Job ID = 2640857 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T10:37:40 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 ) 2019-08-24T10:37:40 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 ) 2019-08-24T10:37:40 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 : 20,758,722 reads read : 41,517,444 reads written : 20,758,722 reads 0-length : 20,758,722 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: 00:03:12 20758722 reads; of these: 20758722 (100.00%) were unpaired; of these: 3662312 (17.64%) aligned 0 times 15435180 (74.36%) aligned exactly 1 time 1661230 (8.00%) aligned >1 times 82.36% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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 8 files... [bam_rmdupse_core] 7146083 / 17096410 = 0.4180 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:45:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.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 19:45:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:45:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:45:27: 1000000 INFO @ Sat, 24 Aug 2019 19:45:34: 2000000 INFO @ Sat, 24 Aug 2019 19:45:41: 3000000 INFO @ Sat, 24 Aug 2019 19:45:47: 4000000 INFO @ Sat, 24 Aug 2019 19:45:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.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 19:45:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:45:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:45:54: 5000000 INFO @ Sat, 24 Aug 2019 19:45:57: 1000000 INFO @ Sat, 24 Aug 2019 19:46:01: 6000000 INFO @ Sat, 24 Aug 2019 19:46:03: 2000000 INFO @ Sat, 24 Aug 2019 19:46:08: 7000000 INFO @ Sat, 24 Aug 2019 19:46:09: 3000000 INFO @ Sat, 24 Aug 2019 19:46:15: 8000000 INFO @ Sat, 24 Aug 2019 19:46:15: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.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 19:46:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:46:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:46:22: 9000000 INFO @ Sat, 24 Aug 2019 19:46:22: 5000000 INFO @ Sat, 24 Aug 2019 19:46:27: 1000000 INFO @ Sat, 24 Aug 2019 19:46:28: 6000000 INFO @ Sat, 24 Aug 2019 19:46:28: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 19:46:28: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 19:46:28: #1 total tags in treatment: 9950327 INFO @ Sat, 24 Aug 2019 19:46:28: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:46:28: #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 19:46:28: #1 tags after filtering in treatment: 9950327 INFO @ Sat, 24 Aug 2019 19:46:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:46:28: #1 finished! INFO @ Sat, 24 Aug 2019 19:46:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:46:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:46:29: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:46:29: 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 19:46:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.05_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/SRX3944353/SRX3944353.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:46:34: 2000000 INFO @ Sat, 24 Aug 2019 19:46:34: 7000000 INFO @ Sat, 24 Aug 2019 19:46:41: 8000000 INFO @ Sat, 24 Aug 2019 19:46:41: 3000000 INFO @ Sat, 24 Aug 2019 19:46:47: 9000000 INFO @ Sat, 24 Aug 2019 19:46:48: 4000000 INFO @ Sat, 24 Aug 2019 19:46:53: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 19:46:53: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 19:46:53: #1 total tags in treatment: 9950327 INFO @ Sat, 24 Aug 2019 19:46:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:46:53: #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 19:46:53: #1 tags after filtering in treatment: 9950327 INFO @ Sat, 24 Aug 2019 19:46:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:46:53: #1 finished! INFO @ Sat, 24 Aug 2019 19:46:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:46:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:46:54: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:46:54: 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 19:46:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.10_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/SRX3944353/SRX3944353.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:46:54: 5000000 INFO @ Sat, 24 Aug 2019 19:47:01: 6000000 INFO @ Sat, 24 Aug 2019 19:47:08: 7000000 INFO @ Sat, 24 Aug 2019 19:47:15: 8000000 INFO @ Sat, 24 Aug 2019 19:47:22: 9000000 INFO @ Sat, 24 Aug 2019 19:47:28: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 19:47:28: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 19:47:28: #1 total tags in treatment: 9950327 INFO @ Sat, 24 Aug 2019 19:47:28: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:47:28: #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 19:47:28: #1 tags after filtering in treatment: 9950327 INFO @ Sat, 24 Aug 2019 19:47:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:47:28: #1 finished! INFO @ Sat, 24 Aug 2019 19:47:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:47:29: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:47:29: 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 19:47:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.20_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/SRX3944353/SRX3944353.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944353/SRX3944353.20_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。