Job ID = 2010757 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T15:30:22 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 ) 2019-07-05T15:30:22 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 ) 2019-07-05T15:33:23 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 ) 2019-07-05T15:34:53 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 ) spots read : 53,677,470 reads read : 53,677,470 reads written : 53,677,470 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: 00:09:41 53677470 reads; of these: 53677470 (100.00%) were unpaired; of these: 2786369 (5.19%) aligned 0 times 46216904 (86.10%) aligned exactly 1 time 4674197 (8.71%) aligned >1 times 94.81% overall alignment rate Time searching: 00:09:41 Overall time: 00:09:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 34868947 / 50891101 = 0.6852 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 @ Sat, 06 Jul 2019 01:10:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 06 Jul 2019 01:10:07: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:10:07: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:10:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 06 Jul 2019 01:10:08: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:10:08: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:10:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 06 Jul 2019 01:10:09: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:10:09: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:10:16: 1000000 INFO @ Sat, 06 Jul 2019 01:10:17: 1000000 INFO @ Sat, 06 Jul 2019 01:10:17: 1000000 INFO @ Sat, 06 Jul 2019 01:10:24: 2000000 INFO @ Sat, 06 Jul 2019 01:10:25: 2000000 INFO @ Sat, 06 Jul 2019 01:10:25: 2000000 INFO @ Sat, 06 Jul 2019 01:10:32: 3000000 INFO @ Sat, 06 Jul 2019 01:10:33: 3000000 INFO @ Sat, 06 Jul 2019 01:10:33: 3000000 INFO @ Sat, 06 Jul 2019 01:10:39: 4000000 INFO @ Sat, 06 Jul 2019 01:10:40: 4000000 INFO @ Sat, 06 Jul 2019 01:10:41: 4000000 INFO @ Sat, 06 Jul 2019 01:10:46: 5000000 INFO @ Sat, 06 Jul 2019 01:10:47: 5000000 INFO @ Sat, 06 Jul 2019 01:10:49: 5000000 INFO @ Sat, 06 Jul 2019 01:10:53: 6000000 INFO @ Sat, 06 Jul 2019 01:10:55: 6000000 INFO @ Sat, 06 Jul 2019 01:10:56: 6000000 INFO @ Sat, 06 Jul 2019 01:11:01: 7000000 INFO @ Sat, 06 Jul 2019 01:11:02: 7000000 INFO @ Sat, 06 Jul 2019 01:11:04: 7000000 INFO @ Sat, 06 Jul 2019 01:11:08: 8000000 INFO @ Sat, 06 Jul 2019 01:11:09: 8000000 INFO @ Sat, 06 Jul 2019 01:11:12: 8000000 INFO @ Sat, 06 Jul 2019 01:11:15: 9000000 INFO @ Sat, 06 Jul 2019 01:11:16: 9000000 INFO @ Sat, 06 Jul 2019 01:11:20: 9000000 INFO @ Sat, 06 Jul 2019 01:11:22: 10000000 INFO @ Sat, 06 Jul 2019 01:11:23: 10000000 INFO @ Sat, 06 Jul 2019 01:11:28: 10000000 INFO @ Sat, 06 Jul 2019 01:11:29: 11000000 INFO @ Sat, 06 Jul 2019 01:11:30: 11000000 INFO @ Sat, 06 Jul 2019 01:11:36: 11000000 INFO @ Sat, 06 Jul 2019 01:11:37: 12000000 INFO @ Sat, 06 Jul 2019 01:11:38: 12000000 INFO @ Sat, 06 Jul 2019 01:11:44: 12000000 INFO @ Sat, 06 Jul 2019 01:11:44: 13000000 INFO @ Sat, 06 Jul 2019 01:11:45: 13000000 INFO @ Sat, 06 Jul 2019 01:11:51: 14000000 INFO @ Sat, 06 Jul 2019 01:11:52: 13000000 INFO @ Sat, 06 Jul 2019 01:11:52: 14000000 INFO @ Sat, 06 Jul 2019 01:11:58: 15000000 INFO @ Sat, 06 Jul 2019 01:11:59: 15000000 INFO @ Sat, 06 Jul 2019 01:11:59: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 01:12:06: 16000000 INFO @ Sat, 06 Jul 2019 01:12:06: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 01:12:06: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 01:12:06: #1 total tags in treatment: 16022154 INFO @ Sat, 06 Jul 2019 01:12:06: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:12:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:12:06: #1 tags after filtering in treatment: 16022154 INFO @ Sat, 06 Jul 2019 01:12:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:12:06: #1 finished! INFO @ Sat, 06 Jul 2019 01:12:06: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:12:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:12:07: 16000000 INFO @ Sat, 06 Jul 2019 01:12:07: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 01:12:07: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 01:12:07: #1 total tags in treatment: 16022154 INFO @ Sat, 06 Jul 2019 01:12:07: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:12:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:12:07: #1 tags after filtering in treatment: 16022154 INFO @ Sat, 06 Jul 2019 01:12:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:12:07: #1 finished! INFO @ Sat, 06 Jul 2019 01:12:07: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:12:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:12:07: 15000000 INFO @ Sat, 06 Jul 2019 01:12:07: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:12:07: Too few paired peaks (0) 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 @ Sat, 06 Jul 2019 01:12:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.20_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/sacCer3/SRX387215/SRX387215.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:12:08: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:12:08: Too few paired peaks (0) 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 @ Sat, 06 Jul 2019 01:12:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.10_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/sacCer3/SRX387215/SRX387215.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:12:15: 16000000 INFO @ Sat, 06 Jul 2019 01:12:15: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 01:12:15: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 01:12:15: #1 total tags in treatment: 16022154 INFO @ Sat, 06 Jul 2019 01:12:15: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:12:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:12:15: #1 tags after filtering in treatment: 16022154 INFO @ Sat, 06 Jul 2019 01:12:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:12:15: #1 finished! INFO @ Sat, 06 Jul 2019 01:12:15: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:12:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:12:17: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:12:17: Too few paired peaks (0) 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 @ Sat, 06 Jul 2019 01:12:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.05_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/sacCer3/SRX387215/SRX387215.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387215/SRX387215.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。