Job ID = 2640747 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:49:50 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 ) 2019-08-24T09:49:50 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 ) 2019-08-24T09:53:37 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 ) 2019-08-24T10:04:29 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 ) spots read : 24,903,486 reads read : 24,903,486 reads written : 24,903,486 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: 00:06:07 24903486 reads; of these: 24903486 (100.00%) were unpaired; of these: 1612024 (6.47%) aligned 0 times 20984115 (84.26%) aligned exactly 1 time 2307347 (9.27%) aligned >1 times 93.53% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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 12 files... [bam_rmdupse_core] 13196753 / 23291462 = 0.5666 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:19:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.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, 24 Aug 2019 19:19:40: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:19:40: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:19:47: 1000000 INFO @ Sat, 24 Aug 2019 19:19:54: 2000000 INFO @ Sat, 24 Aug 2019 19:20:00: 3000000 INFO @ Sat, 24 Aug 2019 19:20:07: 4000000 INFO @ Sat, 24 Aug 2019 19:20:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.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, 24 Aug 2019 19:20:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:20:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:20:14: 5000000 INFO @ Sat, 24 Aug 2019 19:20:17: 1000000 INFO @ Sat, 24 Aug 2019 19:20:20: 6000000 INFO @ Sat, 24 Aug 2019 19:20:24: 2000000 INFO @ Sat, 24 Aug 2019 19:20:27: 7000000 INFO @ Sat, 24 Aug 2019 19:20:32: 3000000 INFO @ Sat, 24 Aug 2019 19:20:34: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:20:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.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, 24 Aug 2019 19:20:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:20:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:20:39: 4000000 INFO @ Sat, 24 Aug 2019 19:20:40: 9000000 INFO @ Sat, 24 Aug 2019 19:20:47: 5000000 INFO @ Sat, 24 Aug 2019 19:20:47: 10000000 INFO @ Sat, 24 Aug 2019 19:20:47: 1000000 INFO @ Sat, 24 Aug 2019 19:20:48: #1 tag size is determined as 49 bps INFO @ Sat, 24 Aug 2019 19:20:48: #1 tag size = 49 INFO @ Sat, 24 Aug 2019 19:20:48: #1 total tags in treatment: 10094709 INFO @ Sat, 24 Aug 2019 19:20:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:20:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:20:48: #1 tags after filtering in treatment: 10094709 INFO @ Sat, 24 Aug 2019 19:20:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:20:48: #1 finished! INFO @ Sat, 24 Aug 2019 19:20:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:20:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:20:49: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:20:49: 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, 24 Aug 2019 19:20:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.05_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/sacCer3/ERX2732438/ERX2732438.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:20:54: 6000000 INFO @ Sat, 24 Aug 2019 19:20:55: 2000000 INFO @ Sat, 24 Aug 2019 19:21:01: 7000000 INFO @ Sat, 24 Aug 2019 19:21:03: 3000000 INFO @ Sat, 24 Aug 2019 19:21:09: 8000000 INFO @ Sat, 24 Aug 2019 19:21:10: 4000000 INFO @ Sat, 24 Aug 2019 19:21:16: 9000000 INFO @ Sat, 24 Aug 2019 19:21:18: 5000000 INFO @ Sat, 24 Aug 2019 19:21:23: 10000000 INFO @ Sat, 24 Aug 2019 19:21:24: #1 tag size is determined as 49 bps INFO @ Sat, 24 Aug 2019 19:21:24: #1 tag size = 49 INFO @ Sat, 24 Aug 2019 19:21:24: #1 total tags in treatment: 10094709 INFO @ Sat, 24 Aug 2019 19:21:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:21:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:21:24: #1 tags after filtering in treatment: 10094709 INFO @ Sat, 24 Aug 2019 19:21:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:21:24: #1 finished! INFO @ Sat, 24 Aug 2019 19:21:24: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:21:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:21:25: 6000000 INFO @ Sat, 24 Aug 2019 19:21:25: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:21:25: 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, 24 Aug 2019 19:21:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.10_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/ERX2732438/ERX2732438.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:21:32: 7000000 INFO @ Sat, 24 Aug 2019 19:21:39: 8000000 INFO @ Sat, 24 Aug 2019 19:21:47: 9000000 INFO @ Sat, 24 Aug 2019 19:21:54: 10000000 INFO @ Sat, 24 Aug 2019 19:21:55: #1 tag size is determined as 49 bps INFO @ Sat, 24 Aug 2019 19:21:55: #1 tag size = 49 INFO @ Sat, 24 Aug 2019 19:21:55: #1 total tags in treatment: 10094709 INFO @ Sat, 24 Aug 2019 19:21:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:21:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:21:55: #1 tags after filtering in treatment: 10094709 INFO @ Sat, 24 Aug 2019 19:21:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:21:55: #1 finished! INFO @ Sat, 24 Aug 2019 19:21:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:21:56: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:21:56: 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, 24 Aug 2019 19:21:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.20_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/sacCer3/ERX2732438/ERX2732438.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732438/ERX2732438.20_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。