Job ID = 1298774 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:38:52 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 ) 2019-06-03T08:38:52 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 ) 2019-06-03T08:40:02 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 ) 2019-06-03T08:40:02 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 ) 2019-06-03T08:41:21 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 ) 2019-06-03T08:41:21 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 ) 2019-06-03T08:44:36 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T08:48:21 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 ) 2019-06-03T08:48:21 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 ) 2019-06-03T08:50:09 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 ) 2019-06-03T08:50:09 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 : 34,009,141 reads read : 34,009,141 reads written : 34,009,141 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: 00:11:13 34009141 reads; of these: 34009141 (100.00%) were unpaired; of these: 1483098 (4.36%) aligned 0 times 25719363 (75.62%) aligned exactly 1 time 6806680 (20.01%) aligned >1 times 95.64% overall alignment rate Time searching: 00:11:13 Overall time: 00:11:13 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] 10454034 / 32526043 = 0.3214 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 18:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.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 18:11:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:11:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.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 18:11:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:11:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.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 18:11:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:11:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:12:01: 1000000 INFO @ Mon, 03 Jun 2019 18:12:01: 1000000 INFO @ Mon, 03 Jun 2019 18:12:03: 1000000 INFO @ Mon, 03 Jun 2019 18:12:08: 2000000 INFO @ Mon, 03 Jun 2019 18:12:09: 2000000 INFO @ Mon, 03 Jun 2019 18:12:13: 2000000 INFO @ Mon, 03 Jun 2019 18:12:16: 3000000 INFO @ Mon, 03 Jun 2019 18:12:16: 3000000 INFO @ Mon, 03 Jun 2019 18:12:23: 3000000 INFO @ Mon, 03 Jun 2019 18:12:24: 4000000 INFO @ Mon, 03 Jun 2019 18:12:24: 4000000 INFO @ Mon, 03 Jun 2019 18:12:32: 5000000 INFO @ Mon, 03 Jun 2019 18:12:32: 5000000 INFO @ Mon, 03 Jun 2019 18:12:33: 4000000 INFO @ Mon, 03 Jun 2019 18:12:39: 6000000 INFO @ Mon, 03 Jun 2019 18:12:39: 6000000 INFO @ Mon, 03 Jun 2019 18:12:43: 5000000 INFO @ Mon, 03 Jun 2019 18:12:47: 7000000 INFO @ Mon, 03 Jun 2019 18:12:47: 7000000 INFO @ Mon, 03 Jun 2019 18:12:53: 6000000 INFO @ Mon, 03 Jun 2019 18:12:54: 8000000 INFO @ Mon, 03 Jun 2019 18:12:55: 8000000 INFO @ Mon, 03 Jun 2019 18:13:02: 9000000 INFO @ Mon, 03 Jun 2019 18:13:02: 9000000 INFO @ Mon, 03 Jun 2019 18:13:03: 7000000 INFO @ Mon, 03 Jun 2019 18:13:10: 10000000 INFO @ Mon, 03 Jun 2019 18:13:10: 10000000 INFO @ Mon, 03 Jun 2019 18:13:13: 8000000 INFO @ Mon, 03 Jun 2019 18:13:17: 11000000 INFO @ Mon, 03 Jun 2019 18:13:18: 11000000 INFO @ Mon, 03 Jun 2019 18:13:22: 9000000 INFO @ Mon, 03 Jun 2019 18:13:25: 12000000 INFO @ Mon, 03 Jun 2019 18:13:25: 12000000 INFO @ Mon, 03 Jun 2019 18:13:32: 13000000 INFO @ Mon, 03 Jun 2019 18:13:32: 10000000 INFO @ Mon, 03 Jun 2019 18:13:33: 13000000 INFO @ Mon, 03 Jun 2019 18:13:40: 14000000 INFO @ Mon, 03 Jun 2019 18:13:40: 14000000 INFO @ Mon, 03 Jun 2019 18:13:42: 11000000 INFO @ Mon, 03 Jun 2019 18:13:47: 15000000 INFO @ Mon, 03 Jun 2019 18:13:48: 15000000 INFO @ Mon, 03 Jun 2019 18:13:52: 12000000 INFO @ Mon, 03 Jun 2019 18:13:55: 16000000 INFO @ Mon, 03 Jun 2019 18:13:56: 16000000 INFO @ Mon, 03 Jun 2019 18:14:02: 13000000 INFO @ Mon, 03 Jun 2019 18:14:02: 17000000 INFO @ Mon, 03 Jun 2019 18:14:03: 17000000 INFO @ Mon, 03 Jun 2019 18:14:10: 18000000 INFO @ Mon, 03 Jun 2019 18:14:11: 18000000 INFO @ Mon, 03 Jun 2019 18:14:12: 14000000 INFO @ Mon, 03 Jun 2019 18:14:18: 19000000 INFO @ Mon, 03 Jun 2019 18:14:19: 19000000 INFO @ Mon, 03 Jun 2019 18:14:22: 15000000 INFO @ Mon, 03 Jun 2019 18:14:25: 20000000 INFO @ Mon, 03 Jun 2019 18:14:26: 20000000 INFO @ Mon, 03 Jun 2019 18:14:32: 16000000 INFO @ Mon, 03 Jun 2019 18:14:33: 21000000 INFO @ Mon, 03 Jun 2019 18:14:35: 21000000 INFO @ Mon, 03 Jun 2019 18:14:42: 17000000 INFO @ Mon, 03 Jun 2019 18:14:42: 22000000 INFO @ Mon, 03 Jun 2019 18:14:43: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:14:43: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:14:43: #1 total tags in treatment: 22072009 INFO @ Mon, 03 Jun 2019 18:14:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:14:43: #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 18:14:43: #1 tags after filtering in treatment: 22072009 INFO @ Mon, 03 Jun 2019 18:14:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:14:43: #1 finished! INFO @ Mon, 03 Jun 2019 18:14:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:14:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:14:44: 22000000 INFO @ Mon, 03 Jun 2019 18:14:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:14:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:14:44: #1 total tags in treatment: 22072009 INFO @ Mon, 03 Jun 2019 18:14:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:14:44: #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 18:14:45: #1 tags after filtering in treatment: 22072009 INFO @ Mon, 03 Jun 2019 18:14:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:14:45: #1 finished! INFO @ Mon, 03 Jun 2019 18:14:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:14:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:14:45: #2 number of paired peaks: 11 WARNING @ Mon, 03 Jun 2019 18:14:45: Too few paired peaks (11) 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 18:14:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.10_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/SRX467051/SRX467051.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:14:47: #2 number of paired peaks: 11 WARNING @ Mon, 03 Jun 2019 18:14:47: Too few paired peaks (11) 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 18:14:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.05_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/SRX467051/SRX467051.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:14:52: 18000000 INFO @ Mon, 03 Jun 2019 18:15:01: 19000000 INFO @ Mon, 03 Jun 2019 18:15:11: 20000000 INFO @ Mon, 03 Jun 2019 18:15:21: 21000000 INFO @ Mon, 03 Jun 2019 18:15:30: 22000000 INFO @ Mon, 03 Jun 2019 18:15:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:15:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:15:31: #1 total tags in treatment: 22072009 INFO @ Mon, 03 Jun 2019 18:15:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:15:31: #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 18:15:32: #1 tags after filtering in treatment: 22072009 INFO @ Mon, 03 Jun 2019 18:15:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:15:32: #1 finished! INFO @ Mon, 03 Jun 2019 18:15:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:15:33: #2 number of paired peaks: 11 WARNING @ Mon, 03 Jun 2019 18:15:33: Too few paired peaks (11) 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 18:15:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.20_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/SRX467051/SRX467051.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467051/SRX467051.20_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。