Job ID = 4289096 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:31:24 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 ) 2019-12-10T04:31:24 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 : 13,088,224 reads read : 26,176,448 reads written : 13,088,224 reads 0-length : 13,088,224 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: 00:02:34 13088224 reads; of these: 13088224 (100.00%) were unpaired; of these: 7726140 (59.03%) aligned 0 times 3717559 (28.40%) aligned exactly 1 time 1644525 (12.56%) aligned >1 times 40.97% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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_rmdupse_core] 3091787 / 5362084 = 0.5766 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:37:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.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 @ Tue, 10 Dec 2019 13:37:34: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:37:34: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:37:43: 1000000 INFO @ Tue, 10 Dec 2019 13:37:54: 2000000 INFO @ Tue, 10 Dec 2019 13:37:57: #1 tag size is determined as 101 bps INFO @ Tue, 10 Dec 2019 13:37:57: #1 tag size = 101 INFO @ Tue, 10 Dec 2019 13:37:57: #1 total tags in treatment: 2270297 INFO @ Tue, 10 Dec 2019 13:37:57: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:37:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:37:57: #1 tags after filtering in treatment: 2270297 INFO @ Tue, 10 Dec 2019 13:37:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:37:57: #1 finished! INFO @ Tue, 10 Dec 2019 13:37:57: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:37:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:37:57: #2 number of paired peaks: 60 WARNING @ Tue, 10 Dec 2019 13:37:57: Too few paired peaks (60) 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 @ Tue, 10 Dec 2019 13:37:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.05_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/SRX5086840/SRX5086840.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:38:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.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 @ Tue, 10 Dec 2019 13:38:04: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:38:04: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:38:14: 1000000 INFO @ Tue, 10 Dec 2019 13:38:24: 2000000 INFO @ Tue, 10 Dec 2019 13:38:27: #1 tag size is determined as 101 bps INFO @ Tue, 10 Dec 2019 13:38:27: #1 tag size = 101 INFO @ Tue, 10 Dec 2019 13:38:27: #1 total tags in treatment: 2270297 INFO @ Tue, 10 Dec 2019 13:38:27: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:38:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:38:27: #1 tags after filtering in treatment: 2270297 INFO @ Tue, 10 Dec 2019 13:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:38:27: #1 finished! INFO @ Tue, 10 Dec 2019 13:38:27: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:38:27: #2 number of paired peaks: 60 WARNING @ Tue, 10 Dec 2019 13:38:27: Too few paired peaks (60) 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 @ Tue, 10 Dec 2019 13:38:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.10_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/SRX5086840/SRX5086840.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:38:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.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 @ Tue, 10 Dec 2019 13:38:34: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:38:34: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:38:44: 1000000 INFO @ Tue, 10 Dec 2019 13:38:54: 2000000 INFO @ Tue, 10 Dec 2019 13:38:57: #1 tag size is determined as 101 bps INFO @ Tue, 10 Dec 2019 13:38:57: #1 tag size = 101 INFO @ Tue, 10 Dec 2019 13:38:57: #1 total tags in treatment: 2270297 INFO @ Tue, 10 Dec 2019 13:38:57: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:38:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:38:57: #1 tags after filtering in treatment: 2270297 INFO @ Tue, 10 Dec 2019 13:38:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:38:57: #1 finished! INFO @ Tue, 10 Dec 2019 13:38:57: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:38:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:38:57: #2 number of paired peaks: 60 WARNING @ Tue, 10 Dec 2019 13:38:57: Too few paired peaks (60) 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 @ Tue, 10 Dec 2019 13:38:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.20_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/SRX5086840/SRX5086840.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086840/SRX5086840.20_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。