Job ID = 1294377 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T21:56:10 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' 2019-06-02T21:56:10 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/SRR5630473' 2019-06-02T21:56:10 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR5630473' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T21:56:10 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 18,583,760 reads read : 37,167,520 reads written : 18,583,760 reads 0-length : 18,583,760 spots read : 18,534,700 reads read : 37,069,400 reads written : 18,534,700 reads 0-length : 18,534,700 2019-06-02T22:28:08 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 ) 2019-06-02T22:28:08 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 ) 2019-06-02T22:28:08 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 ) 2019-06-02T22:30:12 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 ) 2019-06-02T22:30:12 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 : 18,441,147 reads read : 36,882,294 reads written : 18,441,147 reads 0-length : 18,441,147 spots read : 18,457,197 reads read : 36,914,394 reads written : 18,457,197 reads 0-length : 18,457,197 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: 00:48:36 74016804 reads; of these: 74016804 (100.00%) were unpaired; of these: 2341974 (3.16%) aligned 0 times 49517089 (66.90%) aligned exactly 1 time 22157741 (29.94%) aligned >1 times 96.84% overall alignment rate Time searching: 00:48:37 Overall time: 00:48:37 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] 18132578 / 71674830 = 0.2530 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 08:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.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 08:50:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:50:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:50:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.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 08:50:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:50:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:50:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.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 08:50:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:50:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:50:38: 1000000 INFO @ Mon, 03 Jun 2019 08:50:40: 1000000 INFO @ Mon, 03 Jun 2019 08:50:42: 1000000 INFO @ Mon, 03 Jun 2019 08:50:46: 2000000 INFO @ Mon, 03 Jun 2019 08:50:49: 2000000 INFO @ Mon, 03 Jun 2019 08:50:53: 2000000 INFO @ Mon, 03 Jun 2019 08:50:54: 3000000 INFO @ Mon, 03 Jun 2019 08:50:58: 3000000 INFO @ Mon, 03 Jun 2019 08:51:03: 4000000 INFO @ Mon, 03 Jun 2019 08:51:05: 3000000 INFO @ Mon, 03 Jun 2019 08:51:08: 4000000 INFO @ Mon, 03 Jun 2019 08:51:11: 5000000 INFO @ Mon, 03 Jun 2019 08:51:16: 4000000 INFO @ Mon, 03 Jun 2019 08:51:18: 5000000 INFO @ Mon, 03 Jun 2019 08:51:19: 6000000 INFO @ Mon, 03 Jun 2019 08:51:27: 7000000 INFO @ Mon, 03 Jun 2019 08:51:27: 5000000 INFO @ Mon, 03 Jun 2019 08:51:28: 6000000 INFO @ Mon, 03 Jun 2019 08:51:35: 8000000 INFO @ Mon, 03 Jun 2019 08:51:37: 7000000 INFO @ Mon, 03 Jun 2019 08:51:38: 6000000 INFO @ Mon, 03 Jun 2019 08:51:43: 9000000 INFO @ Mon, 03 Jun 2019 08:51:46: 8000000 INFO @ Mon, 03 Jun 2019 08:51:49: 7000000 INFO @ Mon, 03 Jun 2019 08:51:51: 10000000 INFO @ Mon, 03 Jun 2019 08:51:56: 9000000 INFO @ Mon, 03 Jun 2019 08:51:59: 11000000 INFO @ Mon, 03 Jun 2019 08:52:01: 8000000 INFO @ Mon, 03 Jun 2019 08:52:05: 10000000 INFO @ Mon, 03 Jun 2019 08:52:07: 12000000 INFO @ Mon, 03 Jun 2019 08:52:12: 9000000 INFO @ Mon, 03 Jun 2019 08:52:15: 11000000 INFO @ Mon, 03 Jun 2019 08:52:15: 13000000 INFO @ Mon, 03 Jun 2019 08:52:23: 10000000 INFO @ Mon, 03 Jun 2019 08:52:23: 14000000 INFO @ Mon, 03 Jun 2019 08:52:24: 12000000 INFO @ Mon, 03 Jun 2019 08:52:31: 15000000 INFO @ Mon, 03 Jun 2019 08:52:33: 13000000 INFO @ Mon, 03 Jun 2019 08:52:34: 11000000 INFO @ Mon, 03 Jun 2019 08:52:39: 16000000 INFO @ Mon, 03 Jun 2019 08:52:43: 14000000 INFO @ Mon, 03 Jun 2019 08:52:46: 12000000 INFO @ Mon, 03 Jun 2019 08:52:47: 17000000 INFO @ Mon, 03 Jun 2019 08:52:53: 15000000 INFO @ Mon, 03 Jun 2019 08:52:55: 18000000 INFO @ Mon, 03 Jun 2019 08:52:57: 13000000 INFO @ Mon, 03 Jun 2019 08:53:03: 16000000 INFO @ Mon, 03 Jun 2019 08:53:03: 19000000 INFO @ Mon, 03 Jun 2019 08:53:08: 14000000 INFO @ Mon, 03 Jun 2019 08:53:11: 20000000 INFO @ Mon, 03 Jun 2019 08:53:12: 17000000 INFO @ Mon, 03 Jun 2019 08:53:19: 15000000 INFO @ Mon, 03 Jun 2019 08:53:19: 21000000 INFO @ Mon, 03 Jun 2019 08:53:21: 18000000 INFO @ Mon, 03 Jun 2019 08:53:27: 22000000 INFO @ Mon, 03 Jun 2019 08:53:30: 16000000 INFO @ Mon, 03 Jun 2019 08:53:31: 19000000 INFO @ Mon, 03 Jun 2019 08:53:35: 23000000 INFO @ Mon, 03 Jun 2019 08:53:40: 20000000 INFO @ Mon, 03 Jun 2019 08:53:41: 17000000 INFO @ Mon, 03 Jun 2019 08:53:43: 24000000 INFO @ Mon, 03 Jun 2019 08:53:49: 21000000 INFO @ Mon, 03 Jun 2019 08:53:51: 25000000 INFO @ Mon, 03 Jun 2019 08:53:52: 18000000 INFO @ Mon, 03 Jun 2019 08:53:58: 22000000 INFO @ Mon, 03 Jun 2019 08:53:59: 26000000 INFO @ Mon, 03 Jun 2019 08:54:03: 19000000 INFO @ Mon, 03 Jun 2019 08:54:07: 27000000 INFO @ Mon, 03 Jun 2019 08:54:07: 23000000 INFO @ Mon, 03 Jun 2019 08:54:15: 20000000 INFO @ Mon, 03 Jun 2019 08:54:15: 28000000 INFO @ Mon, 03 Jun 2019 08:54:17: 24000000 INFO @ Mon, 03 Jun 2019 08:54:23: 29000000 INFO @ Mon, 03 Jun 2019 08:54:26: 21000000 INFO @ Mon, 03 Jun 2019 08:54:27: 25000000 INFO @ Mon, 03 Jun 2019 08:54:31: 30000000 INFO @ Mon, 03 Jun 2019 08:54:36: 26000000 INFO @ Mon, 03 Jun 2019 08:54:37: 22000000 INFO @ Mon, 03 Jun 2019 08:54:39: 31000000 INFO @ Mon, 03 Jun 2019 08:54:45: 27000000 INFO @ Mon, 03 Jun 2019 08:54:47: 32000000 INFO @ Mon, 03 Jun 2019 08:54:48: 23000000 INFO @ Mon, 03 Jun 2019 08:54:55: 28000000 INFO @ Mon, 03 Jun 2019 08:54:55: 33000000 INFO @ Mon, 03 Jun 2019 08:54:59: 24000000 INFO @ Mon, 03 Jun 2019 08:55:03: 34000000 INFO @ Mon, 03 Jun 2019 08:55:04: 29000000 INFO @ Mon, 03 Jun 2019 08:55:10: 25000000 INFO @ Mon, 03 Jun 2019 08:55:11: 35000000 INFO @ Mon, 03 Jun 2019 08:55:13: 30000000 INFO @ Mon, 03 Jun 2019 08:55:19: 36000000 INFO @ Mon, 03 Jun 2019 08:55:21: 26000000 INFO @ Mon, 03 Jun 2019 08:55:23: 31000000 INFO @ Mon, 03 Jun 2019 08:55:27: 37000000 INFO @ Mon, 03 Jun 2019 08:55:32: 32000000 INFO @ Mon, 03 Jun 2019 08:55:32: 27000000 INFO @ Mon, 03 Jun 2019 08:55:35: 38000000 INFO @ Mon, 03 Jun 2019 08:55:41: 33000000 INFO @ Mon, 03 Jun 2019 08:55:43: 39000000 INFO @ Mon, 03 Jun 2019 08:55:43: 28000000 INFO @ Mon, 03 Jun 2019 08:55:50: 34000000 INFO @ Mon, 03 Jun 2019 08:55:51: 40000000 INFO @ Mon, 03 Jun 2019 08:55:54: 29000000 INFO @ Mon, 03 Jun 2019 08:55:59: 41000000 INFO @ Mon, 03 Jun 2019 08:56:00: 35000000 INFO @ Mon, 03 Jun 2019 08:56:05: 30000000 INFO @ Mon, 03 Jun 2019 08:56:07: 42000000 INFO @ Mon, 03 Jun 2019 08:56:10: 36000000 INFO @ Mon, 03 Jun 2019 08:56:16: 43000000 INFO @ Mon, 03 Jun 2019 08:56:16: 31000000 INFO @ Mon, 03 Jun 2019 08:56:19: 37000000 INFO @ Mon, 03 Jun 2019 08:56:23: 44000000 INFO @ Mon, 03 Jun 2019 08:56:28: 32000000 INFO @ Mon, 03 Jun 2019 08:56:29: 38000000 INFO @ Mon, 03 Jun 2019 08:56:32: 45000000 INFO @ Mon, 03 Jun 2019 08:56:38: 39000000 INFO @ Mon, 03 Jun 2019 08:56:39: 33000000 INFO @ Mon, 03 Jun 2019 08:56:40: 46000000 INFO @ Mon, 03 Jun 2019 08:56:48: 40000000 INFO @ Mon, 03 Jun 2019 08:56:48: 47000000 INFO @ Mon, 03 Jun 2019 08:56:50: 34000000 INFO @ Mon, 03 Jun 2019 08:56:56: 48000000 INFO @ Mon, 03 Jun 2019 08:56:58: 41000000 INFO @ Mon, 03 Jun 2019 08:57:01: 35000000 INFO @ Mon, 03 Jun 2019 08:57:04: 49000000 INFO @ Mon, 03 Jun 2019 08:57:07: 42000000 INFO @ Mon, 03 Jun 2019 08:57:12: 50000000 INFO @ Mon, 03 Jun 2019 08:57:12: 36000000 INFO @ Mon, 03 Jun 2019 08:57:16: 43000000 INFO @ Mon, 03 Jun 2019 08:57:20: 51000000 INFO @ Mon, 03 Jun 2019 08:57:24: 37000000 INFO @ Mon, 03 Jun 2019 08:57:26: 44000000 INFO @ Mon, 03 Jun 2019 08:57:28: 52000000 INFO @ Mon, 03 Jun 2019 08:57:35: 