Job ID = 1292381 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T09:10:48 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' 2019-06-02T09:10:48 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/sra61/SRR/006820/SRR6983680' 2019-06-02T09:10:48 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR6983680' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:10:48 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:45:26 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' 2019-06-02T09:45:26 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/sra61/SRR/006820/SRR6983680' 2019-06-02T09:45:26 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR6983680' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:45:26 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 130,414,596 reads read : 260,829,192 reads written : 130,414,596 reads 0-length : 130,414,596 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: 00:31:42 130414596 reads; of these: 130414596 (100.00%) were unpaired; of these: 1943441 (1.49%) aligned 0 times 109335087 (83.84%) aligned exactly 1 time 19136068 (14.67%) aligned >1 times 98.51% overall alignment rate Time searching: 00:31:42 Overall time: 00:31:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 56 files... [bam_rmdupse_core] 91446175 / 128471155 = 0.7118 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 @ Sun, 02 Jun 2019 20:14:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 20:14:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:14:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:14:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 20:14:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:14:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:14:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 20:14:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:14:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:14:18: 1000000 INFO @ Sun, 02 Jun 2019 20:14:19: 1000000 INFO @ Sun, 02 Jun 2019 20:14:20: 1000000 INFO @ Sun, 02 Jun 2019 20:14:24: 2000000 INFO @ Sun, 02 Jun 2019 20:14:25: 2000000 INFO @ Sun, 02 Jun 2019 20:14:27: 2000000 INFO @ Sun, 02 Jun 2019 20:14:30: 3000000 INFO @ Sun, 02 Jun 2019 20:14:31: 3000000 INFO @ Sun, 02 Jun 2019 20:14:34: 3000000 INFO @ Sun, 02 Jun 2019 20:14:36: 4000000 INFO @ Sun, 02 Jun 2019 20:14:38: 4000000 INFO @ Sun, 02 Jun 2019 20:14:42: 4000000 INFO @ Sun, 02 Jun 2019 20:14:42: 5000000 INFO @ Sun, 02 Jun 2019 20:14:44: 5000000 INFO @ Sun, 02 Jun 2019 20:14:49: 6000000 INFO @ Sun, 02 Jun 2019 20:14:50: 5000000 INFO @ Sun, 02 Jun 2019 20:14:51: 6000000 INFO @ Sun, 02 Jun 2019 20:14:55: 7000000 INFO @ Sun, 02 Jun 2019 20:14:57: 7000000 INFO @ Sun, 02 Jun 2019 20:14:57: 6000000 INFO @ Sun, 02 Jun 2019 20:15:01: 8000000 INFO @ Sun, 02 Jun 2019 20:15:03: 8000000 INFO @ Sun, 02 Jun 2019 20:15:05: 7000000 INFO @ Sun, 02 Jun 2019 20:15:07: 9000000 INFO @ Sun, 02 Jun 2019 20:15:10: 9000000 INFO @ Sun, 02 Jun 2019 20:15:12: 8000000 INFO @ Sun, 02 Jun 2019 20:15:13: 10000000 INFO @ Sun, 02 Jun 2019 20:15:16: 10000000 INFO @ Sun, 02 Jun 2019 20:15:19: 9000000 INFO @ Sun, 02 Jun 2019 20:15:19: 11000000 INFO @ Sun, 02 Jun 2019 20:15:22: 11000000 INFO @ Sun, 02 Jun 2019 20:15:25: 12000000 INFO @ Sun, 02 Jun 2019 20:15:26: 10000000 INFO @ Sun, 02 Jun 2019 20:15:29: 12000000 INFO @ Sun, 02 Jun 2019 20:15:31: 13000000 INFO @ Sun, 02 Jun 2019 20:15:33: 11000000 INFO @ Sun, 02 Jun 2019 20:15:35: 13000000 INFO @ Sun, 02 Jun 2019 20:15:38: 14000000 INFO @ Sun, 02 Jun 2019 20:15:41: 12000000 INFO @ Sun, 02 Jun 2019 20:15:42: 14000000 INFO @ Sun, 02 Jun 2019 20:15:46: 15000000 INFO @ Sun, 02 Jun 2019 20:15:48: 15000000 INFO @ Sun, 02 Jun 2019 20:15:49: 13000000 INFO @ Sun, 02 Jun 2019 20:15:53: 16000000 INFO @ Sun, 02 Jun 2019 20:15:55: 16000000 INFO @ Sun, 02 Jun 2019 20:15:56: 14000000 INFO @ Sun, 02 Jun 2019 20:16:01: 17000000 INFO @ Sun, 02 Jun 2019 20:16:01: 17000000 INFO @ Sun, 02 Jun 2019 20:16:04: 15000000 INFO @ Sun, 02 Jun 2019 20:16:08: 18000000 INFO @ Sun, 02 Jun 2019 20:16:08: 18000000 INFO @ Sun, 02 Jun 2019 20:16:11: 16000000 INFO @ Sun, 02 Jun 2019 20:16:15: 19000000 INFO @ Sun, 02 Jun 2019 20:16:16: 19000000 INFO @ Sun, 02 Jun 2019 20:16:19: 17000000 INFO @ Sun, 02 Jun 2019 20:16:21: 20000000 INFO @ Sun, 02 Jun 2019 20:16:24: 20000000 INFO @ Sun, 02 Jun 2019 20:16:26: 18000000 INFO @ Sun, 02 Jun 2019 20:16:28: 21000000 INFO @ Sun, 02 Jun 2019 20:16:31: 21000000 INFO @ Sun, 02 Jun 2019 20:16:34: 19000000 INFO @ Sun, 02 Jun 2019 20:16:34: 22000000 INFO @ Sun, 02 Jun 2019 20:16:38: 22000000 INFO @ Sun, 02 Jun 2019 20:16:40: 23000000 INFO @ Sun, 02 Jun 2019 20:16:41: 20000000 INFO @ Sun, 02 Jun 2019 20:16:45: 23000000 INFO @ Sun, 02 Jun 2019 20:16:47: 24000000 INFO @ Sun, 02 Jun 2019 20:16:48: 21000000 INFO @ Sun, 02 Jun 2019 20:16:52: 24000000 INFO @ Sun, 02 Jun 2019 20:16:53: 25000000 INFO @ Sun, 02 Jun 2019 20:16:56: 22000000 INFO @ Sun, 02 Jun 2019 20:16:59: 26000000 INFO @ Sun, 02 Jun 2019 20:17:00: 25000000 INFO @ Sun, 02 Jun 2019 20:17:03: 23000000 INFO @ Sun, 02 Jun 2019 20:17:06: 27000000 INFO @ Sun, 02 Jun 2019 20:17:07: 26000000 INFO @ Sun, 02 Jun 2019 20:17:10: 24000000 INFO @ Sun, 02 Jun 2019 20:17:12: 28000000 INFO @ Sun, 02 Jun 2019 20:17:14: 27000000 INFO @ Sun, 02 Jun 2019 20:17:17: 25000000 INFO @ Sun, 02 Jun 2019 20:17:18: 29000000 INFO @ Sun, 02 Jun 2019 20:17:21: 28000000 INFO @ Sun, 02 Jun 2019 20:17:24: 26000000 INFO @ Sun, 02 Jun 2019 20:17:24: 30000000 INFO @ Sun, 02 Jun 2019 20:17:28: 29000000 INFO @ Sun, 02 Jun 2019 20:17:30: 31000000 INFO @ Sun, 02 Jun 2019 20:17:31: 27000000 INFO @ Sun, 02 Jun 2019 20:17:36: 30000000 INFO @ Sun, 02 Jun 2019 20:17:37: 32000000 INFO @ Sun, 02 Jun 2019 20:17:38: 28000000 INFO @ Sun, 02 Jun 2019 20:17:43: 31000000 INFO @ Sun, 02 Jun 2019 20:17:43: 33000000 INFO @ Sun, 02 Jun 2019 20:17:45: 29000000 INFO @ Sun, 02 Jun 2019 20:17:49: 34000000 INFO @ Sun, 02 Jun 2019 20:17:50: 32000000 INFO @ Sun, 02 Jun 2019 20:17:52: 30000000 INFO @ Sun, 02 Jun 2019 20:17:55: 35000000 INFO @ Sun, 02 Jun 2019 20:17:57: 33000000 INFO @ Sun, 02 Jun 2019 20:17:59: 31000000 INFO @ Sun, 02 Jun 2019 20:18:02: 36000000 INFO @ Sun, 02 Jun 2019 20:18:04: 34000000 INFO @ Sun, 02 Jun 2019 20:18:06: 32000000 INFO @ Sun, 02 Jun 2019 20:18:08: 37000000 INFO @ Sun, 02 Jun 2019 20:18:08: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 20:18:08: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 20:18:08: #1 total tags in treatment: 37024980 INFO @ Sun, 02 Jun 2019 20:18:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:18:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:18:09: #1 tags after filtering in treatment: 37024980 INFO @ Sun, 02 Jun 2019 20:18:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:18:09: #1 finished! INFO @ Sun, 02 Jun 2019 20:18:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:18:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:18:11: 35000000 INFO @ Sun, 02 Jun 2019 20:18:12: #2 number of paired peaks: 0 WARNING @ Sun, 02 Jun 2019 20:18:12: 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 @ Sun, 02 Jun 2019 20:18:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.10_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/ce10/SRX3923758/SRX3923758.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:18:13: 33000000 INFO @ Sun, 02 Jun 2019 20:18:18: 36000000 INFO @ Sun, 02 Jun 2019 20:18:20: 34000000 INFO @ Sun, 02 Jun 2019 20:18:25: 37000000 INFO @ Sun, 02 Jun 2019 20:18:26: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 20:18:26: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 20:18:26: #1 total tags in treatment: 37024980 INFO @ Sun, 02 Jun 2019 20:18:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:18:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:18:26: #1 tags after filtering in treatment: 37024980 INFO @ Sun, 02 Jun 2019 20:18:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:18:26: #1 finished! INFO @ Sun, 02 Jun 2019 20:18:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:18:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:18:28: 35000000 INFO @ Sun, 02 Jun 2019 20:18:30: #2 number of paired peaks: 0 WARNING @ Sun, 02 Jun 2019 20:18:30: 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 @ Sun, 02 Jun 2019 20:18:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.05_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/ce10/SRX3923758/SRX3923758.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:18:35: 36000000 INFO @ Sun, 02 Jun 2019 20:18:42: 37000000 INFO @ Sun, 02 Jun 2019 20:18:42: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 20:18:42: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 20:18:42: #1 total tags in treatment: 37024980 INFO @ Sun, 02 Jun 2019 20:18:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:18:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:18:43: #1 tags after filtering in treatment: 37024980 INFO @ Sun, 02 Jun 2019 20:18:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:18:43: #1 finished! INFO @ Sun, 02 Jun 2019 20:18:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:18:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:18:46: #2 number of paired peaks: 0 WARNING @ Sun, 02 Jun 2019 20:18:46: 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 @ Sun, 02 Jun 2019 20:18:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.20_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/ce10/SRX3923758/SRX3923758.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX3923758/SRX3923758.20_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。