Job ID = 1294378 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T21:56:25 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' 2019-06-02T21:56:25 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/sra48/SRR/005498/SRR5630478' 2019-06-02T21:56:25 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR5630478' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T21:56:25 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 15,240,467 reads read : 30,480,934 reads written : 15,240,467 reads 0-length : 15,240,467 spots read : 15,160,615 reads read : 30,321,230 reads written : 15,160,615 reads 0-length : 15,160,615 spots read : 15,108,371 reads read : 30,216,742 reads written : 15,108,371 reads 0-length : 15,108,371 2019-06-02T22:25:29 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' 1900-01-00T00:00:00 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' 2019-06-02T22:25:29 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/sra48/SRR/005498/SRR5630481' 2019-06-02T22:25:29 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/sra48/SRR/005498/SRR5630481' 2019-06-02T22:25:29 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR5630481' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T22:25:29 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR5630481' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T22:25:29 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T22:25:29 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T22:37:22 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 : 15,076,582 reads read : 30,153,164 reads written : 15,076,582 reads 0-length : 15,076,582 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: 00:40:02 60586035 reads; of these: 60586035 (100.00%) were unpaired; of these: 2019762 (3.33%) aligned 0 times 40726596 (67.22%) aligned exactly 1 time 17839677 (29.45%) aligned >1 times 96.67% overall alignment rate Time searching: 00:40:02 Overall time: 00:40:02 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] 14476884 / 58566273 = 0.2472 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 08:39:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.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 08:39:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:39:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:39:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.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 08:39:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:39:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:39:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.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 08:39:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:39:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:39:14: 1000000 INFO @ Mon, 03 Jun 2019 08:39:16: 1000000 INFO @ Mon, 03 Jun 2019 08:39:16: 1000000 INFO @ Mon, 03 Jun 2019 08:39:22: 2000000 INFO @ Mon, 03 Jun 2019 08:39:26: 2000000 INFO @ Mon, 03 Jun 2019 08:39:26: 2000000 INFO @ Mon, 03 Jun 2019 08:39:31: 3000000 INFO @ Mon, 03 Jun 2019 08:39:37: 3000000 INFO @ Mon, 03 Jun 2019 08:39:37: 3000000 INFO @ Mon, 03 Jun 2019 08:39:39: 4000000 INFO @ Mon, 03 Jun 2019 08:39:46: 4000000 INFO @ Mon, 03 Jun 2019 08:39:47: 4000000 INFO @ Mon, 03 Jun 2019 08:39:47: 5000000 INFO @ Mon, 03 Jun 2019 08:39:55: 6000000 INFO @ Mon, 03 Jun 2019 08:39:56: 5000000 INFO @ Mon, 03 Jun 2019 08:39:57: 5000000 INFO @ Mon, 03 Jun 2019 08:40:03: 7000000 INFO @ Mon, 03 Jun 2019 08:40:06: 6000000 INFO @ Mon, 03 Jun 2019 08:40:07: 6000000 INFO @ Mon, 03 Jun 2019 08:40:12: 8000000 INFO @ Mon, 03 Jun 2019 08:40:16: 7000000 INFO @ Mon, 03 Jun 2019 08:40:17: 7000000 INFO @ Mon, 03 Jun 2019 08:40:21: 9000000 INFO @ Mon, 03 Jun 2019 08:40:26: 8000000 INFO @ Mon, 03 Jun 