Job ID = 2011682 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:12:21 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 ) 2019-07-05T17:12:28 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 ) 2019-07-05T17:13:58 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 ) 2019-07-05T17:13:58 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 ) 2019-07-05T17:23:13 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 ) 2019-07-05T17:26:38 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 ) 2019-07-05T17:28:48 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 21,392,698 reads read : 42,785,396 reads written : 42,785,396 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: 00:31:58 21392698 reads; of these: 21392698 (100.00%) were paired; of these: 4601185 (21.51%) aligned concordantly 0 times 13984156 (65.37%) aligned concordantly exactly 1 time 2807357 (13.12%) aligned concordantly >1 times ---- 4601185 pairs aligned concordantly 0 times; of these: 2229749 (48.46%) aligned discordantly 1 time ---- 2371436 pairs aligned 0 times concordantly or discordantly; of these: 4742872 mates make up the pairs; of these: 3424834 (72.21%) aligned 0 times 364579 (7.69%) aligned exactly 1 time 953459 (20.10%) aligned >1 times 92.00% overall alignment rate Time searching: 00:31:58 Overall time: 00:31:58 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] 656002 / 18881993 = 0.0347 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 03:40:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.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 03:40:17: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:40:17: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:40:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.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 03:40:18: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:40:18: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:40:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.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 03:40:19: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:40:19: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:40:30: 1000000 INFO @ Sat, 06 Jul 2019 03:40:30: 1000000 INFO @ Sat, 06 Jul 2019 03:40:33: 1000000 INFO @ Sat, 06 Jul 2019 03:40:41: 2000000 INFO @ Sat, 06 Jul 2019 03:40:43: 2000000 INFO @ Sat, 06 Jul 2019 03:40:49: 2000000 INFO @ Sat, 06 Jul 2019 03:40:52: 3000000 INFO @ Sat, 06 Jul 2019 03:40:55: 3000000 INFO @ Sat, 06 Jul 2019 03:41:03: 4000000 INFO @ Sat, 06 Jul 2019 03:41:04: 3000000 INFO @ Sat, 06 Jul 2019 03:41:08: 4000000 INFO @ Sat, 06 Jul 2019 03:41:14: 5000000 INFO @ Sat, 06 Jul 2019 03:41:20: 4000000 INFO @ Sat, 06 Jul 2019 03:41:21: 5000000 INFO @ Sat, 06 Jul 2019 03:41:25: 6000000 INFO @ Sat, 06 Jul 2019 03:41:34: 6000000 INFO @ Sat, 06 Jul 2019 03:41:35: 5000000 INFO @ Sat, 06 Jul 2019 03:41:36: 7000000 INFO @ Sat, 06 Jul 2019 03:41:47: 7000000 INFO @ Sat, 06 Jul 2019 03:41:47: 8000000 INFO @ Sat, 06 Jul 2019 03:41:50: 6000000 INFO @ Sat, 06 Jul 2019 03:41:58: 9000000 INFO @ Sat, 06 Jul 2019 03:42:00: 8000000 INFO @ Sat, 06 Jul 2019 03:42:06: 7000000 INFO @ Sat, 06 Jul 2019 03:42:08: 10000000 INFO @ Sat, 06 Jul 2019 03:42:13: 9000000 INFO @ Sat, 06 Jul 2019 03:42:20: 11000000 INFO @ Sat, 06 Jul 2019 03:42:21: 8000000 INFO @ Sat, 06 Jul 2019 03:42:26: 10000000 INFO @ Sat, 06 Jul 2019 03:42:31: 12000000 INFO @ Sat, 06 Jul 2019 03:42:37: 9000000 INFO @ Sat, 06 Jul 2019 03:42:39: 11000000 INFO @ Sat, 06 Jul 2019 03:42:42: 13000000 INFO @ Sat, 06 Jul 2019 03:42:52: 10000000 INFO @ Sat, 06 Jul 2019 03:42:52: 12000000 INFO @ Sat, 06 Jul 2019 03:42:55: 14000000 INFO @ Sat, 06 Jul 2019 03:43:05: 13000000 INFO @ Sat, 06 Jul 2019 03:43:07: 11000000 INFO @ Sat, 06 Jul 2019 03:43:07: 15000000 INFO @ Sat, 06 Jul 2019 03:43:18: 16000000 INFO @ Sat, 06 Jul 2019 03:43:18: 14000000 INFO @ Sat, 06 Jul 2019 03:43:23: 12000000 INFO @ Sat, 06 Jul 2019 03:43:31: 17000000 INFO @ Sat, 06 Jul 2019 03:43:32: 15000000 INFO @ Sat, 06 Jul 2019 03:43:38: 13000000 INFO @ Sat, 06 Jul 2019 03:43:42: 18000000 INFO @ Sat, 06 Jul 2019 03:43:45: 16000000 INFO @ Sat, 06 Jul 2019 03:43:53: 14000000 INFO @ Sat, 06 Jul 2019 03:43:56: 19000000 INFO @ Sat, 06 Jul 2019 03:43:58: 17000000 INFO @ Sat, 06 Jul 2019 03:44:09: 15000000 INFO @ Sat, 06 Jul 2019 03:44:12: 18000000 INFO @ Sat, 06 Jul 2019 03:44:12: 20000000 INFO @ Sat, 06 Jul 2019 03:44:24: 16000000 INFO @ Sat, 06 Jul 2019 03:44:25: 19000000 INFO @ Sat, 06 Jul 2019 03:44:28: 21000000 INFO @ Sat, 06 Jul 2019 03:44:39: 20000000 INFO @ Sat, 06 Jul 2019 03:44:39: 17000000 INFO @ Sat, 06 Jul 2019 03:44:45: 22000000 INFO @ Sat, 06 Jul 2019 03:44:52: 21000000 INFO @ Sat, 06 Jul 2019 03:44:55: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:45:01: 23000000 INFO @ Sat, 06 Jul 2019 03:45:05: 22000000 INFO @ Sat, 06 Jul 2019 03:45:10: 19000000 INFO @ Sat, 06 Jul 2019 03:45:17: 24000000 INFO @ Sat, 06 Jul 2019 03:45:19: 23000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:45:25: 20000000 INFO @ Sat, 06 Jul 2019 03:45:32: 24000000 INFO @ Sat, 06 Jul 2019 03:45:34: 25000000 INFO @ Sat, 06 Jul 2019 03:45:40: 21000000 INFO @ Sat, 06 Jul 2019 03:45:45: 25000000 INFO @ Sat, 06 Jul 2019 03:45:50: 26000000 INFO @ Sat, 06 Jul 2019 03:45:55: 22000000 INFO @ Sat, 06 Jul 2019 03:45:58: 26000000 INFO @ Sat, 06 Jul 2019 03:46:06: 27000000 INFO @ Sat, 06 Jul 2019 03:46:11: 23000000 INFO @ Sat, 06 Jul 2019 03:46:11: 27000000 INFO @ Sat, 06 Jul 2019 03:46:22: 28000000 INFO @ Sat, 06 Jul 2019 03:46:24: 28000000 INFO @ Sat, 06 Jul 2019 03:46:26: 24000000 INFO @ Sat, 06 Jul 2019 03:46:38: 29000000 INFO @ Sat, 06 Jul 2019 03:46:39: 29000000 INFO @ Sat, 06 Jul 2019 03:46:42: 25000000 INFO @ Sat, 06 Jul 2019 03:46:51: 30000000 INFO @ Sat, 06 Jul 2019 03:46:55: 30000000 INFO @ Sat, 06 Jul 2019 03:46:57: 26000000 INFO @ Sat, 06 Jul 2019 03:47:04: 31000000 INFO @ Sat, 06 Jul 2019 03:47:11: 31000000 INFO @ Sat, 06 Jul 2019 03:47:12: 27000000 INFO @ Sat, 06 Jul 2019 03:47:17: 32000000 INFO @ Sat, 06 Jul 2019 03:47:28: 32000000 INFO @ Sat, 06 Jul 2019 03:47:28: 28000000 INFO @ Sat, 06 Jul 2019 03:47:30: 33000000 INFO @ Sat, 06 Jul 2019 03:47:43: 29000000 INFO @ Sat, 06 Jul 2019 03:47:43: 34000000 INFO @ Sat, 06 Jul 2019 03:47:44: 33000000 INFO @ Sat, 06 Jul 2019 03:47:56: 35000000 INFO @ Sat, 06 Jul 2019 03:47:58: 30000000 INFO @ Sat, 06 Jul 2019 03:48:00: 34000000 INFO @ Sat, 06 Jul 2019 03:48:10: 36000000 INFO @ Sat, 06 Jul 2019 03:48:13: 31000000 INFO @ Sat, 06 Jul 2019 03:48:16: 35000000 INFO @ Sat, 06 Jul 2019 03:48:23: 37000000 INFO @ Sat, 06 Jul 2019 03:48:29: 32000000 INFO @ Sat, 06 Jul 2019 03:48:32: 36000000 INFO @ Sat, 06 Jul 2019 03:48:36: 38000000 INFO @ Sat, 06 Jul 2019 03:48:37: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:48:37: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:48:37: #1 total tags in treatment: 16187652 INFO @ Sat, 06 Jul 2019 03:48:37: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:48:37: #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: 10631666 INFO @ Sat, 06 Jul 2019 03:48:37: #1 Redundant rate of treatment: 0.34 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 03:48:44: 33000000 INFO @ Sat, 06 Jul 2019 03:48:48: 37000000 INFO @ Sat, 06 Jul 2019 03:48:58: 34000000 INFO @ Sat, 06 Jul 2019 03:49:03: 38000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.05_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/SRX4560563/SRX4560563.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:49:04: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:49:04: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:49:04: #1 total tags in treatment: 16187652 INFO @ Sat, 06 Jul 2019 03:49:04: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:49:04: #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 03:49:04: #1 tags after filtering in treatment: 10631666 INFO @ Sat, 06 Jul 2019 03:49:04: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 03:49:04: #1 finished! INFO @ Sat, 06 Jul 2019 03:49:04: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:49:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:49:05: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:49:05: 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 03:49:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.20_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/SRX4560563/SRX4560563.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:49:13: 35000000 INFO @ Sat, 06 Jul 2019 03:49:26: 36000000 INFO @ Sat, 06 Jul 2019 03:49:40: 37000000 INFO @ Sat, 06 Jul 2019 03:49:54: 38000000 INFO @ Sat, 06 Jul 2019 03:49:55: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:49:55: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:49:55: #1 total tags in treatment: 16187652 INFO @ Sat, 06 Jul 2019 03:49:55: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:49:55: #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 03:49:55: #1 tags after filtering in treatment: 10631666 INFO @ Sat, 06 Jul 2019 03:49:55: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 03:49:55: #1 finished! INFO @ Sat, 06 Jul 2019 03:49:55: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:49:56: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:49:56: 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 03:49:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.10_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/SRX4560563/SRX4560563.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560563/SRX4560563.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling