Job ID = 1294371 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:04:29 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 ) 2019-06-02T22:18:33 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 ) 2019-06-02T22:26:38 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 ) 2019-06-02T22:28:04 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 ) 2019-06-02T22:30:26 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 ) 2019-06-02T22:32:02 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 : 80,920,758 reads read : 80,920,758 reads written : 80,920,758 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: 00:27:28 80920758 reads; of these: 80920758 (100.00%) were unpaired; of these: 5790636 (7.16%) aligned 0 times 56003935 (69.21%) aligned exactly 1 time 19126187 (23.64%) aligned >1 times 92.84% overall alignment rate Time searching: 00:27:28 Overall time: 00:27:28 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] 33703265 / 75130122 = 0.4486 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 08:22:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.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 08:22:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:22:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:22:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.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 08:22:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:22:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:22:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.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 08:22:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:22:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:22:35: 1000000 INFO @ Mon, 03 Jun 2019 08:22:35: 1000000 INFO @ Mon, 03 Jun 2019 08:22:36: 1000000 INFO @ Mon, 03 Jun 2019 08:22:42: 2000000 INFO @ Mon, 03 Jun 2019 08:22:42: 2000000 INFO @ Mon, 03 Jun 2019 08:22:46: 2000000 INFO @ Mon, 03 Jun 2019 08:22:50: 3000000 INFO @ Mon, 03 Jun 2019 08:22:50: 3000000 INFO @ Mon, 03 Jun 2019 08:22:55: 3000000 INFO @ Mon, 03 Jun 2019 08:22:58: 4000000 INFO @ Mon, 03 Jun 2019 08:22:58: 4000000 INFO @ Mon, 03 Jun 2019 08:23:05: 4000000 INFO @ Mon, 03 Jun 2019 08:23:06: 5000000 INFO @ Mon, 03 Jun 2019 08:23:06: 5000000 INFO @ Mon, 03 Jun 2019 08:23:14: 6000000 INFO @ Mon, 03 Jun 2019 08:23:14: 5000000 INFO @ Mon, 03 Jun 2019 08:23:16: 6000000 INFO @ Mon, 03 Jun 2019 08:23:22: 7000000 INFO @ Mon, 03 Jun 2019 08:23:24: 6000000 INFO @ Mon, 03 Jun 2019 08:23:25: 7000000 INFO @ Mon, 03 Jun 2019 08:23:29: 8000000 INFO @ Mon, 03 Jun 2019 08:23:33: 7000000 INFO @ Mon, 03 Jun 2019 08:23:34: 8000000 INFO @ Mon, 03 Jun 2019 08:23:37: 9000000 INFO @ Mon, 03 Jun 2019 08:23:43: 9000000 INFO @ Mon, 03 Jun 2019 08:23:43: 8000000 INFO @ Mon, 03 Jun 2019 08:23:44: 10000000 INFO @ Mon, 03 Jun 2019 08:23:52: 10000000 INFO @ Mon, 03 Jun 2019 08:23:52: 11000000 INFO @ Mon, 03 Jun 2019 08:23:52: 9000000 INFO @ Mon, 03 Jun 2019 08:24:00: 12000000 INFO @ Mon, 03 Jun 2019 08:24:00: 11000000 INFO @ Mon, 03 Jun 2019 08:24:02: 10000000 INFO @ Mon, 03 Jun 2019 08:24:07: 13000000 INFO @ Mon, 03 Jun 2019 08:24:09: 12000000 INFO @ Mon, 03 Jun 2019 08:24:10: 11000000 INFO @ Mon, 03 Jun 2019 08:24:15: 14000000 INFO @ Mon, 03 Jun 2019 08:24:18: 13000000 INFO @ Mon, 03 Jun 2019 08:24:20: 12000000 INFO @ Mon, 03 Jun 2019 08:24:22: 15000000 INFO @ Mon, 03 Jun 2019 08:24:27: 14000000 INFO @ Mon, 03 Jun 2019 08:24:29: 13000000 INFO @ Mon, 03 Jun 2019 08:24:30: 16000000 INFO @ Mon, 03 Jun 2019 08:24:36: 15000000 INFO @ Mon, 03 Jun 2019 08:24:38: 17000000 INFO @ Mon, 03 Jun 2019 08:24:39: 14000000 INFO @ Mon, 03 Jun 2019 08:24:45: 16000000 INFO @ Mon, 03 Jun 2019 08:24:45: 18000000 INFO @ Mon, 03 Jun 2019 08:24:48: 15000000 INFO @ Mon, 03 Jun 2019 08:24:53: 19000000 INFO @ Mon, 03 Jun 2019 08:24:54: 17000000 INFO @ Mon, 03 Jun 2019 08:24:57: 16000000 INFO @ Mon, 03 Jun 2019 08:25:01: 20000000 INFO @ Mon, 03 Jun 2019 08:25:03: 18000000 INFO @ Mon, 03 Jun 2019 08:25:07: 17000000 INFO @ Mon, 03 Jun 2019 08:25:08: 21000000 INFO @ Mon, 03 Jun 2019 08:25:12: 19000000 INFO @ Mon, 03 Jun 2019 08:25:16: 22000000 INFO @ Mon, 03 Jun 2019 08:25:16: 18000000 INFO @ Mon, 03 Jun 2019 08:25:21: 20000000 INFO @ Mon, 03 Jun 2019 08:25:23: 23000000 INFO @ Mon, 03 Jun 2019 08:25:25: 19000000 INFO @ Mon, 03 Jun 2019 08:25:30: 21000000 INFO @ Mon, 03 Jun 2019 08:25:31: 24000000 INFO @ Mon, 03 Jun 2019 08:25:35: 20000000 INFO @ Mon, 03 Jun 2019 08:25:39: 22000000 INFO @ Mon, 03 Jun 2019 08:25:39: 25000000 INFO @ Mon, 03 Jun 2019 08:25:44: 21000000 INFO @ Mon, 03 Jun 2019 08:25:46: 26000000 INFO @ Mon, 03 Jun 2019 08:25:47: 23000000 INFO @ Mon, 03 Jun 2019 08:25:54: 22000000 INFO @ Mon, 03 Jun 2019 08:25:54: 27000000 INFO @ Mon, 03 Jun 2019 08:25:56: 24000000 INFO @ Mon, 03 Jun 2019 08:26:01: 28000000 INFO @ Mon, 03 Jun 2019 08:26:03: 23000000 INFO @ Mon, 03 Jun 2019 08:26:05: 25000000 INFO @ Mon, 03 Jun 2019 08:26:09: 29000000 INFO @ Mon, 03 Jun 2019 08:26:12: 24000000 INFO @ Mon, 03 Jun 2019 08:26:14: 26000000 INFO @ Mon, 03 Jun 2019 08:26:16: 30000000 INFO @ Mon, 03 Jun 2019 08:26:21: 25000000 INFO @ Mon, 03 Jun 2019 08:26:22: 27000000 INFO @ Mon, 03 Jun 2019 08:26:24: 31000000 INFO @ Mon, 03 Jun 2019 08:26:31: 26000000 INFO @ Mon, 03 Jun 2019 08:26:31: 28000000 INFO @ Mon, 03 Jun 2019 08:26:31: 32000000 INFO @ Mon, 03 Jun 2019 08:26:39: 33000000 INFO @ Mon, 03 Jun 2019 08:26:39: 27000000 INFO @ Mon, 03 Jun 2019 08:26:40: 29000000 INFO @ Mon, 03 Jun 2019 08:26:46: 34000000 INFO @ Mon, 03 Jun 2019 08:26:47: 28000000 INFO @ Mon, 03 Jun 2019 08:26:49: 30000000 INFO @ Mon, 03 Jun 2019 08:26:54: 35000000 INFO @ Mon, 03 Jun 2019 08:26:56: 29000000 INFO @ Mon, 03 Jun 2019 08:26:58: 31000000 INFO @ Mon, 03 Jun 2019 08:27:02: 36000000 INFO @ Mon, 03 Jun 2019 08:27:05: 30000000 INFO @ Mon, 03 Jun 2019 08:27:07: 32000000 INFO @ Mon, 03 Jun 2019 08:27:09: 37000000 INFO @ Mon, 03 Jun 2019 08:27:15: 31000000 INFO @ Mon, 03 Jun 2019 08:27:16: 33000000 INFO @ Mon, 03 Jun 2019 08:27:17: 38000000 INFO @ Mon, 03 Jun 2019 08:27:24: 32000000 INFO @ Mon, 03 Jun 2019 08:27:24: 39000000 INFO @ Mon, 03 Jun 2019 08:27:25: 34000000 INFO @ Mon, 03 Jun 2019 08:27:32: 40000000 INFO @ Mon, 03 Jun 2019 08:27:33: 33000000 INFO @ Mon, 03 Jun 2019 08:27:33: 35000000 INFO @ Mon, 03 Jun 2019 08:27:40: 41000000 INFO @ Mon, 03 Jun 2019 08:27:42: 36000000 INFO @ Mon, 03 Jun 2019 08:27:42: 34000000 INFO @ Mon, 03 Jun 2019 08:27:43: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 