Job ID = 2011859 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:52:02 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 ) 2019-07-05T17:54:16 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 ) 2019-07-05T17:56:07 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 ) 2019-07-05T18:06:10 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 : 34,800,170 reads read : 69,600,340 reads written : 69,600,340 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: 00:27:28 34800170 reads; of these: 34800170 (100.00%) were paired; of these: 1745375 (5.02%) aligned concordantly 0 times 27842588 (80.01%) aligned concordantly exactly 1 time 5212207 (14.98%) aligned concordantly >1 times ---- 1745375 pairs aligned concordantly 0 times; of these: 139880 (8.01%) aligned discordantly 1 time ---- 1605495 pairs aligned 0 times concordantly or discordantly; of these: 3210990 mates make up the pairs; of these: 2721734 (84.76%) aligned 0 times 351108 (10.93%) aligned exactly 1 time 138148 (4.30%) aligned >1 times 96.09% overall alignment rate Time searching: 00:27:28 Overall time: 00:27:28 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] 10390564 / 33132884 = 0.3136 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 03:54:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.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 03:54:28: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:54:28: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:54:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.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 03:54:29: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:54:29: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:54:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.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 03:54:30: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:54:30: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:54:35: 1000000 INFO @ Sat, 06 Jul 2019 03:54:36: 1000000 INFO @ Sat, 06 Jul 2019 03:54:37: 1000000 INFO @ Sat, 06 Jul 2019 03:54:41: 2000000 INFO @ Sat, 06 Jul 2019 03:54:44: 2000000 INFO @ Sat, 06 Jul 2019 03:54:47: 2000000 INFO @ Sat, 06 Jul 2019 03:54:48: 3000000 INFO @ Sat, 06 Jul 2019 03:54:53: 3000000 INFO @ Sat, 06 Jul 2019 03:54:54: 4000000 INFO @ Sat, 06 Jul 2019 03:54:58: 3000000 INFO @ Sat, 06 Jul 2019 03:55:00: 5000000 INFO @ Sat, 06 Jul 2019 03:55:04: 4000000 INFO @ Sat, 06 Jul 2019 03:55:06: 6000000 INFO @ Sat, 06 Jul 2019 03:55:08: 4000000 INFO @ Sat, 06 Jul 2019 03:55:12: 7000000 INFO @ Sat, 06 Jul 2019 03:55:13: 5000000 INFO @ Sat, 06 Jul 2019 03:55:18: 8000000 INFO @ Sat, 06 Jul 2019 03:55:18: 5000000 INFO @ Sat, 06 Jul 2019 03:55:24: 6000000 INFO @ Sat, 06 Jul 2019 03:55:24: 9000000 INFO @ Sat, 06 Jul 2019 03:55:29: 6000000 INFO @ Sat, 06 Jul 2019 03:55:31: 10000000 INFO @ Sat, 06 Jul 2019 03:55:34: 7000000 INFO @ Sat, 06 Jul 2019 03:55:37: 11000000 INFO @ Sat, 06 Jul 2019 03:55:40: 7000000 INFO @ Sat, 06 Jul 2019 03:55:43: 12000000 INFO @ Sat, 06 Jul 2019 03:55:45: 8000000 INFO @ Sat, 06 Jul 2019 03:55:49: 13000000 INFO @ Sat, 06 Jul 2019 03:55:50: 8000000 INFO @ Sat, 06 Jul 2019 03:55:55: 14000000 INFO @ Sat, 06 Jul 2019 03:55:55: 9000000 INFO @ Sat, 06 Jul 2019 03:56:00: 9000000 INFO @ Sat, 06 Jul 2019 03:56:01: 15000000 INFO @ Sat, 06 Jul 2019 03:56:05: 10000000 INFO @ Sat, 06 Jul 2019 03:56:07: 16000000 INFO @ Sat, 06 Jul 2019 03:56:11: 10000000 INFO @ Sat, 06 Jul 2019 03:56:13: 17000000 INFO @ Sat, 06 Jul 2019 03:56:16: 11000000 INFO @ Sat, 06 Jul 2019 03:56:19: 18000000 INFO @ Sat, 06 Jul 2019 03:56:21: 11000000 INFO @ Sat, 06 Jul 2019 03:56:25: 19000000 INFO @ Sat, 06 Jul 2019 03:56:26: 12000000 INFO @ Sat, 06 Jul 2019 03:56:31: 20000000 INFO @ Sat, 06 Jul 2019 03:56:31: 12000000 INFO @ Sat, 06 Jul 2019 03:56:36: 13000000 INFO @ Sat, 06 Jul 2019 03:56:36: 21000000 INFO @ Sat, 06 Jul 2019 03:56:41: 13000000 INFO @ Sat, 06 Jul 2019 03:56:42: 22000000 INFO @ Sat, 06 Jul 2019 03:56:46: 14000000 INFO @ Sat, 06 Jul 2019 03:56:48: 23000000 INFO @ Sat, 06 Jul 2019 03:56:51: 14000000 INFO @ Sat, 06 Jul 2019 03:56:54: 24000000 INFO @ Sat, 06 Jul 2019 03:56:56: 15000000 INFO @ Sat, 06 Jul 2019 03:57:00: 25000000 INFO @ Sat, 06 Jul 2019 03:57:01: 15000000 INFO @ Sat, 06 Jul 2019 03:57:06: 16000000 INFO @ Sat, 06 Jul 2019 03:57:06: 26000000 INFO @ Sat, 06 Jul 2019 03:57:11: 16000000 INFO @ Sat, 06 Jul 2019 03:57:12: 27000000 INFO @ Sat, 06 Jul 2019 03:57:16: 17000000 INFO @ Sat, 06 Jul 2019 03:57:18: 28000000 INFO @ Sat, 06 Jul 2019 03:57:21: 17000000 INFO @ Sat, 06 Jul 2019 03:57:24: 29000000 INFO @ Sat, 06 Jul 2019 03:57:26: 18000000 INFO @ Sat, 06 Jul 2019 03:57:30: 30000000 INFO @ Sat, 06 Jul 2019 03:57:31: 18000000 INFO @ Sat, 06 Jul 2019 03:57:36: 19000000 INFO @ Sat, 06 Jul 2019 03:57:36: 31000000 INFO @ Sat, 06 Jul 2019 03:57:41: 19000000 INFO @ Sat, 06 Jul 2019 03:57:42: 32000000 INFO @ Sat, 06 Jul 2019 03:57:46: 20000000 INFO @ Sat, 06 Jul 2019 03:57:48: 33000000 INFO @ Sat, 06 Jul 2019 03:57:51: 20000000 INFO @ Sat, 06 Jul 2019 03:57:54: 34000000 INFO @ Sat, 06 Jul 2019 03:57:55: 21000000 INFO @ Sat, 06 Jul 2019 03:58:00: 35000000 INFO @ Sat, 06 Jul 2019 03:58:00: 21000000 INFO @ Sat, 06 Jul 2019 03:58:05: 22000000 INFO @ Sat, 06 Jul 2019 03:58:06: 36000000 INFO @ Sat, 06 Jul 2019 03:58:10: 22000000 INFO @ Sat, 06 Jul 2019 03:58:11: 37000000 INFO @ Sat, 06 Jul 2019 03:58:15: 23000000 INFO @ Sat, 06 Jul 2019 03:58:17: 38000000 INFO @ Sat, 06 Jul 2019 03:58:20: 23000000 INFO @ Sat, 06 Jul 2019 03:58:23: 39000000 INFO @ Sat, 06 Jul 2019 03:58:25: 24000000 INFO @ Sat, 06 Jul 2019 03:58:29: 40000000 INFO @ Sat, 06 Jul 2019 03:58:30: 24000000 INFO @ Sat, 06 Jul 2019 03:58:35: 25000000 INFO @ Sat, 06 Jul 2019 03:58:35: 41000000 INFO @ Sat, 06 Jul 2019 03:58:40: 25000000 INFO @ Sat, 06 Jul 2019 03:58:41: 42000000 INFO @ Sat, 06 Jul 2019 03:58:44: 26000000 INFO @ Sat, 06 Jul 2019 03:58:47: 43000000 INFO @ Sat, 06 Jul 2019 03:58:49: 26000000 INFO @ Sat, 06 Jul 2019 03:58:53: 44000000 INFO @ Sat, 06 Jul 2019 03:58:54: 27000000 INFO @ Sat, 06 Jul 2019 03:58:59: 45000000 INFO @ Sat, 06 Jul 2019 03:58:59: 27000000 INFO @ Sat, 06 Jul 2019 03:59:04: 28000000 INFO @ Sat, 06 Jul 2019 03:59:05: 46000000 INFO @ Sat, 06 Jul 2019 03:59:06: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:59:06: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:59:06: #1 total tags in treatment: 22680831 INFO @ Sat, 06 Jul 2019 03:59:06: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:59:06: #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 03:59:06: #1 tags after filtering in treatment: 11094348 INFO @ Sat, 06 Jul 2019 03:59:06: #1 Redundant rate of treatment: 0.51 INFO @ Sat, 06 Jul 2019 03:59:06: #1 finished! INFO @ Sat, 06 Jul 2019 03:59:06: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:59:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:59:07: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:59:07: 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 03:59:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.10_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/SRX5170656/SRX5170656.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:59:09: 28000000 INFO @ Sat, 06 Jul 2019 03:59:14: 29000000 INFO @ Sat, 06 Jul 2019 03:59:19: 29000000 INFO @ Sat, 06 Jul 2019 03:59:24: 30000000 INFO @ Sat, 06 Jul 2019 03:59:29: 30000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:59:33: 31000000 INFO @ Sat, 06 Jul 2019 03:59:39: 31000000 INFO @ Sat, 06 Jul 2019 03:59:43: 32000000 INFO @ Sat, 06 Jul 2019 03:59:48: 32000000 INFO @ Sat, 06 Jul 2019 03:59:53: 33000000 INFO @ Sat, 06 Jul 2019 03:59:58: 33000000 INFO @ Sat, 06 Jul 2019 04:00:03: 34000000 INFO @ Sat, 06 Jul 2019 04:00:08: 34000000 INFO @ Sat, 06 Jul 2019 04:00:13: 35000000 INFO @ Sat, 06 Jul 2019 04:00:18: 35000000 INFO @ Sat, 06 Jul 2019 04:00:22: 36000000 INFO @ Sat, 06 Jul 2019 04:00:27: 36000000 INFO @ Sat, 06 Jul 2019 04:00:32: 37000000 INFO @ Sat, 06 Jul 2019 04:00:37: 37000000 INFO @ Sat, 06 Jul 2019 04:00:42: 38000000 INFO @ Sat, 06 Jul 2019 04:00:47: 38000000 INFO @ Sat, 06 Jul 2019 04:00:51: 39000000 INFO @ Sat, 06 Jul 2019 04:00:56: 39000000 INFO @ Sat, 06 Jul 2019 04:01:01: 40000000 INFO @ Sat, 06 Jul 2019 04:01:06: 40000000 INFO @ Sat, 06 Jul 2019 04:01:10: 41000000 INFO @ Sat, 06 Jul 2019 04:01:15: 41000000 INFO @ Sat, 06 Jul 2019 04:01:20: 42000000 INFO @ Sat, 06 Jul 2019 04:01:25: 42000000 INFO @ Sat, 06 Jul 2019 04:01:29: 43000000 INFO @ Sat, 06 Jul 2019 04:01:34: 43000000 INFO @ Sat, 06 Jul 2019 04:01:39: 44000000 INFO @ Sat, 06 Jul 2019 04:01:44: 44000000 INFO @ Sat, 06 Jul 2019 04:01:49: 45000000 INFO @ Sat, 06 Jul 2019 04:01:54: 45000000 INFO @ Sat, 06 Jul 2019 04:01:58: 46000000 INFO @ Sat, 06 Jul 2019 04:01:59: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 04:01:59: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 04:01:59: #1 total tags in treatment: 22680831 INFO @ Sat, 06 Jul 2019 04:01:59: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:01:59: #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 04:02:00: #1 tags after filtering in treatment: 11094348 INFO @ Sat, 06 Jul 2019 04:02:00: #1 Redundant rate of treatment: 0.51 INFO @ Sat, 06 Jul 2019 04:02:00: #1 finished! INFO @ Sat, 06 Jul 2019 04:02:00: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:02:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:02:01: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:02:01: 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 04:02:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.20_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/SRX5170656/SRX5170656.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 04:02:02: 46000000 INFO @ Sat, 06 Jul 2019 04:02:03: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 04:02:03: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 04:02:03: #1 total tags in treatment: 22680831 INFO @ Sat, 06 Jul 2019 04:02:03: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:02:03: #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 04:02:04: #1 tags after filtering in treatment: 11094348 INFO @ Sat, 06 Jul 2019 04:02:04: #1 Redundant rate of treatment: 0.51 INFO @ Sat, 06 Jul 2019 04:02:04: #1 finished! INFO @ Sat, 06 Jul 2019 04:02:04: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:02:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:02:05: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:02:05: 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 04:02:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.05_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/SRX5170656/SRX5170656.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170656/SRX5170656.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling