Job ID = 1307635 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:25:03 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 ) 2019-06-03T13:26:44 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 ) 2019-06-03T13:26:53 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 ) 2019-06-03T13:26:53 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 ) 2019-06-03T13:26:53 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 ) 2019-06-03T13:26:53 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 ) 2019-06-03T13:27:34 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 ) 2019-06-03T13:34:35 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 : 34,567,824 reads read : 69,135,648 reads written : 34,567,824 reads 0-length : 34,567,824 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: 00:13:38 34567824 reads; of these: 34567824 (100.00%) were unpaired; of these: 1338840 (3.87%) aligned 0 times 27381201 (79.21%) aligned exactly 1 time 5847783 (16.92%) aligned >1 times 96.13% overall alignment rate Time searching: 00:13:38 Overall time: 00:13:38 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 16 files... [bam_rmdupse_core] 4668876 / 33228984 = 0.1405 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 23:05:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.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 23:05:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:05:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:05:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.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 23:05:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:05:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:05:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.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 23:05:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:05:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:05:41: 1000000 INFO @ Mon, 03 Jun 2019 23:05:42: 1000000 INFO @ Mon, 03 Jun 2019 23:05:43: 1000000 INFO @ Mon, 03 Jun 2019 23:05:48: 2000000 INFO @ Mon, 03 Jun 2019 23:05:50: 2000000 INFO @ Mon, 03 Jun 2019 23:05:52: 2000000 INFO @ Mon, 03 Jun 2019 23:05:55: 3000000 INFO @ Mon, 03 Jun 2019 23:05:58: 3000000 INFO @ Mon, 03 Jun 2019 23:06:01: 3000000 INFO @ Mon, 03 Jun 2019 23:06:02: 4000000 INFO @ Mon, 03 Jun 2019 23:06:06: 4000000 INFO @ Mon, 03 Jun 2019 23:06:09: 5000000 INFO @ Mon, 03 Jun 2019 23:06:10: 4000000 INFO @ Mon, 03 Jun 2019 23:06:13: 5000000 INFO @ Mon, 03 Jun 2019 23:06:16: 6000000 INFO @ Mon, 03 Jun 2019 23:06:19: 5000000 INFO @ Mon, 03 Jun 2019 23:06:21: 6000000 INFO @ Mon, 03 Jun 2019 23:06:24: 7000000 INFO @ Mon, 03 Jun 2019 23:06:28: 6000000 INFO @ Mon, 03 Jun 2019 23:06:30: 7000000 INFO @ Mon, 03 Jun 2019 23:06:32: 8000000 INFO @ Mon, 03 Jun 2019 23:06:37: 7000000 INFO @ Mon, 03 Jun 2019 23:06:38: 8000000 INFO @ Mon, 03 Jun 2019 23:06:40: 9000000 INFO @ Mon, 03 Jun 2019 23:06:45: 9000000 INFO @ Mon, 03 Jun 2019 23:06:46: 8000000 INFO @ Mon, 03 Jun 2019 23:06:47: 10000000 INFO @ Mon, 03 Jun 2019 23:06:53: 10000000 INFO @ Mon, 03 Jun 2019 23:06:54: 11000000 INFO @ Mon, 03 Jun 2019 23:06:55: 9000000 INFO @ Mon, 03 Jun 2019 23:07:01: 11000000 INFO @ Mon, 03 Jun 2019 23:07:01: 12000000 INFO @ Mon, 03 Jun 2019 23:07:04: 10000000 INFO @ Mon, 03 Jun 2019 23:07:08: 13000000 INFO @ Mon, 03 Jun 2019 23:07:08: 12000000 INFO @ Mon, 03 Jun 2019 23:07:13: 11000000 INFO @ Mon, 03 Jun 2019 23:07:15: 14000000 INFO @ Mon, 03 Jun 2019 23:07:16: 13000000 INFO @ Mon, 03 Jun 2019 23:07:22: 12000000 INFO @ Mon, 03 Jun 2019 23:07:22: 15000000 INFO @ Mon, 03 Jun 2019 23:07:23: 14000000 INFO @ Mon, 03 Jun 2019 23:07:29: 16000000 INFO @ Mon, 03 Jun 2019 23:07:31: 13000000 INFO @ Mon, 03 Jun 2019 23:07:31: 15000000 INFO @ Mon, 03 Jun 2019 23:07:36: 17000000 INFO @ Mon, 03 Jun 2019 23:07:39: 16000000 INFO @ Mon, 03 Jun 2019 23:07:39: 14000000 INFO @ Mon, 03 Jun 2019 23:07:43: 18000000 INFO @ Mon, 03 Jun 2019 23:07:46: 17000000 INFO @ Mon, 03 Jun 2019 23:07:48: 15000000 INFO @ Mon, 03 Jun 2019 23:07:50: 19000000 INFO @ Mon, 03 Jun 2019 23:07:54: 18000000 INFO @ Mon, 03 Jun 2019 23:07:57: 20000000 INFO @ Mon, 03 Jun 2019 23:07:57: 16000000 INFO @ Mon, 03 Jun 2019 23:08:02: 19000000 INFO @ Mon, 03 Jun 2019 23:08:03: 21000000 INFO @ Mon, 03 Jun 2019 23:08:06: 17000000 INFO @ Mon, 03 Jun 2019 23:08:09: 20000000 INFO @ Mon, 03 Jun 2019 23:08:10: 22000000 INFO @ Mon, 03 Jun 2019 23:08:15: 18000000 INFO @ Mon, 03 Jun 2019 23:08:17: 21000000 INFO @ Mon, 03 Jun 2019 23:08:17: 23000000 INFO @ Mon, 03 Jun 2019 23:08:23: 19000000 INFO @ Mon, 03 Jun 2019 23:08:24: 22000000 INFO @ Mon, 03 Jun 2019 23:08:24: 24000000 INFO @ Mon, 03 Jun 2019 23:08:31: 25000000 INFO @ Mon, 03 Jun 2019 23:08:32: 23000000 INFO @ Mon, 03 Jun 2019 23:08:32: 20000000 INFO @ Mon, 03 Jun 2019 23:08:39: 26000000 INFO @ Mon, 03 Jun 2019 23:08:40: 24000000 INFO @ Mon, 03 Jun 2019 23:08:41: 21000000 INFO @ Mon, 03 Jun 2019 23:08:47: 27000000 INFO @ Mon, 03 Jun 2019 23:08:48: 25000000 INFO @ Mon, 03 Jun 2019 23:08:50: 22000000 INFO @ Mon, 03 Jun 2019 23:08:55: 28000000 INFO @ Mon, 03 Jun 2019 23:08:56: 26000000 INFO @ Mon, 03 Jun 2019 23:08:59: 23000000 INFO @ Mon, 03 Jun 2019 23:08:59: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:08:59: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:08:59: #1 total tags in treatment: 28560108 INFO @ Mon, 03 Jun 2019 23:08:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:08:59: #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 23:09:00: #1 tags after filtering in treatment: 28560108 INFO @ Mon, 03 Jun 2019 23:09:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:09:00: #1 finished! INFO @ Mon, 03 Jun 2019 23:09:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:09:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:09:02: #2 number of paired peaks: 36 WARNING @ Mon, 03 Jun 2019 23:09:02: Too few paired peaks (36) 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 23:09:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.05_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/SRX5343102/SRX5343102.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:09:04: 27000000 INFO @ Mon, 03 Jun 2019 23:09:08: 24000000 INFO @ Mon, 03 Jun 2019 23:09:11: 28000000 INFO @ Mon, 03 Jun 2019 23:09:16: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:09:16: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:09:16: #1 total tags in treatment: 28560108 INFO @ Mon, 03 Jun 2019 23:09:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:09:16: #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 23:09:16: #1 tags after filtering in treatment: 28560108 INFO @ Mon, 03 Jun 2019 23:09:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:09:16: #1 finished! INFO @ Mon, 03 Jun 2019 23:09:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:09:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:09:17: 25000000 INFO @ Mon, 03 Jun 2019 23:09:19: #2 number of paired peaks: 36 WARNING @ Mon, 03 Jun 2019 23:09:19: Too few paired peaks (36) 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 23:09:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.20_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/SRX5343102/SRX5343102.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:09:25: 26000000 INFO @ Mon, 03 Jun 2019 23:09:34: 27000000 INFO @ Mon, 03 Jun 2019 23:09:42: 28000000 INFO @ Mon, 03 Jun 2019 23:09:47: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:09:47: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:09:47: #1 total tags in treatment: 28560108 INFO @ Mon, 03 Jun 2019 23:09:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:09:47: #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 23:09:48: #1 tags after filtering in treatment: 28560108 INFO @ Mon, 03 Jun 2019 23:09:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:09:48: #1 finished! INFO @ Mon, 03 Jun 2019 23:09:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:09:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:09:50: #2 number of paired peaks: 36 WARNING @ Mon, 03 Jun 2019 23:09:50: Too few paired peaks (36) 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 23:09:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.10_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/SRX5343102/SRX5343102.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343102/SRX5343102.10_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。