08:27:43: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 08:27:43: #1 total tags in treatment: 41426857 INFO @ Mon, 03 Jun 2019 08:27:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:27:43: #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 08:27:44: #1 tags after filtering in treatment: 41426857 INFO @ Mon, 03 Jun 2019 08:27:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:27:44: #1 finished! INFO @ Mon, 03 Jun 2019 08:27:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:27:47: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 08:27:47: 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 08:27:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.10_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/SRX271405/SRX271405.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:27:51: 37000000 INFO @ Mon, 03 Jun 2019 08:27:52: 35000000 INFO @ Mon, 03 Jun 2019 08:28:00: 38000000 INFO @ Mon, 03 Jun 2019 08:28:01: 36000000 INFO @ Mon, 03 Jun 2019 08:28:08: 39000000 INFO @ Mon, 03 Jun 2019 08:28:10: 37000000 INFO @ Mon, 03 Jun 2019 08:28:17: 40000000 INFO @ Mon, 03 Jun 2019 08:28:19: 38000000 INFO @ Mon, 03 Jun 2019 08:28:26: 41000000 INFO @ Mon, 03 Jun 2019 08:28:28: 39000000 INFO @ Mon, 03 Jun 2019 08:28:30: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 08:28:30: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 08:28:30: #1 total tags in treatment: 41426857 INFO @ Mon, 03 Jun 2019 08:28:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:28:30: #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 08:28:31: #1 tags after filtering in treatment: 41426857 INFO @ Mon, 03 Jun 2019 08:28:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:28:31: #1 finished! INFO @ Mon, 03 Jun 2019 08:28:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:28:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:28:34: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 08:28:34: 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 08:28:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.05_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/SRX271405/SRX271405.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:28:37: 40000000 INFO @ Mon, 03 Jun 2019 08:28:46: 41000000 INFO @ Mon, 03 Jun 2019 08:28:50: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 08:28:50: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 08:28:50: #1 total tags in treatment: 41426857 INFO @ Mon, 03 Jun 2019 08:28:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:28:50: #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 08:28:51: #1 tags after filtering in treatment: 41426857 INFO @ Mon, 03 Jun 2019 08:28:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:28:51: #1 finished! INFO @ Mon, 03 Jun 2019 08:28:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:28:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:28:55: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 08:28:55: 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 08:28:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.20_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/SRX271405/SRX271405.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX271405/SRX271405.20_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。