000 INFO @ Sat, 06 Jul 2019 03:49:32: 30000000 INFO @ Sat, 06 Jul 2019 03:49:34: 30000000 INFO @ Sat, 06 Jul 2019 03:49:38: 25000000 INFO @ Sat, 06 Jul 2019 03:49:39: 31000000 INFO @ Sat, 06 Jul 2019 03:49:41: 31000000 INFO @ Sat, 06 Jul 2019 03:49:46: 32000000 INFO @ Sat, 06 Jul 2019 03:49:47: 26000000 INFO @ Sat, 06 Jul 2019 03:49:48: 32000000 INFO @ Sat, 06 Jul 2019 03:49:53: 33000000 INFO @ Sat, 06 Jul 2019 03:49:54: 33000000 INFO @ Sat, 06 Jul 2019 03:49:57: 27000000 INFO @ Sat, 06 Jul 2019 03:50:00: 34000000 INFO @ Sat, 06 Jul 2019 03:50:01: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:50:06: 28000000 INFO @ Sat, 06 Jul 2019 03:50:07: 35000000 INFO @ Sat, 06 Jul 2019 03:50:08: 35000000 INFO @ Sat, 06 Jul 2019 03:50:14: 36000000 INFO @ Sat, 06 Jul 2019 03:50:15: 36000000 INFO @ Sat, 06 Jul 2019 03:50:16: 29000000 INFO @ Sat, 06 Jul 2019 03:50:21: 37000000 INFO @ Sat, 06 Jul 2019 03:50:22: 37000000 INFO @ Sat, 06 Jul 2019 03:50:25: 30000000 INFO @ Sat, 06 Jul 2019 03:50:27: 38000000 INFO @ Sat, 06 Jul 2019 03:50:29: 38000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:50:34: 39000000 INFO @ Sat, 06 Jul 2019 03:50:35: 31000000 INFO @ Sat, 06 Jul 2019 03:50:36: 39000000 INFO @ Sat, 06 Jul 2019 03:50:41: 40000000 INFO @ Sat, 06 Jul 2019 03:50:43: 40000000 INFO @ Sat, 06 Jul 2019 03:50:44: 32000000 INFO @ Sat, 06 Jul 2019 03:50:48: 41000000 INFO @ Sat, 06 Jul 2019 03:50:50: 41000000 INFO @ Sat, 06 Jul 2019 03:50:54: 33000000 INFO @ Sat, 06 Jul 2019 03:50:55: 42000000 INFO @ Sat, 06 Jul 2019 03:50:57: 42000000 INFO @ Sat, 06 Jul 2019 03:51:02: 43000000 INFO @ Sat, 06 Jul 2019 03:51:03: 34000000 INFO @ Sat, 06 Jul 2019 03:51:04: 43000000 INFO @ Sat, 06 Jul 2019 03:51:09: 44000000 INFO @ Sat, 06 Jul 2019 03:51:11: 44000000 INFO @ Sat, 06 Jul 2019 03:51:13: 35000000 INFO @ Sat, 06 Jul 2019 03:51:16: 45000000 INFO @ Sat, 06 Jul 2019 03:51:17: 45000000 INFO @ Sat, 06 Jul 2019 03:51:22: 36000000 INFO @ Sat, 06 Jul 2019 03:51:23: 46000000 INFO @ Sat, 06 Jul 2019 03:51:24: 46000000 INFO @ Sat, 06 Jul 2019 03:51:30: 47000000 INFO @ Sat, 06 Jul 2019 03:51:31: 47000000 INFO @ Sat, 06 Jul 2019 03:51:31: 37000000 INFO @ Sat, 06 Jul 2019 03:51:37: 48000000 INFO @ Sat, 06 Jul 2019 03:51:38: 48000000 INFO @ Sat, 06 Jul 2019 03:51:41: 38000000 INFO @ Sat, 06 Jul 2019 03:51:43: 49000000 INFO @ Sat, 06 Jul 2019 03:51:45: 49000000 INFO @ Sat, 06 Jul 2019 03:51:50: 39000000 INFO @ Sat, 06 Jul 2019 03:51:50: 50000000 INFO @ Sat, 06 Jul 2019 03:51:52: 50000000 INFO @ Sat, 06 Jul 2019 03:51:57: 51000000 INFO @ Sat, 06 Jul 2019 03:51:59: 40000000 INFO @ Sat, 06 Jul 2019 03:51:59: 51000000 INFO @ Sat, 06 Jul 2019 03:52:01: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:52:01: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:52:01: #1 total tags in treatment: 25075958 INFO @ Sat, 06 Jul 2019 03:52:01: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:52:01: #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 03:52:01: #1 tags after filtering in treatment: 14083402 INFO @ Sat, 06 Jul 2019 03:52:01: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 06 Jul 2019 03:52:01: #1 finished! INFO @ Sat, 06 Jul 2019 03:52:01: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:52:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:52:02: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:52:02: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:52:02: #1 total tags in treatment: 25075958 INFO @ Sat, 06 Jul 2019 03:52:02: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:52:02: #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 03:52:02: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:52:02: 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 03:52:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.05_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/SRX5170655/SRX5170655.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:52:03: #1 tags after filtering in treatment: 14083402 INFO @ Sat, 06 Jul 2019 03:52:03: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 06 Jul 2019 03:52:03: #1 finished! INFO @ Sat, 06 Jul 2019 03:52:03: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:52:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:52:04: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:52:04: 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 03:52:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.20_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/SRX5170655/SRX5170655.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:52:08: 41000000 INFO @ Sat, 06 Jul 2019 03:52:16: 42000000 INFO @ Sat, 06 Jul 2019 03:52:25: 43000000 INFO @ Sat, 06 Jul 2019 03:52:34: 44000000 INFO @ Sat, 06 Jul 2019 03:52:43: 45000000 INFO @ Sat, 06 Jul 2019 03:52:51: 46000000 INFO @ Sat, 06 Jul 2019 03:53:00: 47000000 INFO @ Sat, 06 Jul 2019 03:53:09: 48000000 INFO @ Sat, 06 Jul 2019 03:53:18: 49000000 INFO @ Sat, 06 Jul 2019 03:53:26: 50000000 INFO @ Sat, 06 Jul 2019 03:53:35: 51000000 INFO @ Sat, 06 Jul 2019 03:53:39: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:53:39: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:53:39: #1 total tags in treatment: 25075958 INFO @ Sat, 06 Jul 2019 03:53:39: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:53:39: #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 03:53:40: #1 tags after filtering in treatment: 14083402 INFO @ Sat, 06 Jul 2019 03:53:40: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 06 Jul 2019 03:53:40: #1 finished! INFO @ Sat, 06 Jul 2019 03:53:40: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:53:41: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:53:41: 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 03:53:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.10_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/SRX5170655/SRX5170655.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170655/SRX5170655.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling