Job ID = 1298412 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:21:33 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 ) 2019-06-03T08:26:24 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 ) 2019-06-03T08:32:22 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 ) 2019-06-03T08:32:22 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 ) 2019-06-03T08:32:22 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 ) 2019-06-03T08:34:59 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 ) 2019-06-03T08:34:59 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 : 28,572,025 reads read : 28,572,025 reads written : 28,572,025 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: 00:09:54 28572025 reads; of these: 28572025 (100.00%) were unpaired; of these: 10347205 (36.21%) aligned 0 times 12473613 (43.66%) aligned exactly 1 time 5751207 (20.13%) aligned >1 times 63.79% overall alignment rate Time searching: 00:09:54 Overall time: 00:09:54 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] 4939420 / 18224820 = 0.2710 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 17:51:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.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 17:51:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:51:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:51:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.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 17:51:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:51:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:51:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.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 17:51:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:51:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:51:38: 1000000 INFO @ Mon, 03 Jun 2019 17:51:39: 1000000 INFO @ Mon, 03 Jun 2019 17:51:40: 1000000 INFO @ Mon, 03 Jun 2019 17:51:47: 2000000 INFO @ Mon, 03 Jun 2019 17:51:50: 2000000 INFO @ Mon, 03 Jun 2019 17:51:51: 2000000 INFO @ Mon, 03 Jun 2019 17:51:56: 3000000 INFO @ Mon, 03 Jun 2019 17:52:01: 3000000 INFO @ Mon, 03 Jun 2019 17:52:02: 3000000 INFO @ Mon, 03 Jun 2019 17:52:04: 4000000 INFO @ Mon, 03 Jun 2019 17:52:10: 4000000 INFO @ Mon, 03 Jun 2019 17:52:12: 4000000 INFO @ Mon, 03 Jun 2019 17:52:13: 5000000 INFO @ Mon, 03 Jun 2019 17:52:20: 5000000 INFO @ Mon, 03 Jun 2019 17:52:22: 6000000 INFO @ Mon, 03 Jun 2019 17:52:23: 5000000 INFO @ Mon, 03 Jun 2019 17:52:30: 6000000 INFO @ Mon, 03 Jun 2019 17:52:31: 7000000 INFO @ Mon, 03 Jun 2019 17:52:33: 6000000 INFO @ Mon, 03 Jun 2019 17:52:40: 8000000 INFO @ Mon, 03 Jun 2019 17:52:41: 7000000 INFO @ Mon, 03 Jun 2019 17:52:44: 7000000 INFO @ Mon, 03 Jun 2019 17:52:49: 9000000 INFO @ Mon, 03 Jun 2019 17:52:51: 8000000 INFO @ Mon, 03 Jun 2019 17:52:55: 8000000 INFO @ Mon, 03 Jun 2019 17:52:57: 10000000 INFO @ Mon, 03 Jun 2019 17:53:01: 9000000 INFO @ Mon, 03 Jun 2019 17:53:05: 9000000 INFO @ Mon, 03 Jun 2019 17:53:06: 11000000 INFO @ Mon, 03 Jun 2019 17:53:12: 10000000 INFO @ Mon, 03 Jun 2019 17:53:15: 12000000 INFO @ Mon, 03 Jun 2019 17:53:16: 10000000 INFO @ Mon, 03 Jun 2019 17:53:22: 11000000 INFO @ Mon, 03 Jun 2019 17:53:24: 13000000 INFO @ Mon, 03 Jun 2019 17:53:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:53:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:53:27: #1 total tags in treatment: 13285400 INFO @ Mon, 03 Jun 2019 17:53:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:53:27: #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 17:53:27: 11000000 INFO @ Mon, 03 Jun 2019 17:53:27: #1 tags after filtering in treatment: 13285400 INFO @ Mon, 03 Jun 2019 17:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:53:27: #1 finished! INFO @ Mon, 03 Jun 2019 17:53:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:53:28: #2 number of paired peaks: 93 WARNING @ Mon, 03 Jun 2019 17:53:28: Too few paired peaks (93) 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 17:53:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.20_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/SRX467029/SRX467029.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:53:33: 12000000 INFO @ Mon, 03 Jun 2019 17:53:37: 12000000 INFO @ Mon, 03 Jun 2019 17:53:43: 13000000 INFO @ Mon, 03 Jun 2019 17:53:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:53:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:53:46: #1 total tags in treatment: 13285400 INFO @ Mon, 03 Jun 2019 17:53:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:53:46: #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 17:53:46: #1 tags after filtering in treatment: 13285400 INFO @ Mon, 03 Jun 2019 17:53:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:53:46: #1 finished! INFO @ Mon, 03 Jun 2019 17:53:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:53:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:53:48: #2 number of paired peaks: 93 WARNING @ Mon, 03 Jun 2019 17:53:48: Too few paired peaks (93) 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 17:53:48: Process for pairing-model is terminated! INFO @ Mon, 03 Jun 2019 17:53:48: 13000000 cut: /home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:53:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:53:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:53:51: #1 total tags in treatment: 13285400 INFO @ Mon, 03 Jun 2019 17:53:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:53:51: #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 17:53:51: #1 tags after filtering in treatment: 13285400 INFO @ Mon, 03 Jun 2019 17:53:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:53:51: #1 finished! INFO @ Mon, 03 Jun 2019 17:53:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:53:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:53:52: #2 number of paired peaks: 93 WARNING @ Mon, 03 Jun 2019 17:53:52: Too few paired peaks (93) 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 17:53:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.05_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/SRX467029/SRX467029.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467029/SRX467029.05_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。