Job ID = 1293959 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T18:31:25 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' 2019-06-02T18:31:25 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/sra5/SRR/000493/SRR504949' 2019-06-02T18:31:34 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR504949' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T18:31:34 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T18:36:33 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 ) 2019-06-02T18:36:33 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 ) 2019-06-02T18:36:33 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 ) 2019-06-02T18:47:51 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 : 72,611,177 reads read : 72,611,177 reads written : 72,611,177 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:28:22 72611177 reads; of these: 72611177 (100.00%) were unpaired; of these: 1920735 (2.65%) aligned 0 times 51425727 (70.82%) aligned exactly 1 time 19264715 (26.53%) aligned >1 times 97.35% overall alignment rate Time searching: 00:28:23 Overall time: 00:28:23 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 32 files... [bam_rmdupse_core] 27945242 / 70690442 = 0.3953 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 @ Mon, 03 Jun 2019 05:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.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 @ Mon, 03 Jun 2019 05:35:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:35:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.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 @ Mon, 03 Jun 2019 05:35:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:35:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.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 @ Mon, 03 Jun 2019 05:35:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:35:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:35:34: 1000000 INFO @ Mon, 03 Jun 2019 05:35:34: 1000000 INFO @ Mon, 03 Jun 2019 05:35:36: 1000000 INFO @ Mon, 03 Jun 2019 05:35:42: 2000000 INFO @ Mon, 03 Jun 2019 05:35:42: 2000000 INFO @ Mon, 03 Jun 2019 05:35:46: 2000000 INFO @ Mon, 03 Jun 2019 05:35:50: 3000000 INFO @ Mon, 03 Jun 2019 05:35:50: 3000000 INFO @ Mon, 03 Jun 2019 05:35:55: 3000000 INFO @ Mon, 03 Jun 2019 05:35:58: 4000000 INFO @ Mon, 03 Jun 2019 05:35:58: 4000000 INFO @ Mon, 03 Jun 2019 05:36:05: 4000000 INFO @ Mon, 03 Jun 2019 05:36:05: 5000000 INFO @ Mon, 03 Jun 2019 05:36:06: 5000000 INFO @ Mon, 03 Jun 2019 05:36:13: 6000000 INFO @ Mon, 03 Jun 2019 05:36:14: 6000000 INFO @ Mon, 03 Jun 2019 05:36:14: 5000000 INFO @ Mon, 03 Jun 2019 05:36:21: 7000000 INFO @ Mon, 03 Jun 2019 05:36:22: 7000000 INFO @ Mon, 03 Jun 2019 05:36:23: 6000000 INFO @ Mon, 03 Jun 2019 05:36:29: 8000000 INFO @ Mon, 03 Jun 2019 05:36:29: 8000000 INFO @ Mon, 03 Jun 2019 05:36:33: 7000000 INFO @ Mon, 03 Jun 2019 05:36:36: 9000000 INFO @ Mon, 03 Jun 2019 05:36:37: 9000000 INFO @ Mon, 03 Jun 2019 05:36:42: 8000000 INFO @ Mon, 03 Jun 2019 05:36:43: 10000000 INFO @ Mon, 03 Jun 2019 05:36:45: 10000000 INFO @ Mon, 03 Jun 2019 05:36:50: 11000000 INFO @ Mon, 03 Jun 2019 05:36:51: 9000000 INFO @ Mon, 03 Jun 2019 05:36:53: 11000000 INFO @ Mon, 03 Jun 2019 05:36:57: 12000000 INFO @ Mon, 03 Jun 2019 05:37:01: 10000000 INFO @ Mon, 03 Jun 2019 05:37:01: 12000000 INFO @ Mon, 03 Jun 2019 05:37:04: 13000000 INFO @ Mon, 03 Jun 2019 05:37:09: 13000000 INFO @ Mon, 03 Jun 2019 05:37:10: 11000000 INFO @ Mon, 03 Jun 2019 05:37:12: 14000000 INFO @ Mon, 03 Jun 2019 05:37:17: 14000000 INFO @ Mon, 03 Jun 2019 05:37:19: 15000000 INFO @ Mon, 03 Jun 2019 05:37:20: 12000000 INFO @ Mon, 03 Jun 2019 05:37:24: 15000000 INFO @ Mon, 03 Jun 2019 05:37:26: 16000000 INFO @ Mon, 03 Jun 2019 05:37:29: 13000000 INFO @ Mon, 03 Jun 2019 05:37:32: 16000000 INFO @ Mon, 03 Jun 2019 05:37:33: 17000000 INFO @ Mon, 03 Jun 2019 05:37:39: 14000000 INFO @ Mon, 03 Jun 2019 05:37:40: 17000000 INFO @ Mon, 03 Jun 2019 05:37:40: 18000000 INFO @ Mon, 03 Jun 2019 05:37:48: 15000000 INFO @ Mon, 03 Jun 2019 05:37:48: 19000000 INFO @ Mon, 03 Jun 2019 05:37:48: 18000000 INFO @ Mon, 03 Jun 2019 05:37:55: 20000000 INFO @ Mon, 03 Jun 2019 05:37:56: 19000000 INFO @ Mon, 03 Jun 2019 05:37:58: 16000000 INFO @ Mon, 03 Jun 2019 05:38:02: 21000000 INFO @ Mon, 03 Jun 2019 05:38:04: 20000000 INFO @ Mon, 03 Jun 2019 05:38:08: 17000000 INFO @ Mon, 03 Jun 2019 05:38:09: 22000000 INFO @ Mon, 03 Jun 2019 05:38:12: 21000000 INFO @ Mon, 03 Jun 2019 05:38:16: 23000000 INFO @ Mon, 03 Jun 2019 05:38:17: 18000000 INFO @ Mon, 03 Jun 2019 05:38:19: 22000000 INFO @ Mon, 03 Jun 2019 05:38:23: 24000000 INFO @ Mon, 03 Jun 2019 05:38:27: 19000000 INFO @ Mon, 03 Jun 2019 05:38:27: 23000000 INFO @ Mon, 03 Jun 2019 05:38:30: 25000000 INFO @ Mon, 03 Jun 2019 05:38:35: 24000000 INFO @ Mon, 03 Jun 2019 05:38:36: 20000000 INFO @ Mon, 03 Jun 2019 05:38:37: 26000000 INFO @ Mon, 03 Jun 2019 05:38:42: 25000000 INFO @ Mon, 03 Jun 2019 05:38:44: 27000000 INFO @ Mon, 03 Jun 2019 05:38:45: 21000000 INFO @ Mon, 03 Jun 2019 05:38:50: 26000000 INFO @ Mon, 03 Jun 2019 05:38:51: 28000000 INFO @ Mon, 03 Jun 2019 05:38:54: 22000000 INFO @ Mon, 03 Jun 2019 05:38:57: 27000000 INFO @ Mon, 03 Jun 2019 05:38:58: 29000000 INFO @ Mon, 03 Jun 2019 05:39:03: 23000000 INFO @ Mon, 03 Jun 2019 05:39:05: 28000000 INFO @ Mon, 03 Jun 2019 05:39:05: 30000000 INFO @ Mon, 03 Jun 2019 05:39:12: 24000000 INFO @ Mon, 03 Jun 2019 05:39:12: 31000000 INFO @ Mon, 03 Jun 2019 05:39:12: 29000000 INFO @ Mon, 03 Jun 2019 05:39:19: 32000000 INFO @ Mon, 03 Jun 2019 05:39:20: 30000000 INFO @ Mon, 03 Jun 2019 05:39:21: 25000000 INFO @ Mon, 03 Jun 2019 05:39:26: 33000000 INFO @ Mon, 03 Jun 2019 05:39:28: 31000000 INFO @ Mon, 03 Jun 2019 05:39:29: 26000000 INFO @ Mon, 03 Jun 2019 05:39:33: 34000000 INFO @ Mon, 03 Jun 2019 05:39:35: 32000000 INFO @ Mon, 03 Jun 2019 05:39:38: 27000000 INFO @ Mon, 03 Jun 2019 05:39:40: 35000000 INFO @ Mon, 03 Jun 2019 05:39:43: 33000000 INFO @ Mon, 03 Jun 2019 05:39:47: 28000000 INFO @ Mon, 03 Jun 2019 05:39:47: 36000000 INFO @ Mon, 03 Jun 2019 05:39:50: 34000000 INFO @ Mon, 03 Jun 2019 05:39:55: 37000000 INFO @ Mon, 03 Jun 2019 05:39:57: 29000000 INFO @ Mon, 03 Jun 2019 05:39:58: 35000000 INFO @ Mon, 03 Jun 2019 05:40:02: 38000000 INFO @ Mon, 03 Jun 2019 05:40:06: 36000000 INFO @ Mon, 03 Jun 2019 05:40:07: 30000000 INFO @ Mon, 03 Jun 2019 05:40:09: 39000000 INFO @ Mon, 03 Jun 2019 05:40:14: 37000000 INFO @ Mon, 03 Jun 2019 05:40:15: 31000000 INFO @ Mon, 03 Jun 2019 05:40:17: 40000000 INFO @ Mon, 03 Jun 2019 05:40:22: 38000000 INFO @ Mon, 03 Jun 2019 05:40:24: 32000000 INFO @ Mon, 03 Jun 2019 05:40:25: 41000000 INFO @ Mon, 03 Jun 2019 05:40:30: 39000000 INFO @ Mon, 03 Jun 2019 05:40:32: 42000000 INFO @ Mon, 03 Jun 2019 05:40:33: 33000000 INFO @ Mon, 03 Jun 2019 05:40:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:40:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:40:38: #1 total tags in treatment: 42745200 INFO @ Mon, 03 Jun 2019 05:40:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:40:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:40:39: #1 tags after filtering in treatment: 42745200 INFO @ Mon, 03 Jun 2019 05:40:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:40:39: #1 finished! INFO @ Mon, 03 Jun 2019 05:40:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:40:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:40:39: 40000000 INFO @ Mon, 03 Jun 2019 05:40:42: 34000000 INFO @ Mon, 03 Jun 2019 05:40:42: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 05:40:42: 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 @ Mon, 03 Jun 2019 05:40:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.10_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/dm3/SRX152093/SRX152093.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:40:48: 41000000 INFO @ Mon, 03 Jun 2019 05:40:51: 35000000 INFO @ Mon, 03 Jun 2019 05:40:55: 42000000 INFO @ Mon, 03 Jun 2019 05:40:59: 36000000 INFO @ Mon, 03 Jun 2019 05:41:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:41:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:41:02: #1 total tags in treatment: 42745200 INFO @ Mon, 03 Jun 2019 05:41:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:41:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:41:02: #1 tags after filtering in treatment: 42745200 INFO @ Mon, 03 Jun 2019 05:41:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:41:02: #1 finished! INFO @ Mon, 03 Jun 2019 05:41:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:41:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:41:06: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 05:41:06: 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 @ Mon, 03 Jun 2019 05:41:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.05_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/dm3/SRX152093/SRX152093.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:41:08: 37000000 INFO @ Mon, 03 Jun 2019 05:41:18: 38000000 INFO @ Mon, 03 Jun 2019 05:41:27: 39000000 INFO @ Mon, 03 Jun 2019 05:41:35: 40000000 INFO @ Mon, 03 Jun 2019 05:41:43: 41000000 INFO @ Mon, 03 Jun 2019 05:41:52: 42000000 INFO @ Mon, 03 Jun 2019 05:41:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:41:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:41:58: #1 total tags in treatment: 42745200 INFO @ Mon, 03 Jun 2019 05:41:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:41:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:41:59: #1 tags after filtering in treatment: 42745200 INFO @ Mon, 03 Jun 2019 05:41:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:41:59: #1 finished! INFO @ Mon, 03 Jun 2019 05:41:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:42:03: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 05:42:03: 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 @ Mon, 03 Jun 2019 05:42:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.20_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/SRX152093/SRX152093.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX152093/SRX152093.20_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。