38000000 INFO @ Mon, 03 Jun 2019 08:57:36: 53000000 INFO @ Mon, 03 Jun 2019 08:57:36: 45000000 INFO @ Mon, 03 Jun 2019 08:57:40: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 08:57:40: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 08:57:40: #1 total tags in treatment: 53542252 INFO @ Mon, 03 Jun 2019 08:57:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:57:40: #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 08:57:42: #1 tags after filtering in treatment: 53542252 INFO @ Mon, 03 Jun 2019 08:57:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:57:42: #1 finished! INFO @ Mon, 03 Jun 2019 08:57:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:57:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:57:45: 46000000 INFO @ Mon, 03 Jun 2019 08:57:46: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 08:57:46: 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 @ Mon, 03 Jun 2019 08:57:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.10_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/SRX2870710/SRX2870710.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:57:47: 39000000 INFO @ Mon, 03 Jun 2019 08:57:54: 47000000 INFO @ Mon, 03 Jun 2019 08:57:58: 40000000 INFO @ Mon, 03 Jun 2019 08:58:04: 48000000 INFO @ Mon, 03 Jun 2019 08:58:09: 41000000 INFO @ Mon, 03 Jun 2019 08:58:13: 49000000 INFO @ Mon, 03 Jun 2019 08:58:21: 42000000 INFO @ Mon, 03 Jun 2019 08:58:22: 50000000 INFO @ Mon, 03 Jun 2019 08:58:31: 51000000 INFO @ Mon, 03 Jun 2019 08:58:32: 43000000 INFO @ Mon, 03 Jun 2019 08:58:40: 52000000 INFO @ Mon, 03 Jun 2019 08:58:43: 44000000 INFO @ Mon, 03 Jun 2019 08:58:49: 53000000 INFO @ Mon, 03 Jun 2019 08:58:54: 45000000 INFO @ Mon, 03 Jun 2019 08:58:55: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 08:58:55: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 08:58:55: #1 total tags in treatment: 53542252 INFO @ Mon, 03 Jun 2019 08:58:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:58:55: #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 08:58:56: #1 tags after filtering in treatment: 53542252 INFO @ Mon, 03 Jun 2019 08:58:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:58:56: #1 finished! INFO @ Mon, 03 Jun 2019 08:58:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:58:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:59:00: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 08:59:00: 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 08:59:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.20_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/SRX2870710/SRX2870710.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:59:05: 46000000 INFO @ Mon, 03 Jun 2019 08:59:16: 47000000 INFO @ Mon, 03 Jun 2019 08:59:27: 48000000 INFO @ Mon, 03 Jun 2019 08:59:38: 49000000 INFO @ Mon, 03 Jun 2019 08:59:49: 50000000 INFO @ Mon, 03 Jun 2019 09:00:00: 51000000 INFO @ Mon, 03 Jun 2019 09:00:11: 52000000 INFO @ Mon, 03 Jun 2019 09:00:21: 53000000 INFO @ Mon, 03 Jun 2019 09:00:27: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 09:00:27: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 09:00:27: #1 total tags in treatment: 53542252 INFO @ Mon, 03 Jun 2019 09:00:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:00:27: #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 09:00:29: #1 tags after filtering in treatment: 53542252 INFO @ Mon, 03 Jun 2019 09:00:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:00:29: #1 finished! INFO @ Mon, 03 Jun 2019 09:00:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:00:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:00:33: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 09:00:33: 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 09:00:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.05_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/SRX2870710/SRX2870710.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2870710/SRX2870710.05_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。