Job ID = 1293879 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:55:27 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' 2019-06-02T17:55:27 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/sos/sra-pub-run-1/SRR453247/SRR453247.2' 2019-06-02T17:55:38 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR453247' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T17:55:38 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T17:56:25 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 ) 2019-06-02T17:56:25 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 ) 2019-06-02T17:56:25 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 ) 2019-06-02T17:56:26 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 : 81,219,748 reads read : 81,219,748 reads written : 81,219,748 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: 00:25:49 81219748 reads; of these: 81219748 (100.00%) were unpaired; of these: 5573470 (6.86%) aligned 0 times 60848952 (74.92%) aligned exactly 1 time 14797326 (18.22%) aligned >1 times 93.14% overall alignment rate Time searching: 00:25:49 Overall time: 00:25:49 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] 38990508 / 75646278 = 0.5154 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 03:52:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.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 03:52:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:52:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:52:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.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 03:52:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:52:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:52:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.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 03:52:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:52:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:52:15: 1000000 INFO @ Mon, 03 Jun 2019 03:52:16: 1000000 INFO @ Mon, 03 Jun 2019 03:52:16: 1000000 INFO @ Mon, 03 Jun 2019 03:52:23: 2000000 INFO @ Mon, 03 Jun 2019 03:52:25: 2000000 INFO @ Mon, 03 Jun 2019 03:52:26: 2000000 INFO @ Mon, 03 Jun 2019 03:52:31: 3000000 INFO @ Mon, 03 Jun 2019 03:52:34: 3000000 INFO @ Mon, 03 Jun 2019 03:52:35: 3000000 INFO @ Mon, 03 Jun 2019 03:52:40: 4000000 INFO @ Mon, 03 Jun 2019 03:52:44: 4000000 INFO @ Mon, 03 Jun 2019 03:52:45: 4000000 INFO @ Mon, 03 Jun 2019 03:52:49: 5000000 INFO @ Mon, 03 Jun 2019 03:52:53: 5000000 INFO @ Mon, 03 Jun 2019 03:52:55: 5000000 INFO @ Mon, 03 Jun 2019 03:52:57: 6000000 INFO @ Mon, 03 Jun 2019 03:53:02: 6000000 INFO @ Mon, 03 Jun 2019 03:53:04: 6000000 INFO @ Mon, 03 Jun 2019 03:53:05: 7000000 INFO @ Mon, 03 Jun 2019 03:53:11: 7000000 INFO @ Mon, 03 Jun 2019 03:53:13: 8000000 INFO @ Mon, 03 Jun 2019 03:53:14: 7000000 INFO @ Mon, 03 Jun 2019 03:53:20: 8000000 INFO @ Mon, 03 Jun 2019 03:53:21: 9000000 INFO @ Mon, 03 Jun 2019 03:53:23: 8000000 INFO @ Mon, 03 Jun 2019 03:53:29: 10000000 INFO @ Mon, 03 Jun 2019 03:53:29: 9000000 INFO @ Mon, 03 Jun 2019 03:53:33: 9000000 INFO @ Mon, 03 Jun 2019 03:53:37: 11000000 INFO @ Mon, 03 Jun 2019 03:53:38: 10000000 INFO @ Mon, 03 Jun 2019 03:53:42: 10000000 INFO @ Mon, 03 Jun 2019 03:53:46: 12000000 INFO @ Mon, 03 Jun 2019 03:53:47: 11000000 INFO @ Mon, 03 Jun 2019 03:53:51: 11000000 INFO @ Mon, 03 Jun 2019 03:53:55: 13000000 INFO @ Mon, 03 Jun 2019 03:53:56: 12000000 INFO @ Mon, 03 Jun 2019 03:54:02: 12000000 INFO @ Mon, 03 Jun 2019 03:54:03: 14000000 INFO @ Mon, 03 Jun 2019 03:54:05: 13000000 INFO @ Mon, 03 Jun 2019 03:54:11: 15000000 INFO @ Mon, 03 Jun 2019 03:54:11: 13000000 INFO @ Mon, 03 Jun 2019 03:54:15: 14000000 INFO @ Mon, 03 Jun 2019 03:54:20: 16000000 INFO @ Mon, 03 Jun 2019 03:54:21: 14000000 INFO @ Mon, 03 Jun 2019 03:54:24: 15000000 INFO @ Mon, 03 Jun 2019 03:54:27: 17000000 INFO @ Mon, 03 Jun 2019 03:54:30: 15000000 INFO @ Mon, 03 Jun 2019 03:54:33: 16000000 INFO @ Mon, 03 Jun 2019 03:54:35: 18000000 INFO @ Mon, 03 Jun 2019 03:54:39: 16000000 INFO @ Mon, 03 Jun 2019 03:54:42: 17000000 INFO @ Mon, 03 Jun 2019 03:54:43: 19000000 INFO @ Mon, 03 Jun 2019 03:54:49: 17000000 INFO @ Mon, 03 Jun 2019 03:54:50: 18000000 INFO @ Mon, 03 Jun 2019 03:54:52: 20000000 INFO @ Mon, 03 Jun 2019 03:54:58: 18000000 INFO @ Mon, 03 Jun 2019 03:54:59: 19000000 INFO @ Mon, 03 Jun 2019 03:55:00: 21000000 INFO @ Mon, 03 Jun 2019 03:55:08: 19000000 INFO @ Mon, 03 Jun 2019 03:55:08: 22000000 INFO @ Mon, 03 Jun 2019 03:55:09: 20000000 INFO @ Mon, 03 Jun 2019 03:55:17: 23000000 INFO @ Mon, 03 Jun 2019 03:55:17: 20000000 INFO @ Mon, 03 Jun 2019 03:55:17: 21000000 INFO @ Mon, 03 Jun 2019 03:55:25: 24000000 INFO @ Mon, 03 Jun 2019 03:55:26: 22000000 INFO @ Mon, 03 Jun 2019 03:55:27: 21000000 INFO @ Mon, 03 Jun 2019 03:55:33: 25000000 INFO @ Mon, 03 Jun 2019 03:55:35: 23000000 INFO @ Mon, 03 Jun 2019 03:55:36: 22000000 INFO @ Mon, 03 Jun 2019 03:55:40: 26000000 INFO @ Mon, 03 Jun 2019 03:55:44: 24000000 INFO @ Mon, 03 Jun 2019 03:55:45: 23000000 INFO @ Mon, 03 Jun 2019 03:55:48: 27000000 INFO @ Mon, 03 Jun 2019 03:55:53: 25000000 INFO @ Mon, 03 Jun 2019 03:55:54: 24000000 INFO @ Mon, 03 Jun 2019 03:55:57: 28000000 INFO @ Mon, 03 Jun 2019 03:56:02: 26000000 INFO @ Mon, 03 Jun 2019 03:56:03: 25000000 INFO @ Mon, 03 Jun 2019 03:56:05: 29000000 INFO @ Mon, 03 Jun 2019 03:56:10: 27000000 INFO @ Mon, 03 Jun 2019 03:56:12: 26000000 INFO @ Mon, 03 Jun 2019 03:56:13: 30000000 INFO @ Mon, 03 Jun 2019 03:56:20: 28000000 INFO @ Mon, 03 Jun 2019 03:56:22: 31000000 INFO @ Mon, 03 Jun 2019 03:56:22: 27000000 INFO @ Mon, 03 Jun 2019 03:56:29: 29000000 INFO @ Mon, 03 Jun 2019 03:56:30: 32000000 INFO @ Mon, 03 Jun 2019 03:56:32: 28000000 INFO @ Mon, 03 Jun 2019 03:56:38: 30000000 INFO @ Mon, 03 Jun 2019 03:56:38: 33000000 INFO @ Mon, 03 Jun 2019 03:56:41: 29000000 INFO @ Mon, 03 Jun 2019 03:56:46: 34000000 INFO @ Mon, 03 Jun 2019 03:56:46: 31000000 INFO @ Mon, 03 Jun 2019 03:56:50: 30000000 INFO @ Mon, 03 Jun 2019 03:56:53: 35000000 INFO @ Mon, 03 Jun 2019 03:56:55: 32000000 INFO @ Mon, 03 Jun 2019 03:56:59: 31000000 INFO @ Mon, 03 Jun 2019 03:57:02: 36000000 INFO @ Mon, 03 Jun 2019 03:57:04: 33000000 INFO @ Mon, 03 Jun 2019 03:57:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:57:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:57:08: #1 total tags in treatment: 36655770 INFO @ Mon, 03 Jun 2019 03:57:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:57:08: #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 03:57:09: 32000000 INFO @ Mon, 03 Jun 2019 03:57:09: #1 tags after filtering in treatment: 36655770 INFO @ Mon, 03 Jun 2019 03:57:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:57:09: #1 finished! INFO @ Mon, 03 Jun 2019 03:57:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:57:12: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 03:57:12: 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 @ Mon, 03 Jun 2019 03:57:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.10_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/SRX135522/SRX135522.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:57:13: 34000000 INFO @ Mon, 03 Jun 2019 03:57:18: 33000000 INFO @ Mon, 03 Jun 2019 03:57:22: 35000000 INFO @ Mon, 03 Jun 2019 03:57:27: 34000000 INFO @ Mon, 03 Jun 2019 03:57:31: 36000000 INFO @ Mon, 03 Jun 2019 03:57:37: 35000000 INFO @ Mon, 03 Jun 2019 03:57:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:57:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:57:37: #1 total tags in treatment: 36655770 INFO @ Mon, 03 Jun 2019 03:57:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:57:37: #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 03:57:38: #1 tags after filtering in treatment: 36655770 INFO @ Mon, 03 Jun 2019 03:57:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:57:38: #1 finished! INFO @ Mon, 03 Jun 2019 03:57:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:57:41: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 03:57:41: 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 03:57:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.05_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/SRX135522/SRX135522.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:57:46: 36000000 INFO @ Mon, 03 Jun 2019 03:57:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:57:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:57:52: #1 total tags in treatment: 36655770 INFO @ Mon, 03 Jun 2019 03:57:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:57:52: #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 03:57:53: #1 tags after filtering in treatment: 36655770 INFO @ Mon, 03 Jun 2019 03:57:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:57:53: #1 finished! INFO @ Mon, 03 Jun 2019 03:57:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:57:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:57:56: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 03:57:56: 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 @ Mon, 03 Jun 2019 03:57:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.20_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/SRX135522/SRX135522.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135522/SRX135522.20_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。