2019 08:40:27: 8000000 INFO @ Mon, 03 Jun 2019 08:40:30: 10000000 INFO @ Mon, 03 Jun 2019 08:40:37: 9000000 INFO @ Mon, 03 Jun 2019 08:40:38: 9000000 INFO @ Mon, 03 Jun 2019 08:40:38: 11000000 INFO @ Mon, 03 Jun 2019 08:40:47: 12000000 INFO @ Mon, 03 Jun 2019 08:40:47: 10000000 INFO @ Mon, 03 Jun 2019 08:40:48: 10000000 INFO @ Mon, 03 Jun 2019 08:40:55: 13000000 INFO @ Mon, 03 Jun 2019 08:40:57: 11000000 INFO @ Mon, 03 Jun 2019 08:40:57: 11000000 INFO @ Mon, 03 Jun 2019 08:41:03: 14000000 INFO @ Mon, 03 Jun 2019 08:41:07: 12000000 INFO @ Mon, 03 Jun 2019 08:41:08: 12000000 INFO @ Mon, 03 Jun 2019 08:41:11: 15000000 INFO @ Mon, 03 Jun 2019 08:41:17: 13000000 INFO @ Mon, 03 Jun 2019 08:41:18: 13000000 INFO @ Mon, 03 Jun 2019 08:41:19: 16000000 INFO @ Mon, 03 Jun 2019 08:41:26: 14000000 INFO @ Mon, 03 Jun 2019 08:41:27: 17000000 INFO @ Mon, 03 Jun 2019 08:41:27: 14000000 INFO @ Mon, 03 Jun 2019 08:41:35: 15000000 INFO @ Mon, 03 Jun 2019 08:41:35: 18000000 INFO @ Mon, 03 Jun 2019 08:41:37: 15000000 INFO @ Mon, 03 Jun 2019 08:41:44: 19000000 INFO @ Mon, 03 Jun 2019 08:41:45: 16000000 INFO @ Mon, 03 Jun 2019 08:41:47: 16000000 INFO @ Mon, 03 Jun 2019 08:41:52: 20000000 INFO @ Mon, 03 Jun 2019 08:41:54: 17000000 INFO @ Mon, 03 Jun 2019 08:41:57: 17000000 INFO @ Mon, 03 Jun 2019 08:42:00: 21000000 INFO @ Mon, 03 Jun 2019 08:42:05: 18000000 INFO @ Mon, 03 Jun 2019 08:42:07: 18000000 INFO @ Mon, 03 Jun 2019 08:42:08: 22000000 INFO @ Mon, 03 Jun 2019 08:42:15: 19000000 INFO @ Mon, 03 Jun 2019 08:42:16: 23000000 INFO @ Mon, 03 Jun 2019 08:42:16: 19000000 INFO @ Mon, 03 Jun 2019 08:42:24: 24000000 INFO @ Mon, 03 Jun 2019 08:42:24: 20000000 INFO @ Mon, 03 Jun 2019 08:42:26: 20000000 INFO @ Mon, 03 Jun 2019 08:42:32: 25000000 INFO @ Mon, 03 Jun 2019 08:42:34: 21000000 INFO @ Mon, 03 Jun 2019 08:42:35: 21000000 INFO @ Mon, 03 Jun 2019 08:42:40: 26000000 INFO @ Mon, 03 Jun 2019 08:42:43: 22000000 INFO @ Mon, 03 Jun 2019 08:42:45: 22000000 INFO @ Mon, 03 Jun 2019 08:42:47: 27000000 INFO @ Mon, 03 Jun 2019 08:42:52: 23000000 INFO @ Mon, 03 Jun 2019 08:42:54: 23000000 INFO @ Mon, 03 Jun 2019 08:42:55: 28000000 INFO @ Mon, 03 Jun 2019 08:43:02: 24000000 INFO @ Mon, 03 Jun 2019 08:43:03: 29000000 INFO @ Mon, 03 Jun 2019 08:43:03: 24000000 INFO @ Mon, 03 Jun 2019 08:43:11: 25000000 INFO @ Mon, 03 Jun 2019 08:43:11: 30000000 INFO @ Mon, 03 Jun 2019 08:43:12: 25000000 INFO @ Mon, 03 Jun 2019 08:43:19: 31000000 INFO @ Mon, 03 Jun 2019 08:43:20: 26000000 INFO @ Mon, 03 Jun 2019 08:43:22: 26000000 INFO @ Mon, 03 Jun 2019 08:43:27: 32000000 INFO @ Mon, 03 Jun 2019 08:43:30: 27000000 INFO @ Mon, 03 Jun 2019 08:43:32: 27000000 INFO @ Mon, 03 Jun 2019 08:43:35: 33000000 INFO @ Mon, 03 Jun 2019 08:43:39: 28000000 INFO @ Mon, 03 Jun 2019 08:43:41: 28000000 INFO @ Mon, 03 Jun 2019 08:43:43: 34000000 INFO @ Mon, 03 Jun 2019 08:43:48: 29000000 INFO @ Mon, 03 Jun 2019 08:43:50: 29000000 INFO @ Mon, 03 Jun 2019 08:43:51: 35000000 INFO @ Mon, 03 Jun 2019 08:43:57: 30000000 INFO @ Mon, 03 Jun 2019 08:43:59: 30000000 INFO @ Mon, 03 Jun 2019 08:43:59: 36000000 INFO @ Mon, 03 Jun 2019 08:44:07: 31000000 INFO @ Mon, 03 Jun 2019 08:44:07: 37000000 INFO @ Mon, 03 Jun 2019 08:44:08: 31000000 INFO @ Mon, 03 Jun 2019 08:44:15: 38000000 INFO @ Mon, 03 Jun 2019 08:44:16: 32000000 INFO @ Mon, 03 Jun 2019 08:44:17: 32000000 INFO @ Mon, 03 Jun 2019 08:44:23: 39000000 INFO @ Mon, 03 Jun 2019 08:44:25: 33000000 INFO @ Mon, 03 Jun 2019 08:44:26: 33000000 INFO @ Mon, 03 Jun 2019 08:44:30: 40000000 INFO @ Mon, 03 Jun 2019 08:44:35: 34000000 INFO @ Mon, 03 Jun 2019 08:44:35: 34000000 INFO @ Mon, 03 Jun 2019 08:44:39: 41000000 INFO @ Mon, 03 Jun 2019 08:44:44: 35000000 INFO @ Mon, 03 Jun 2019 08:44:45: 35000000 INFO @ Mon, 03 Jun 2019 08:44:47: 42000000 INFO @ Mon, 03 Jun 2019 08:44:54: 36000000 INFO @ Mon, 03 Jun 2019 08:44:55: 36000000 INFO @ Mon, 03 Jun 2019 08:44:55: 43000000 INFO @ Mon, 03 Jun 2019 08:45:03: 44000000 INFO @ Mon, 03 Jun 2019 08:45:03: 37000000 INFO @ Mon, 03 Jun 2019 08:45:04: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 08:45:04: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 08:45:04: #1 total tags in treatment: 44089389 INFO @ Mon, 03 Jun 2019 08:45:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:45:04: #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 08:45:04: 37000000 INFO @ Mon, 03 Jun 2019 08:45:05: #1 tags after filtering in treatment: 44089389 INFO @ Mon, 03 Jun 2019 08:45:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:45:05: #1 finished! INFO @ Mon, 03 Jun 2019 08:45:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:45:09: #2 number of paired peaks: 22 WARNING @ Mon, 03 Jun 2019 08:45:09: Too few paired peaks (22) 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 08:45:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.05_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/SRX2870711/SRX2870711.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:45:13: 38000000 INFO @ Mon, 03 Jun 2019 08:45:13: 38000000 INFO @ Mon, 03 Jun 2019 08:45:22: 39000000 INFO @ Mon, 03 Jun 2019 08:45:23: 39000000 INFO @ Mon, 03 Jun 2019 08:45:31: 40000000 INFO @ Mon, 03 Jun 2019 08:45:32: 40000000 INFO @ Mon, 03 Jun 2019 08:45:40: 41000000 INFO @ Mon, 03 Jun 2019 08:45:42: 41000000 INFO @ Mon, 03 Jun 2019 08:45:49: 42000000 INFO @ Mon, 03 Jun 2019 08:45:52: 42000000 INFO @ Mon, 03 Jun 2019 08:45:58: 43000000 INFO @ Mon, 03 Jun 2019 08:46:01: 43000000 INFO @ Mon, 03 Jun 2019 08:46:07: 44000000 INFO @ Mon, 03 Jun 2019 08:46:09: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 08:46:09: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 08:46:09: #1 total tags in treatment: 44089389 INFO @ Mon, 03 Jun 2019 08:46:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:46:09: #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 08:46:10: #1 tags after filtering in treatment: 44089389 INFO @ Mon, 03 Jun 2019 08:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:46:10: #1 finished! INFO @ Mon, 03 Jun 2019 08:46:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:46:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:46:11: 44000000 INFO @ Mon, 03 Jun 2019 08:46:12: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 08:46:12: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 08:46:12: #1 total tags in treatment: 44089389 INFO @ Mon, 03 Jun 2019 08:46:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:46:12: #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 08:46:13: #1 tags after filtering in treatment: 44089389 INFO @ Mon, 03 Jun 2019 08:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:46:13: #1 finished! INFO @ Mon, 03 Jun 2019 08:46:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:46:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:46:13: #2 number of paired peaks: 22 WARNING @ Mon, 03 Jun 2019 08:46:13: Too few paired peaks (22) 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 08:46:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.20_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/SRX2870711/SRX2870711.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:46:17: #2 number of paired peaks: 22 WARNING @ Mon, 03 Jun 2019 08:46:17: Too few paired peaks (22) 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 08:46:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.10_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/SRX2870711/SRX2870711.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2870711/SRX2870711.10_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。