Job ID = 4289056 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:26:25 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 ) spots read : 17,996,522 reads read : 17,996,522 reads written : 17,996,522 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: 00:03:20 17996522 reads; of these: 17996522 (100.00%) were unpaired; of these: 1723623 (9.58%) aligned 0 times 14063179 (78.14%) aligned exactly 1 time 2209720 (12.28%) aligned >1 times 90.42% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 9977397 / 16272899 = 0.6131 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:36:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.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 13:36:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:36:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:36:09: 1000000 INFO @ Tue, 10 Dec 2019 13:36:18: 2000000 INFO @ Tue, 10 Dec 2019 13:36:26: 3000000 INFO @ Tue, 10 Dec 2019 13:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.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 13:36:30: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:36:30: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:36:35: 4000000 INFO @ Tue, 10 Dec 2019 13:36:40: 1000000 INFO @ Tue, 10 Dec 2019 13:36:43: 5000000 INFO @ Tue, 10 Dec 2019 13:36:50: 2000000 INFO @ Tue, 10 Dec 2019 13:36:52: 6000000 INFO @ Tue, 10 Dec 2019 13:36:54: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 13:36:54: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 13:36:54: #1 total tags in treatment: 6295502 INFO @ Tue, 10 Dec 2019 13:36:54: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:36:54: #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 13:36:54: #1 tags after filtering in treatment: 6295502 INFO @ Tue, 10 Dec 2019 13:36:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:36:54: #1 finished! INFO @ Tue, 10 Dec 2019 13:36:54: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:36:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:36:55: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:36:55: 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 @ Tue, 10 Dec 2019 13:36:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.05_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/SRX3479953/SRX3479953.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:37:00: 3000000 INFO @ Tue, 10 Dec 2019 13:37:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.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 13:37:00: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:37:00: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:37:09: 4000000 INFO @ Tue, 10 Dec 2019 13:37:09: 1000000 INFO @ Tue, 10 Dec 2019 13:37:18: 2000000 INFO @ Tue, 10 Dec 2019 13:37:19: 5000000 INFO @ Tue, 10 Dec 2019 13:37:27: 3000000 INFO @ Tue, 10 Dec 2019 13:37:28: 6000000 INFO @ Tue, 10 Dec 2019 13:37:31: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 13:37:31: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 13:37:31: #1 total tags in treatment: 6295502 INFO @ Tue, 10 Dec 2019 13:37:31: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:37:31: #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 13:37:31: #1 tags after filtering in treatment: 6295502 INFO @ Tue, 10 Dec 2019 13:37:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:37:31: #1 finished! INFO @ Tue, 10 Dec 2019 13:37:31: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:37:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:37:32: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:37:32: 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 @ Tue, 10 Dec 2019 13:37:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:37:35: 4000000 INFO @ Tue, 10 Dec 2019 13:37:44: 5000000 INFO @ Tue, 10 Dec 2019 13:37:52: 6000000 INFO @ Tue, 10 Dec 2019 13:37:54: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 13:37:54: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 13:37:54: #1 total tags in treatment: 6295502 INFO @ Tue, 10 Dec 2019 13:37:54: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:37:54: #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 13:37:54: #1 tags after filtering in treatment: 6295502 INFO @ Tue, 10 Dec 2019 13:37:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:37:54: #1 finished! INFO @ Tue, 10 Dec 2019 13:37:54: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:37:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:37:55: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:37:55: 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 @ Tue, 10 Dec 2019 13:37:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.20_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/SRX3479953/SRX3479953.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3479953/SRX3479953.20_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。