Job ID = 1293880 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:55:34 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' 2019-06-02T17:55:34 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/SRR453248/SRR453248.2' 2019-06-02T17:55:34 fasterq-dump.2.9.6 err: invalid accession 'SRR453248' 2019-06-02T18:02:34 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 ) 2019-06-02T18:02:34 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 : 105,154,728 reads read : 105,154,728 reads written : 105,154,728 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: 00:44:54 105154728 reads; of these: 105154728 (100.00%) were unpaired; of these: 7104646 (6.76%) aligned 0 times 63084220 (59.99%) aligned exactly 1 time 34965862 (33.25%) aligned >1 times 93.24% overall alignment rate Time searching: 00:44:54 Overall time: 00:44:54 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 40 files... [bam_rmdupse_core] 47247314 / 98050082 = 0.4819 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 04:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.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 04:12:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:12:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.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 04:12:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:12:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.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 04:12:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:12:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:13:03: 1000000 INFO @ Mon, 03 Jun 2019 04:13:04: 1000000 INFO @ Mon, 03 Jun 2019 04:13:04: 1000000 INFO @ Mon, 03 Jun 2019 04:13:10: 2000000 INFO @ Mon, 03 Jun 2019 04:13:12: 2000000 INFO @ Mon, 03 Jun 2019 04:13:12: 2000000 INFO @ Mon, 03 Jun 2019 04:13:17: 3000000 INFO @ Mon, 03 Jun 2019 04:13:19: 3000000 INFO @ Mon, 03 Jun 2019 04:13:20: 3000000 INFO @ Mon, 03 Jun 2019 04:13:24: 4000000 INFO @ Mon, 03 Jun 2019 04:13:26: 4000000 INFO @ Mon, 03 Jun 2019 04:13:28: 4000000 INFO @ Mon, 03 Jun 2019 04:13:30: 5000000 INFO @ Mon, 03 Jun 2019 04:13:33: 5000000 INFO @ Mon, 03 Jun 2019 04:13:36: 5000000 INFO @ Mon, 03 Jun 2019 04:13:37: 6000000 INFO @ Mon, 03 Jun 2019 04:13:41: 6000000 INFO @ Mon, 03 Jun 2019 04:13:44: 6000000 INFO @ Mon, 03 Jun 2019 04:13:44: 7000000 INFO @ Mon, 03 Jun 2019 04:13:48: 7000000 INFO @ Mon, 03 Jun 2019 04:13:51: 8000000 INFO @ Mon, 03 Jun 2019 04:13:52: 7000000 INFO @ Mon, 03 Jun 2019 04:13:56: 8000000 INFO @ Mon, 03 Jun 2019 04:13:58: 9000000 INFO @ Mon, 03 Jun 2019 04:13:59: 8000000 INFO @ Mon, 03 Jun 2019 04:14:03: 9000000 INFO @ Mon, 03 Jun 2019 04:14:04: 10000000 INFO @ Mon, 03 Jun 2019 04:14:07: 9000000 INFO @ Mon, 03 Jun 2019 04:14:10: 10000000 INFO @ Mon, 03 Jun 2019 04:14:11: 11000000 INFO @ Mon, 03 Jun 2019 04:14:15: 10000000 INFO @ Mon, 03 Jun 2019 04:14:18: 11000000 INFO @ Mon, 03 Jun 2019 04:14:18: 12000000 INFO @ Mon, 03 Jun 2019 04:14:23: 11000000 INFO @ Mon, 03 Jun 2019 04:14:24: 13000000 INFO @ Mon, 03 Jun 2019 04:14:25: 12000000 INFO @ Mon, 03 Jun 2019 04:14:31: 14000000 INFO @ Mon, 03 Jun 2019 04:14:32: 12000000 INFO @ Mon, 03 Jun 2019 04:14:32: 13000000 INFO @ Mon, 03 Jun 2019 04:14:38: 15000000 INFO @ Mon, 03 Jun 2019 04:14:39: 13000000 INFO @ Mon, 03 Jun 2019 04:14:39: 14000000 INFO @ Mon, 03 Jun 2019 04:14:44: 16000000 INFO @ Mon, 03 Jun 2019 04:14:47: 15000000 INFO @ Mon, 03 Jun 2019 04:14:47: 14000000 INFO @ Mon, 03 Jun 2019 04:14:51: 17000000 INFO @ Mon, 03 Jun 2019 04:14:54: 16000000 INFO @ Mon, 03 Jun 2019 04:14:54: 15000000 INFO @ Mon, 03 Jun 2019 04:14:58: 18000000 INFO @ Mon, 03 Jun 2019 04:15:01: 17000000 INFO @ Mon, 03 Jun 2019 04:15:02: 16000000 INFO @ Mon, 03 Jun 2019 04:15:04: 19000000 INFO @ Mon, 03 Jun 2019 04:15:08: 18000000 INFO @ Mon, 03 Jun 2019 04:15:09: 17000000 INFO @ Mon, 03 Jun 2019 04:15:11: 20000000 INFO @ Mon, 03 Jun 2019 04:15:15: 19000000 INFO @ Mon, 03 Jun 2019 04:15:17: 18000000 INFO @ Mon, 03 Jun 2019 04:15:18: 21000000 INFO @ Mon, 03 Jun 2019 04:15:22: 20000000 INFO @ Mon, 03 Jun 2019 04:15:24: 22000000 INFO @ Mon, 03 Jun 2019 04:15:24: 19000000 INFO @ Mon, 03 Jun 2019 04:15:29: 21000000 INFO @ Mon, 03 Jun 2019 04:15:31: 23000000 INFO @ Mon, 03 Jun 2019 04:15:32: 20000000 INFO @ Mon, 03 Jun 2019 04:15:37: 22000000 INFO @ Mon, 03 Jun 2019 04:15:37: 24000000 INFO @ Mon, 03 Jun 2019 04:15:39: 21000000 INFO @ Mon, 03 Jun 2019 04:15:44: 23000000 INFO @ Mon, 03 Jun 2019 04:15:45: 25000000 INFO @ Mon, 03 Jun 2019 04:15:47: 22000000 INFO @ Mon, 03 Jun 2019 04:15:51: 24000000 INFO @ Mon, 03 Jun 2019 04:15:53: 26000000 INFO @ Mon, 03 Jun 2019 04:15:54: 23000000 INFO @ Mon, 03 Jun 2019 04:15:58: 25000000 INFO @ Mon, 03 Jun 2019 04:16:00: 27000000 INFO @ Mon, 03 Jun 2019 04:16:02: 24000000 INFO @ Mon, 03 Jun 2019 04:16:06: 26000000 INFO @ Mon, 03 Jun 2019 04:16:07: 28000000 INFO @ Mon, 03 Jun 2019 04:16:09: 25000000 INFO @ Mon, 03 Jun 2019 04:16:13: 29000000 INFO @ Mon, 03 Jun 2019 04:16:13: 27000000 INFO @ Mon, 03 Jun 2019 04:16:18: 26000000 INFO @ Mon, 03 Jun 2019 04:16:20: 30000000 INFO @ Mon, 03 Jun 2019 04:16:21: 28000000 INFO @ Mon, 03 Jun 2019 04:16:25: 27000000 INFO @ Mon, 03 Jun 2019 04:16:26: 31000000 INFO @ Mon, 03 Jun 2019 04:16:28: 29000000 INFO @ Mon, 03 Jun 2019 04:16:33: 28000000 INFO @ Mon, 03 Jun 2019 04:16:33: 32000000 INFO @ Mon, 03 Jun 2019 04:16:35: 30000000 INFO @ Mon, 03 Jun 2019 04:16:41: 33000000 INFO @ Mon, 03 Jun 2019 04:16:41: 29000000 INFO @ Mon, 03 Jun 2019 04:16:42: 31000000 INFO @ Mon, 03 Jun 2019 04:16:47: 34000000 INFO @ Mon, 03 Jun 2019 04:16:48: 30000000 INFO @ Mon, 03 Jun 2019 04:16:49: 32000000 INFO @ Mon, 03 Jun 2019 04:16:54: 35000000 INFO @ Mon, 03 Jun 2019 04:16:56: 31000000 INFO @ Mon, 03 Jun 2019 04:16:57: 33000000 INFO @ Mon, 03 Jun 2019 04:17:01: 36000000 INFO @ Mon, 03 Jun 2019 04:17:03: 32000000 INFO @ Mon, 03 Jun 2019 04:17:04: 34000000 INFO @ Mon, 03 Jun 2019 04:17:08: 37000000 INFO @ Mon, 03 Jun 2019 04:17:11: 33000000 INFO @ Mon, 03 Jun 2019 04:17:11: 35000000 INFO @ Mon, 03 Jun 2019 04:17:14: 38000000 INFO @ Mon, 03 Jun 2019 04:17:18: 34000000 INFO @ Mon, 03 Jun 2019 04:17:18: 36000000 INFO @ Mon, 03 Jun 2019 04:17:21: 39000000 INFO @ Mon, 03 Jun 2019 04:17:26: 35000000 INFO @ Mon, 03 Jun 2019 04:17:26: 37000000 INFO @ Mon, 03 Jun 2019 04:17:28: 40000000 INFO @ Mon, 03 Jun 2019 04:17:33: 38000000 INFO @ Mon, 03 Jun 2019 04:17:33: 36000000 INFO @ Mon, 03 Jun 2019 04:17:35: 41000000 INFO @ Mon, 03 Jun 2019 04:17:41: 39000000 INFO @ Mon, 03 Jun 2019 04:17:41: 37000000 INFO @ Mon, 03 Jun 2019 04:17:42: 42000000 INFO @ Mon, 03 Jun 2019 04:17:48: 40000000 INFO @ Mon, 03 Jun 2019 04:17:49: 43000000 INFO @ Mon, 03 Jun 2019 04:17:49: 38000000 INFO @ Mon, 03 Jun 2019 04:17:55: 44000000 INFO @ Mon, 03 Jun 2019 04:17:56: 41000000 INFO @ Mon, 03 Jun 2019 04:17:57: 39000000 INFO @ Mon, 03 Jun 2019 04:18:02: 45000000 INFO @ Mon, 03 Jun 2019 04:18:03: 42000000 INFO @ Mon, 03 Jun 2019 04:18:05: 40000000 INFO @ Mon, 03 Jun 2019 04:18:09: 46000000 INFO @ Mon, 03 Jun 2019 04:18:11: 43000000 INFO @ Mon, 03 Jun 2019 04:18:13: 41000000 INFO @ Mon, 03 Jun 2019 04:18:16: 47000000 INFO @ Mon, 03 Jun 2019 04:18:18: 44000000 INFO @ Mon, 03 Jun 2019 04:18:21: 42000000 INFO @ Mon, 03 Jun 2019 04:18:22: 48000000 INFO @ Mon, 03 Jun 2019 04:18:25: 45000000 INFO @ Mon, 03 Jun 2019 04:18:29: 49000000 INFO @ Mon, 03 Jun 2019 04:18:29: 43000000 INFO @ Mon, 03 Jun 2019 04:18:32: 46000000 INFO @ Mon, 03 Jun 2019 04:18:35: 50000000 INFO @ Mon, 03 Jun 2019 04:18:37: 44000000 INFO @ Mon, 03 Jun 2019 04:18:39: 47000000 INFO @ Mon, 03 Jun 2019 04:18:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:18:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:18:41: #1 total tags in treatment: 50802768 INFO @ Mon, 03 Jun 2019 04:18:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:18:41: #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 04:18:42: #1 tags after filtering in treatment: 50802768 INFO @ Mon, 03 Jun 2019 04:18:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:18:42: #1 finished! INFO @ Mon, 03 Jun 2019 04:18:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:18:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:18:44: 45000000 INFO @ Mon, 03 Jun 2019 04:18:47: 48000000 INFO @ Mon, 03 Jun 2019 04:18:47: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 04:18:47: 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 04:18:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.20_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/SRX135523/SRX135523.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:18:52: 46000000 INFO @ Mon, 03 Jun 2019 04:18:54: 49000000 INFO @ Mon, 03 Jun 2019 04:18:59: 47000000 INFO @ Mon, 03 Jun 2019 04:19:01: 50000000 INFO @ Mon, 03 Jun 2019 04:19:07: 48000000 INFO @ Mon, 03 Jun 2019 04:19:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:19:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:19:07: #1 total tags in treatment: 50802768 INFO @ Mon, 03 Jun 2019 04:19:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:19:07: #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 04:19:08: #1 tags after filtering in treatment: 50802768 INFO @ Mon, 03 Jun 2019 04:19:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:19:08: #1 finished! INFO @ Mon, 03 Jun 2019 04:19:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:19:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:19:12: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 04:19:12: 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 04:19:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.05_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/SRX135523/SRX135523.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:19:14: 49000000 INFO @ Mon, 03 Jun 2019 04:19:22: 50000000 INFO @ Mon, 03 Jun 2019 04:19:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:19:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:19:28: #1 total tags in treatment: 50802768 INFO @ Mon, 03 Jun 2019 04:19:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:19:28: #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 04:19:29: #1 tags after filtering in treatment: 50802768 INFO @ Mon, 03 Jun 2019 04:19:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:19:29: #1 finished! INFO @ Mon, 03 Jun 2019 04:19:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:19:33: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 04:19:33: 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 04:19:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.10_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/SRX135523/SRX135523.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135523/SRX135523.10_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。