Job ID = 1299230 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:00:43 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' 2019-06-03T09:00:43 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/sra36/SRR/001146/SRR1174423' 2019-06-03T09:00:43 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_table_names( 'SRR1174423' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T09:01:07 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' 2019-06-03T09:01:07 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/sra36/SRR/001146/SRR1174423' 2019-06-03T09:01:07 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR1174423' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T09:01:07 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T09:05:13 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 ) 2019-06-03T09:11:54 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 ) 2019-06-03T09:12:59 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 ) 2019-06-03T09:17:14 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 ) 2019-06-03T09:17:14 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 ) 2019-06-03T09:24:23 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 ) 2019-06-03T09:24:23 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 : 21,202,663 reads read : 42,405,326 reads written : 42,405,326 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:40:34 21202663 reads; of these: 21202663 (100.00%) were paired; of these: 2245717 (10.59%) aligned concordantly 0 times 15039204 (70.93%) aligned concordantly exactly 1 time 3917742 (18.48%) aligned concordantly >1 times ---- 2245717 pairs aligned concordantly 0 times; of these: 94140 (4.19%) aligned discordantly 1 time ---- 2151577 pairs aligned 0 times concordantly or discordantly; of these: 4303154 mates make up the pairs; of these: 3783637 (87.93%) aligned 0 times 396591 (9.22%) aligned exactly 1 time 122926 (2.86%) aligned >1 times 91.08% overall alignment rate Time searching: 00:40:35 Overall time: 00:40:35 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 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2005401 / 19027622 = 0.1054 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 19:40:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.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 19:40:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:40:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:40:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.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 19:40:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:40:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.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 19:40:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:40:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:41:03: 1000000 INFO @ Mon, 03 Jun 2019 19:41:05: 1000000 INFO @ Mon, 03 Jun 2019 19:41:05: 1000000 INFO @ Mon, 03 Jun 2019 19:41:11: 2000000 INFO @ Mon, 03 Jun 2019 19:41:14: 2000000 INFO @ Mon, 03 Jun 2019 19:41:14: 2000000 INFO @ Mon, 03 Jun 2019 19:41:19: 3000000 INFO @ Mon, 03 Jun 2019 19:41:23: 3000000 INFO @ Mon, 03 Jun 2019 19:41:23: 3000000 INFO @ Mon, 03 Jun 2019 19:41:26: 4000000 INFO @ Mon, 03 Jun 2019 19:41:32: 4000000 INFO @ Mon, 03 Jun 2019 19:41:32: 4000000 INFO @ Mon, 03 Jun 2019 19:41:34: 5000000 INFO @ Mon, 03 Jun 2019 19:41:41: 5000000 INFO @ Mon, 03 Jun 2019 19:41:41: 5000000 INFO @ Mon, 03 Jun 2019 19:41:41: 6000000 INFO @ Mon, 03 Jun 2019 19:41:49: 7000000 INFO @ Mon, 03 Jun 2019 19:41:50: 6000000 INFO @ Mon, 03 Jun 2019 19:41:50: 6000000 INFO @ Mon, 03 Jun 2019 19:41:56: 8000000 INFO @ Mon, 03 Jun 2019 19:41:59: 7000000 INFO @ Mon, 03 Jun 2019 19:41:59: 7000000 INFO @ Mon, 03 Jun 2019 19:42:04: 9000000 INFO @ Mon, 03 Jun 2019 19:42:09: 8000000 INFO @ Mon, 03 Jun 2019 19:42:09: 8000000 INFO @ Mon, 03 Jun 2019 19:42:12: 10000000 INFO @ Mon, 03 Jun 2019 19:42:18: 9000000 INFO @ Mon, 03 Jun 2019 19:42:18: 9000000 INFO @ Mon, 03 Jun 2019 19:42:19: 11000000 INFO @ Mon, 03 Jun 2019 19:42:27: 12000000 INFO @ Mon, 03 Jun 2019 19:42:27: 10000000 INFO @ Mon, 03 Jun 2019 19:42:27: 10000000 INFO @ Mon, 03 Jun 2019 19:42:34: 13000000 INFO @ Mon, 03 Jun 2019 19:42:36: 11000000 INFO @ Mon, 03 Jun 2019 19:42:36: 11000000 INFO @ Mon, 03 Jun 2019 19:42:42: 14000000 INFO @ Mon, 03 Jun 2019 19:42:45: 12000000 INFO @ Mon, 03 Jun 2019 19:42:45: 12000000 INFO @ Mon, 03 Jun 2019 19:42:50: 15000000 INFO @ Mon, 03 Jun 2019 19:42:54: 13000000 INFO @ Mon, 03 Jun 2019 19:42:54: 13000000 INFO @ Mon, 03 Jun 2019 19:42:57: 16000000 INFO @ Mon, 03 Jun 2019 19:43:04: 14000000 INFO @ Mon, 03 Jun 2019 19:43:04: 14000000 INFO @ Mon, 03 Jun 2019 19:43:05: 17000000 INFO @ Mon, 03 Jun 2019 19:43:12: 18000000 INFO @ Mon, 03 Jun 2019 19:43:13: 15000000 INFO @ Mon, 03 Jun 2019 19:43:13: 15000000 INFO @ Mon, 03 Jun 2019 19:43:20: 19000000 INFO @ Mon, 03 Jun 2019 19:43:22: 16000000 INFO @ Mon, 03 Jun 2019 19:43:22: 16000000 INFO @ Mon, 03 Jun 2019 19:43:27: 20000000 INFO @ Mon, 03 Jun 2019 