Job ID = 1308045 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:36:14 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T13:36:14 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra76/SRR/008340/SRR8540830' 2019-06-03T13:36:14 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8540830' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T13:36:14 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T14:06:15 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 ) 2019-06-03T14:13:52 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 : 53,659,973 reads read : 107,319,946 reads written : 53,659,973 reads 0-length : 53,659,973 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:32:26 53659973 reads; of these: 53659973 (100.00%) were unpaired; of these: 1833339 (3.42%) aligned 0 times 35206533 (65.61%) aligned exactly 1 time 16620101 (30.97%) aligned >1 times 96.58% overall alignment rate Time searching: 00:32:26 Overall time: 00:32:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 8572652 / 51826634 = 0.1654 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 @ Tue, 04 Jun 2019 00:15:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 04 Jun 2019 00:15:59: #1 read tag files... INFO @ Tue, 04 Jun 2019 00:15:59: #1 read treatment tags... INFO @ Tue, 04 Jun 2019 00:15:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 04 Jun 2019 00:15:59: #1 read tag files... INFO @ Tue, 04 Jun 2019 00:15:59: #1 read treatment tags... INFO @ Tue, 04 Jun 2019 00:15:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 04 Jun 2019 00:15:59: #1 read tag files... INFO @ Tue, 04 Jun 2019 00:15:59: #1 read treatment tags... INFO @ Tue, 04 Jun 2019 00:16:09: 1000000 INFO @ Tue, 04 Jun 2019 00:16:10: 1000000 INFO @ Tue, 04 Jun 2019 00:16:11: 1000000 INFO @ Tue, 04 Jun 2019 00:16:18: 2000000 INFO @ Tue, 04 Jun 2019 00:16:20: 2000000 INFO @ Tue, 04 Jun 2019 00:16:22: 2000000 INFO @ Tue, 04 Jun 2019 00:16:27: 3000000 INFO @ Tue, 04 Jun 2019 00:16:29: 3000000 INFO @ Tue, 04 Jun 2019 00:16:33: 3000000 INFO @ Tue, 04 Jun 2019 00:16:36: 4000000 INFO @ Tue, 04 Jun 2019 00:16:39: 4000000 INFO @ Tue, 04 Jun 2019 00:16:43: 4000000 INFO @ Tue, 04 Jun 2019 00:16:44: 5000000 INFO @ Tue, 04 Jun 2019 00:16:48: 5000000 INFO @ Tue, 04 Jun 2019 00:16:53: 6000000 INFO @ Tue, 04 Jun 2019 00:16:54: 5000000 INFO @ Tue, 04 Jun 2019 00:16:57: 6000000 INFO @ Tue, 04 Jun 2019 00:17:02: 7000000 INFO @ Tue, 04 Jun 2019 00:17:05: 6000000 INFO @ Tue, 04 Jun 2019 00:17:06: 7000000 INFO @ Tue, 04 Jun 2019 00:17:10: 8000000 INFO @ Tue, 04 Jun 2019 00:17:15: 7000000 INFO @ Tue, 04 Jun 2019 00:17:16: 8000000 INFO @ Tue, 04 Jun 2019 00:17:19: 9000000 INFO @ Tue, 04 Jun 2019 00:17:24: 9000000 INFO @ Tue, 04 Jun 2019 00:17:26: 8000000 INFO @ Tue, 04 Jun 2019 00:17:28: 10000000 INFO @ Tue, 04 Jun 2019 00:17:34: 10000000 INFO @ Tue, 04 Jun 2019 00:17:37: 9000000 INFO @ Tue, 04 Jun 2019 00:17:37: 11000000 INFO @ Tue, 04 Jun 2019 00:17:45: 11000000 INFO @ Tue, 04 Jun 2019 00:17:46: 12000000 INFO @ Tue, 04 Jun 2019 00:17:48: 10000000 INFO @ Tue, 04 Jun 2019 00:17:54: 12000000 INFO @ Tue, 04 Jun 2019 00:17:55: 13000000 INFO @ Tue, 04 Jun 2019 00:17:58: 11000000 INFO @ Tue, 04 Jun 2019 00:18:03: 13000000 INFO @ Tue, 04 Jun 2019 00:18:03: 14000000 INFO @ Tue, 04 Jun 2019 00:18:09: 12000000 INFO @ Tue, 04 Jun 2019 00:18:12: 15000000 INFO @ Tue, 04 Jun 2019 00:18:12: 14000000 INFO @ Tue, 04 Jun 2019 00:18:20: 13000000 INFO @ Tue, 04 Jun 2019 00:18:21: 16000000 INFO @ Tue, 04 Jun 2019 00:18:21: 15000000 INFO @ Tue, 04 Jun 2019 00:18:30: 17000000 INFO @ Tue, 04 Jun 2019 00:18:30: 14000000 INFO @ Tue, 04 Jun 2019 00:18:31: 16000000 INFO @ Tue, 04 Jun 2019 00:18:38: 18000000 INFO @ Tue, 04 Jun 2019 00:18:40: 17000000 INFO @ Tue, 04 Jun 2019 00:18:41: 15000000 INFO @ Tue, 04 Jun 2019 00:18:47: 19000000 INFO @ Tue, 04 Jun 2019 00:18:49: 18000000 INFO @ Tue, 04 Jun 2019 00:18:52: 16000000 INFO @ Tue, 04 Jun 2019 00:18:56: 20000000 INFO @ Tue, 04 Jun 2019 00:18:58: 19000000 INFO @ Tue, 04 Jun 2019 00:19:03: 17000000 INFO @ Tue, 04 Jun 2019 00:19:05: 21000000 INFO @ Tue, 04 Jun 2019 00:19:09: 20000000 INFO @ Tue, 04 Jun 2019 00:19:13: 18000000 INFO @ Tue, 04 Jun 2019 00:19:13: 22000000 INFO @ Tue, 04 Jun 2019 00:19:18: 21000000 INFO @ Tue, 04 Jun 2019 00:19:22: 23000000 INFO @ Tue, 04 Jun 2019 00:19:24: 19000000 INFO @ Tue, 04 Jun 2019 00:19:27: 22000000 INFO @ Tue, 04 Jun 2019 00:19:31: 24000000 INFO @ Tue, 04 Jun 2019 00:19:34: 20000000 INFO @ Tue, 04 Jun 2019 00:19:36: 23000000 INFO @ Tue, 04 Jun 2019 00:19:39: 25000000 INFO @ Tue, 04 Jun 2019 00:19:45: 21000000 INFO @ Tue, 04 Jun 2019 00:19:45: 24000000 INFO @ Tue, 04 Jun 2019 00:19:48: 26000000 INFO @ Tue, 04 Jun 2019 00:19:54: 25000000 INFO @ Tue, 04 Jun 2019 00:19:56: 22000000 INFO @ Tue, 04 Jun 2019 00:19:57: 27000000 INFO @ Tue, 04 Jun 2019 00:20:03: 26000000 INFO @ Tue, 04 Jun 2019 00:20:05: 28000000 INFO @ Tue, 04 Jun 2019 00:20:06: 23000000 INFO @ Tue, 04 Jun 2019 00:20:12: 27000000 INFO @ Tue, 04 Jun 2019 00:20:14: 29000000 INFO @ Tue, 04 Jun 2019 00:20:17: 24000000 INFO @ Tue, 04 Jun 2019 00:20:21: 28000000 INFO @ Tue, 04 Jun 2019 00:20:23: 30000000 INFO @ Tue, 04 Jun 2019 00:20:27: 25000000 INFO @ Tue, 04 Jun 2019 00:20:31: 29000000 INFO @ Tue, 04 Jun 2019 00:20:32: 31000000 INFO @ Tue, 04 Jun 2019 00:20:38: 26000000 INFO @ Tue, 04 Jun 2019 00:20:40: 32000000 INFO @ Tue, 04 Jun 2019 00:20:41: 30000000 INFO @ Tue, 04 Jun 2019 00:20:49: 27000000 INFO @ Tue, 04 Jun 2019 00:20:49: 33000000 INFO @ Tue, 04 Jun 2019 00:20:50: 31000000 INFO @ Tue, 04 Jun 2019 00:20:57: 34000000 INFO @ Tue, 04 Jun 2019 00:20:58: 28000000 INFO @ Tue, 04 Jun 2019 00:20:59: 32000000 INFO @ Tue, 04 Jun 2019 00:21:06: 35000000 INFO @ Tue, 04 Jun 2019 00:21:08: 33000000 INFO @ Tue, 04 Jun 2019 00:21:09: 29000000 INFO @ Tue, 04 Jun 2019 00:21:15: 36000000 INFO @ Tue, 04 Jun 2019 00:21:17: 34000000 INFO @ Tue, 04 Jun 2019 00:21:19: 30000000 INFO @ Tue, 04 Jun 2019 00:21:23: 37000000 INFO @ Tue, 04 Jun 2019 00:21:26: 35000000 INFO @ Tue, 04 Jun 2019 00:21:30: 31000000 INFO @ Tue, 04 Jun 2019 00:21:32: 38000000 INFO @ Tue, 04 Jun 2019 00:21:35: 36000000 INFO @ Tue, 04 Jun 2019 00:21:40: 32000000 INFO @ Tue, 04 Jun 2019 00:21:41: 39000000 INFO @ Tue, 04 Jun 2019 00:21:45: 37000000 INFO @ Tue, 04 Jun 2019 00:21:50: 40000000 INFO @ Tue, 04 Jun 2019 00:21:51: 33000000 INFO @ Tue, 04 Jun 2019 00:21:54: 38000000 INFO @ Tue, 04 Jun 2019 00:21:59: 41000000 INFO @ Tue, 04 Jun 2019 00:22:02: 34000000 INFO @ Tue, 04 Jun 2019 00:22:04: 39000000 INFO @ Tue, 04 Jun 2019 00:22:07: 42000000 INFO @ Tue, 04 Jun 2019 00:22:12: 35000000 INFO @ Tue, 04 Jun 2019 00:22:13: 40000000 INFO @ Tue, 04 Jun 2019 00:22:16: 43000000 INFO @ Tue, 04 Jun 2019 00:22:18: #1 tag size is determined as 65 bps INFO @ Tue, 04 Jun 2019 00:22:18: #1 tag size = 65 INFO @ Tue, 04 Jun 2019 00:22:18: #1 total tags in treatment: 43253982 INFO @ Tue, 04 Jun 