Job ID = 2590162 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T10:53:25 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 ) 2019-08-12T10:53:27 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 : 28,232,537 reads read : 28,232,537 reads written : 28,232,537 rm: cannot remove ‘[DSE]RR*’: 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: 00:07:53 28232537 reads; of these: 28232537 (100.00%) were unpaired; of these: 1992411 (7.06%) aligned 0 times 22241232 (78.78%) aligned exactly 1 time 3998894 (14.16%) aligned >1 times 92.94% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4083291 / 26240126 = 0.1556 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, 12 Aug 2019 20:18:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 20:18:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:18:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:18:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 20:18:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:18:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:18:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 20:18:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:18:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:18:15: 1000000 INFO @ Mon, 12 Aug 2019 20:18:16: 1000000 INFO @ Mon, 12 Aug 2019 20:18:16: 1000000 INFO @ Mon, 12 Aug 2019 20:18:23: 2000000 INFO @ Mon, 12 Aug 2019 20:18:24: 2000000 INFO @ Mon, 12 Aug 2019 20:18:25: 2000000 INFO @ Mon, 12 Aug 2019 20:18:31: 3000000 INFO @ Mon, 12 Aug 2019 20:18:32: 3000000 INFO @ Mon, 12 Aug 2019 20:18:34: 3000000 INFO @ Mon, 12 Aug 2019 20:18:39: 4000000 INFO @ Mon, 12 Aug 2019 20:18:39: 4000000 INFO @ Mon, 12 Aug 2019 20:18:44: 4000000 INFO @ Mon, 12 Aug 2019 20:18:46: 5000000 INFO @ Mon, 12 Aug 2019 20:18:47: 5000000 INFO @ Mon, 12 Aug 2019 20:18:53: 5000000 INFO @ Mon, 12 Aug 2019 20:18:54: 6000000 INFO @ Mon, 12 Aug 2019 20:18:55: 6000000 INFO @ Mon, 12 Aug 2019 20:19:02: 6000000 INFO @ Mon, 12 Aug 2019 20:19:02: 7000000 INFO @ Mon, 12 Aug 2019 20:19:03: 7000000 INFO @ Mon, 12 Aug 2019 20:19:10: 8000000 INFO @ Mon, 12 Aug 2019 20:19:10: 8000000 INFO @ Mon, 12 Aug 2019 20:19:11: 7000000 INFO @ Mon, 12 Aug 2019 20:19:17: 9000000 INFO @ Mon, 12 Aug 2019 20:19:18: 9000000 INFO @ Mon, 12 Aug 2019 20:19:20: 8000000 INFO @ Mon, 12 Aug 2019 20:19:25: 10000000 INFO @ Mon, 12 Aug 2019 20:19:28: 10000000 INFO @ Mon, 12 Aug 2019 20:19:30: 9000000 INFO @ Mon, 12 Aug 2019 20:19:33: 11000000 INFO @ Mon, 12 Aug 2019 20:19:38: 11000000 INFO @ Mon, 12 Aug 2019 20:19:39: 10000000 INFO @ Mon, 12 Aug 2019 20:19:41: 12000000 INFO @ Mon, 12 Aug 2019 20:19:48: 12000000 INFO @ Mon, 12 Aug 2019 20:19:49: 11000000 INFO @ Mon, 12 Aug 2019 20:19:49: 13000000 INFO @ Mon, 12 Aug 2019 20:19:57: 14000000 INFO @ Mon, 12 Aug 2019 20:19:58: 13000000 INFO @ Mon, 12 Aug 2019 20:19:59: 12000000 INFO @ Mon, 12 Aug 2019 20:20:06: 15000000 INFO @ Mon, 12 Aug 2019 20:20:07: 14000000 INFO @ Mon, 12 Aug 2019 20:20:09: 13000000 INFO @ Mon, 12 Aug 2019 20:20:14: 16000000 INFO @ Mon, 12 Aug 2019 20:20:18: 15000000 INFO @ Mon, 12 Aug 2019 20:20:19: 14000000 INFO @ Mon, 12 Aug 2019 20:20:22: 17000000 INFO @ Mon, 12 Aug 2019 20:20:28: 16000000 INFO @ Mon, 12 Aug 2019 20:20:29: 15000000 INFO @ Mon, 12 Aug 2019 20:20:31: 18000000 INFO @ Mon, 12 Aug 2019 20:20:39: 17000000 INFO @ Mon, 12 Aug 2019 20:20:39: 19000000 INFO @ Mon, 12 Aug 2019 20:20:39: 16000000 INFO @ Mon, 12 Aug 2019 20:20:47: 20000000 INFO @ Mon, 12 Aug 2019 20:20:49: 18000000 INFO @ Mon, 12 Aug 2019 20:20:50: 17000000 INFO @ Mon, 12 Aug 2019 20:20:55: 21000000 INFO @ Mon, 12 Aug 2019 20:20:59: 19000000 INFO @ Mon, 12 Aug 2019 20:21:00: 18000000 INFO @ Mon, 12 Aug 2019 20:21:03: 22000000 INFO @ Mon, 12 Aug 2019 20:21:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:21:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:21:05: #1 total tags in treatment: 22156835 INFO @ Mon, 12 Aug 2019 20:21:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:21:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:21:05: #1 tags after filtering in treatment: 22156835 INFO @ Mon, 12 Aug 2019 20:21:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:21:05: #1 finished! INFO @ Mon, 12 Aug 2019 20:21:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:21:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:21:07: #2 number of paired peaks: 74 WARNING @ Mon, 12 Aug 2019 20:21:07: Too few paired peaks (74) 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, 12 Aug 2019 20:21:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.10_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/ce10/SRX495032/SRX495032.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:21:09: 20000000 INFO @ Mon, 12 Aug 2019 20:21:10: 19000000 INFO @ Mon, 12 Aug 2019 20:21:19: 21000000 INFO @ Mon, 12 Aug 2019 20:21:20: 20000000 INFO @ Mon, 12 Aug 2019 20:21:29: 22000000 INFO @ Mon, 12 Aug 2019 20:21:30: 21000000 INFO @ Mon, 12 Aug 2019 20:21:31: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:21:31: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:21:31: #1 total tags in treatment: 22156835 INFO @ Mon, 12 Aug 2019 20:21:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:21:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:21:31: #1 tags after filtering in treatment: 22156835 INFO @ Mon, 12 Aug 2019 20:21:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:21:31: #1 finished! INFO @ Mon, 12 Aug 2019 20:21:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:21:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:21:33: #2 number of paired peaks: 74 WARNING @ Mon, 12 Aug 2019 20:21:33: Too few paired peaks (74) 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, 12 Aug 2019 20:21:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.20_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/ce10/SRX495032/SRX495032.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:21:39: 22000000 INFO @ Mon, 12 Aug 2019 20:21:41: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:21:41: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:21:41: #1 total tags in treatment: 22156835 INFO @ Mon, 12 Aug 2019 20:21:41: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:21:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:21:41: #1 tags after filtering in treatment: 22156835 INFO @ Mon, 12 Aug 2019 20:21:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:21:41: #1 finished! INFO @ Mon, 12 Aug 2019 20:21:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:21:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:21:43: #2 number of paired peaks: 74 WARNING @ Mon, 12 Aug 2019 20:21:43: Too few paired peaks (74) 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, 12 Aug 2019 20:21:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.05_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/ce10/SRX495032/SRX495032.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX495032/SRX495032.05_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。