19:43:31: 17000000 INFO @ Mon, 03 Jun 2019 19:43:31: 17000000 INFO @ Mon, 03 Jun 2019 19:43:35: 21000000 INFO @ Mon, 03 Jun 2019 19:43:40: 18000000 INFO @ Mon, 03 Jun 2019 19:43:40: 18000000 INFO @ Mon, 03 Jun 2019 19:43:42: 22000000 INFO @ Mon, 03 Jun 2019 19:43:49: 19000000 INFO @ Mon, 03 Jun 2019 19:43:49: 19000000 INFO @ Mon, 03 Jun 2019 19:43:50: 23000000 INFO @ Mon, 03 Jun 2019 19:43:58: 24000000 INFO @ Mon, 03 Jun 2019 19:43:58: 20000000 INFO @ Mon, 03 Jun 2019 19:43:58: 20000000 INFO @ Mon, 03 Jun 2019 19:44:05: 25000000 INFO @ Mon, 03 Jun 2019 19:44:07: 21000000 INFO @ Mon, 03 Jun 2019 19:44:07: 21000000 INFO @ Mon, 03 Jun 2019 19:44:12: 26000000 INFO @ Mon, 03 Jun 2019 19:44:16: 22000000 INFO @ Mon, 03 Jun 2019 19:44:16: 22000000 INFO @ Mon, 03 Jun 2019 19:44:20: 27000000 INFO @ Mon, 03 Jun 2019 19:44:25: 23000000 INFO @ Mon, 03 Jun 2019 19:44:25: 23000000 INFO @ Mon, 03 Jun 2019 19:44:28: 28000000 INFO @ Mon, 03 Jun 2019 19:44:34: 24000000 INFO @ Mon, 03 Jun 2019 19:44:34: 24000000 INFO @ Mon, 03 Jun 2019 19:44:35: 29000000 INFO @ Mon, 03 Jun 2019 19:44:42: 25000000 INFO @ Mon, 03 Jun 2019 19:44:42: 30000000 INFO @ Mon, 03 Jun 2019 19:44:43: 25000000 INFO @ Mon, 03 Jun 2019 19:44:50: 31000000 INFO @ Mon, 03 Jun 2019 19:44:51: 26000000 INFO @ Mon, 03 Jun 2019 19:44:52: 26000000 INFO @ Mon, 03 Jun 2019 19:44:57: 32000000 INFO @ Mon, 03 Jun 2019 19:45:00: 27000000 INFO @ Mon, 03 Jun 2019 19:45:01: 27000000 INFO @ Mon, 03 Jun 2019 19:45:05: 33000000 INFO @ Mon, 03 Jun 2019 19:45:09: 28000000 INFO @ Mon, 03 Jun 2019 19:45:09: 28000000 INFO @ Mon, 03 Jun 2019 19:45:13: 34000000 INFO @ Mon, 03 Jun 2019 19:45:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:45:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:45:17: #1 total tags in treatment: 16954336 INFO @ Mon, 03 Jun 2019 19:45:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:45:17: #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 19:45:18: #1 tags after filtering in treatment: 14355998 INFO @ Mon, 03 Jun 2019 19:45:18: #1 Redundant rate of treatment: 0.15 INFO @ Mon, 03 Jun 2019 19:45:18: #1 finished! INFO @ Mon, 03 Jun 2019 19:45:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:45:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:45:18: 29000000 INFO @ Mon, 03 Jun 2019 19:45:18: 29000000 INFO @ Mon, 03 Jun 2019 19:45:19: #2 number of paired peaks: 7 WARNING @ Mon, 03 Jun 2019 19:45:19: 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 @ Mon, 03 Jun 2019 19:45:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.05_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/SRX474570/SRX474570.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:45:27: 30000000 INFO @ Mon, 03 Jun 2019 19:45:27: 30000000 INFO @ Mon, 03 Jun 2019 19:45:36: 31000000 INFO @ Mon, 03 Jun 2019 19:45:36: 31000000 INFO @ Mon, 03 Jun 2019 19:45:45: 32000000 INFO @ Mon, 03 Jun 2019 19:45:45: 32000000 INFO @ Mon, 03 Jun 2019 19:45:53: 33000000 INFO @ Mon, 03 Jun 2019 19:45:54: 33000000 INFO @ Mon, 03 Jun 2019 19:46:02: 34000000 INFO @ Mon, 03 Jun 2019 19:46:03: 34000000 INFO @ Mon, 03 Jun 2019 19:46:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:46:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:46:07: #1 total tags in treatment: 16954336 INFO @ Mon, 03 Jun 2019 19:46:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:46:07: #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 19:46:08: #1 tags after filtering in treatment: 14355998 INFO @ Mon, 03 Jun 2019 19:46:08: #1 Redundant rate of treatment: 0.15 INFO @ Mon, 03 Jun 2019 19:46:08: #1 finished! INFO @ Mon, 03 Jun 2019 19:46:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:46:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:46:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:46:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:46:09: #1 total tags in treatment: 16954336 INFO @ Mon, 03 Jun 2019 19:46:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:46:09: #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 19:46:09: #2 number of paired peaks: 7 WARNING @ Mon, 03 Jun 2019 19:46:09: 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 @ Mon, 03 Jun 2019 19:46:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.10_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/SRX474570/SRX474570.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:46:09: #1 tags after filtering in treatment: 14355998 INFO @ Mon, 03 Jun 2019 19:46:09: #1 Redundant rate of treatment: 0.15 INFO @ Mon, 03 Jun 2019 19:46:09: #1 finished! INFO @ Mon, 03 Jun 2019 19:46:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:46:10: #2 number of paired peaks: 7 WARNING @ Mon, 03 Jun 2019 19:46:10: 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 @ Mon, 03 Jun 2019 19:46:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.20_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/SRX474570/SRX474570.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474570/SRX474570.20_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。