2019 00:22:18: #1 user defined the maximum tags... INFO @ Tue, 04 Jun 2019 00:22:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Jun 2019 00:22:19: #1 tags after filtering in treatment: 43253982 INFO @ Tue, 04 Jun 2019 00:22:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 04 Jun 2019 00:22:19: #1 finished! INFO @ Tue, 04 Jun 2019 00:22:19: #2 Build Peak Model... INFO @ Tue, 04 Jun 2019 00:22:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Jun 2019 00:22:22: 41000000 INFO @ Tue, 04 Jun 2019 00:22:23: #2 number of paired peaks: 7 WARNING @ Tue, 04 Jun 2019 00:22:23: Too few paired peaks (7) 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 @ Tue, 04 Jun 2019 00:22:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.10_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/dm3/SRX5343130/SRX5343130.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 04 Jun 2019 00:22:23: 36000000 INFO @ Tue, 04 Jun 2019 00:22:31: 42000000 INFO @ Tue, 04 Jun 2019 00:22:33: 37000000 INFO @ Tue, 04 Jun 2019 00:22:40: 43000000 INFO @ Tue, 04 Jun 2019 00:22:43: #1 tag size is determined as 65 bps INFO @ Tue, 04 Jun 2019 00:22:43: #1 tag size = 65 INFO @ Tue, 04 Jun 2019 00:22:43: #1 total tags in treatment: 43253982 INFO @ Tue, 04 Jun 2019 00:22:43: #1 user defined the maximum tags... INFO @ Tue, 04 Jun 2019 00:22:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Jun 2019 00:22:43: #1 tags after filtering in treatment: 43253982 INFO @ Tue, 04 Jun 2019 00:22:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 04 Jun 2019 00:22:43: #1 finished! INFO @ Tue, 04 Jun 2019 00:22:43: #2 Build Peak Model... INFO @ Tue, 04 Jun 2019 00:22:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Jun 2019 00:22:44: 38000000 INFO @ Tue, 04 Jun 2019 00:22:47: #2 number of paired peaks: 7 WARNING @ Tue, 04 Jun 2019 00:22:47: Too few paired peaks (7) 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 @ Tue, 04 Jun 2019 00:22:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.05_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/dm3/SRX5343130/SRX5343130.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 04 Jun 2019 00:22:54: 39000000 INFO @ Tue, 04 Jun 2019 00:23:04: 40000000 INFO @ Tue, 04 Jun 2019 00:23:15: 41000000 INFO @ Tue, 04 Jun 2019 00:23:24: 42000000 INFO @ Tue, 04 Jun 2019 00:23:35: 43000000 INFO @ Tue, 04 Jun 2019 00:23:38: #1 tag size is determined as 65 bps INFO @ Tue, 04 Jun 2019 00:23:38: #1 tag size = 65 INFO @ Tue, 04 Jun 2019 00:23:38: #1 total tags in treatment: 43253982 INFO @ Tue, 04 Jun 2019 00:23:38: #1 user defined the maximum tags... INFO @ Tue, 04 Jun 2019 00:23:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Jun 2019 00:23:39: #1 tags after filtering in treatment: 43253982 INFO @ Tue, 04 Jun 2019 00:23:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 04 Jun 2019 00:23:39: #1 finished! INFO @ Tue, 04 Jun 2019 00:23:39: #2 Build Peak Model... INFO @ Tue, 04 Jun 2019 00:23:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Jun 2019 00:23:42: #2 number of paired peaks: 7 WARNING @ Tue, 04 Jun 2019 00:23:42: Too few paired peaks (7) 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 @ Tue, 04 Jun 2019 00:23:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.20_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/dm3/SRX5343130/SRX5343130.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343130/SRX5343130.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。