Job ID = 1304622 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:53:34 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 ) 2019-06-03T11:53:34 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 ) 2019-06-03T11:53:34 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 ) 2019-06-03T11:53:34 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 ) 2019-06-03T11:57:44 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 ) 2019-06-03T12:02:00 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 ) 2019-06-03T12:02:40 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 : 21,457,757 reads read : 21,457,757 reads written : 21,457,757 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: 00:06:54 21457757 reads; of these: 21457757 (100.00%) were unpaired; of these: 411895 (1.92%) aligned 0 times 15998975 (74.56%) aligned exactly 1 time 5046887 (23.52%) aligned >1 times 98.08% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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 8 files... [bam_rmdupse_core] 4332081 / 21045862 = 0.2058 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 21:16:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.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 21:16:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:16:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:16:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.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 21:16:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:16:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:16:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.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 21:16:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:16:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:16:36: 1000000 INFO @ Mon, 03 Jun 2019 21:16:36: 1000000 INFO @ Mon, 03 Jun 2019 21:16:37: 1000000 INFO @ Mon, 03 Jun 2019 21:16:44: 2000000 INFO @ Mon, 03 Jun 2019 21:16:45: 2000000 INFO @ Mon, 03 Jun 2019 21:16:47: 2000000 INFO @ Mon, 03 Jun 2019 21:16:52: 3000000 INFO @ Mon, 03 Jun 2019 21:16:54: 3000000 INFO @ Mon, 03 Jun 2019 21:16:57: 3000000 INFO @ Mon, 03 Jun 2019 21:17:00: 4000000 INFO @ Mon, 03 Jun 2019 21:17:03: 4000000 INFO @ Mon, 03 Jun 2019 21:17:06: 4000000 INFO @ Mon, 03 Jun 2019 21:17:08: 5000000 INFO @ Mon, 03 Jun 2019 21:17:12: 5000000 INFO @ Mon, 03 Jun 2019 21:17:16: 6000000 INFO @ Mon, 03 Jun 2019 21:17:16: 5000000 INFO @ Mon, 03 Jun 2019 21:17:22: 6000000 INFO @ Mon, 03 Jun 2019 21:17:24: 7000000 INFO @ Mon, 03 Jun 2019 21:17:26: 6000000 INFO @ Mon, 03 Jun 2019 21:17:31: 7000000 INFO @ Mon, 03 Jun 2019 21:17:31: 8000000 INFO @ Mon, 03 Jun 2019 21:17:35: 7000000 INFO @ Mon, 03 Jun 2019 21:17:39: 9000000 INFO @ Mon, 03 Jun 2019 21:17:40: 8000000 INFO @ Mon, 03 Jun 2019 21:17:45: 8000000 INFO @ Mon, 03 Jun 2019 21:17:47: 10000000 INFO @ Mon, 03 Jun 2019 21:17:49: 9000000 INFO @ Mon, 03 Jun 2019 21:17:55: 11000000 INFO @ Mon, 03 Jun 2019 21:17:55: 9000000 INFO @ Mon, 03 Jun 2019 21:17:59: 10000000 INFO @ Mon, 03 Jun 2019 21:18:02: 12000000 INFO @ Mon, 03 Jun 2019 21:18:05: 10000000 INFO @ Mon, 03 Jun 2019 21:18:07: 11000000 INFO @ Mon, 03 Jun 2019 21:18:10: 13000000 INFO @ Mon, 03 Jun 2019 21:18:14: 11000000 INFO @ Mon, 03 Jun 2019 21:18:15: 12000000 INFO @ Mon, 03 Jun 2019 21:18:17: 14000000 INFO @ Mon, 03 Jun 2019 21:18:23: 13000000 INFO @ Mon, 03 Jun 2019 21:18:23: 12000000 INFO @ Mon, 03 Jun 2019 21:18:25: 15000000 INFO @ Mon, 03 Jun 2019 21:18:32: 14000000 INFO @ Mon, 03 Jun 2019 21:18:33: 16000000 INFO @ Mon, 03 Jun 2019 21:18:33: 13000000 INFO @ Mon, 03 Jun 2019 21:18:38: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:18:38: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:18:38: #1 total tags in treatment: 16713781 INFO @ Mon, 03 Jun 2019 21:18:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:18:38: #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 21:18:39: #1 tags after filtering in treatment: 16713781 INFO @ Mon, 03 Jun 2019 21:18:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:18:39: #1 finished! INFO @ Mon, 03 Jun 2019 21:18:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:18:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:18:40: #2 number of paired peaks: 50 WARNING @ Mon, 03 Jun 2019 21:18:40: Too few paired peaks (50) 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 21:18:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.10_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/SRX495198/SRX495198.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:18:41: 15000000 INFO @ Mon, 03 Jun 2019 21:18:43: 14000000 INFO @ Mon, 03 Jun 2019 21:18:50: 16000000 INFO @ Mon, 03 Jun 2019 21:18:53: 15000000 INFO @ Mon, 03 Jun 2019 21:18:56: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:18:56: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:18:56: #1 total tags in treatment: 16713781 INFO @ Mon, 03 Jun 2019 21:18:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:18:56: #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 21:18:56: #1 tags after filtering in treatment: 16713781 INFO @ Mon, 03 Jun 2019 21:18:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:18:56: #1 finished! INFO @ Mon, 03 Jun 2019 21:18:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:18:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:18:58: #2 number of paired peaks: 50 WARNING @ Mon, 03 Jun 2019 21:18:58: Too few paired peaks (50) 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 21:18:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.05_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/SRX495198/SRX495198.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:19:03: 16000000 INFO @ Mon, 03 Jun 2019 21:19:09: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:19:09: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:19:09: #1 total tags in treatment: 16713781 INFO @ Mon, 03 Jun 2019 21:19:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:19:09: #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 21:19:10: #1 tags after filtering in treatment: 16713781 INFO @ Mon, 03 Jun 2019 21:19:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:19:10: #1 finished! INFO @ Mon, 03 Jun 2019 21:19:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:19:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:19:11: #2 number of paired peaks: 50 WARNING @ Mon, 03 Jun 2019 21:19:11: Too few paired peaks (50) 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 21:19:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.20_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/SRX495198/SRX495198.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495198/SRX495198.20_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。