Job ID = 1298803 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:34:51 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 ) 2019-06-03T08:34:51 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 ) 2019-06-03T08:34:51 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 ) 2019-06-03T08:37:41 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 ) 2019-06-03T08:40:30 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 ) 2019-06-03T08:43:03 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 ) spots read : 18,176,876 reads read : 18,176,876 reads written : 18,176,876 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: 00:06:16 18176876 reads; of these: 18176876 (100.00%) were unpaired; of these: 907378 (4.99%) aligned 0 times 13289099 (73.11%) aligned exactly 1 time 3980399 (21.90%) aligned >1 times 95.01% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 3181582 / 17269498 = 0.1842 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 17:54:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.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 17:54:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:54:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:54:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.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 17:54:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:54:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:54:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.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 17:54:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:54:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:54:54: 1000000 INFO @ Mon, 03 Jun 2019 17:54:54: 1000000 INFO @ Mon, 03 Jun 2019 17:54:54: 1000000 INFO @ Mon, 03 Jun 2019 17:55:02: 2000000 INFO @ Mon, 03 Jun 2019 17:55:03: 2000000 INFO @ Mon, 03 Jun 2019 17:55:04: 2000000 INFO @ Mon, 03 Jun 2019 17:55:11: 3000000 INFO @ Mon, 03 Jun 2019 17:55:13: 3000000 INFO @ Mon, 03 Jun 2019 17:55:13: 3000000 INFO @ Mon, 03 Jun 2019 17:55:19: 4000000 INFO @ Mon, 03 Jun 2019 17:55:22: 4000000 INFO @ Mon, 03 Jun 2019 17:55:23: 4000000 INFO @ Mon, 03 Jun 2019 17:55:28: 5000000 INFO @ Mon, 03 Jun 2019 17:55:31: 5000000 INFO @ Mon, 03 Jun 2019 17:55:32: 5000000 INFO @ Mon, 03 Jun 2019 17:55:38: 6000000 INFO @ Mon, 03 Jun 2019 17:55:40: 6000000 INFO @ Mon, 03 Jun 2019 17:55:41: 6000000 INFO @ Mon, 03 Jun 2019 17:55:46: 7000000 INFO @ Mon, 03 Jun 2019 17:55:49: 7000000 INFO @ Mon, 03 Jun 2019 17:55:50: 7000000 INFO @ Mon, 03 Jun 2019 17:55:55: 8000000 INFO @ Mon, 03 Jun 2019 17:55:57: 8000000 INFO @ Mon, 03 Jun 2019 17:55:59: 8000000 INFO @ Mon, 03 Jun 2019 17:56:03: 9000000 INFO @ Mon, 03 Jun 2019 17:56:06: 9000000 INFO @ Mon, 03 Jun 2019 17:56:09: 9000000 INFO @ Mon, 03 Jun 2019 17:56:13: 10000000 INFO @ Mon, 03 Jun 2019 17:56:15: 10000000 INFO @ Mon, 03 Jun 2019 17:56:18: 10000000 INFO @ Mon, 03 Jun 2019 17:56:22: 11000000 INFO @ Mon, 03 Jun 2019 17:56:24: 11000000 INFO @ Mon, 03 Jun 2019 17:56:28: 11000000 INFO @ Mon, 03 Jun 2019 17:56:31: 12000000 INFO @ Mon, 03 Jun 2019 17:56:33: 12000000 INFO @ Mon, 03 Jun 2019 17:56:37: 12000000 INFO @ Mon, 03 Jun 2019 17:56:40: 13000000 INFO @ Mon, 03 Jun 2019 17:56:42: 13000000 INFO @ Mon, 03 Jun 2019 17:56:46: 13000000 INFO @ Mon, 03 Jun 2019 17:56:50: 14000000 INFO @ Mon, 03 Jun 2019 17:56:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:56:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:56:50: #1 total tags in treatment: 14087916 INFO @ Mon, 03 Jun 2019 17:56:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:56:50: #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 17:56:51: #1 tags after filtering in treatment: 14087916 INFO @ Mon, 03 Jun 2019 17:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:56:51: #1 finished! INFO @ Mon, 03 Jun 2019 17:56:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:56:51: 14000000 INFO @ Mon, 03 Jun 2019 17:56:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:56:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:56:52: #1 total tags in treatment: 14087916 INFO @ Mon, 03 Jun 2019 17:56:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:56:52: #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 17:56:52: #2 number of paired peaks: 90 WARNING @ Mon, 03 Jun 2019 17:56:52: Too few paired peaks (90) 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 17:56:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.10_peaks.narrowPeak: No such file or directory INFO @ Mon, 03 Jun 2019 17:56:52: #1 tags after filtering in treatment: 14087916 INFO @ Mon, 03 Jun 2019 17:56:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:56:52: #1 finished! INFO @ Mon, 03 Jun 2019 17:56:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:56:52: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:56:53: #2 number of paired peaks: 90 WARNING @ Mon, 03 Jun 2019 17:56:53: Too few paired peaks (90) 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 17:56:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.05_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/SRX467052/SRX467052.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:56:56: 14000000 INFO @ Mon, 03 Jun 2019 17:56:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:56:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:56:56: #1 total tags in treatment: 14087916 INFO @ Mon, 03 Jun 2019 17:56:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:56:56: #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 17:56:57: #1 tags after filtering in treatment: 14087916 INFO @ Mon, 03 Jun 2019 17:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:56:57: #1 finished! INFO @ Mon, 03 Jun 2019 17:56:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:56:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:56:58: #2 number of paired peaks: 90 WARNING @ Mon, 03 Jun 2019 17:56:58: Too few paired peaks (90) 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 17:56:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.20_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/SRX467052/SRX467052.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467052/SRX467052.20_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。