Job ID = 4289127 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:40:05 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 ) 2019-12-10T04:40:05 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 : 31,925,916 reads read : 63,851,832 reads written : 31,925,916 reads 0-length : 31,925,916 spots read : 25,590,752 reads read : 51,181,504 reads written : 25,590,752 reads 0-length : 25,590,752 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: 00:07:08 57516668 reads; of these: 57516668 (100.00%) were unpaired; of these: 41647290 (72.41%) aligned 0 times 10361371 (18.01%) aligned exactly 1 time 5508007 (9.58%) aligned >1 times 27.59% overall alignment rate Time searching: 00:07:08 Overall time: 00:07:08 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] 7776981 / 15869378 = 0.4901 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.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 14:01:26: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:01:26: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:01:37: 1000000 INFO @ Tue, 10 Dec 2019 14:01:47: 2000000 INFO @ Tue, 10 Dec 2019 14:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.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 14:01:56: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:01:56: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:01:58: 3000000 INFO @ Tue, 10 Dec 2019 14:02:06: 1000000 INFO @ Tue, 10 Dec 2019 14:02:08: 4000000 INFO @ Tue, 10 Dec 2019 14:02:16: 2000000 INFO @ Tue, 10 Dec 2019 14:02:18: 5000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:02:26: 3000000 INFO @ Tue, 10 Dec 2019 14:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.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 14:02:26: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:02:26: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:02:29: 6000000 INFO @ Tue, 10 Dec 2019 14:02:36: 4000000 INFO @ Tue, 10 Dec 2019 14:02:37: 1000000 INFO @ Tue, 10 Dec 2019 14:02:40: 7000000 INFO @ Tue, 10 Dec 2019 14:02:47: 5000000 INFO @ Tue, 10 Dec 2019 14:02:49: 2000000 INFO @ Tue, 10 Dec 2019 14:02:51: 8000000 INFO @ Tue, 10 Dec 2019 14:02:52: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 14:02:52: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 14:02:52: #1 total tags in treatment: 8092397 INFO @ Tue, 10 Dec 2019 14:02:52: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:02:52: #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 14:02:52: #1 tags after filtering in treatment: 8092397 INFO @ Tue, 10 Dec 2019 14:02:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:02:52: #1 finished! INFO @ Tue, 10 Dec 2019 14:02:52: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:02:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:02:53: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:02:53: 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 14:02:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.05_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/SRX5486254/SRX5486254.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:02:59: 6000000 INFO @ Tue, 10 Dec 2019 14:03:00: 3000000 INFO @ Tue, 10 Dec 2019 14:03:09: 7000000 INFO @ Tue, 10 Dec 2019 14:03:11: 4000000 INFO @ Tue, 10 Dec 2019 14:03:19: 8000000 INFO @ Tue, 10 Dec 2019 14:03:20: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 14:03:20: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 14:03:20: #1 total tags in treatment: 8092397 INFO @ Tue, 10 Dec 2019 14:03:20: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:03:20: #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 14:03:20: #1 tags after filtering in treatment: 8092397 INFO @ Tue, 10 Dec 2019 14:03:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:03:20: #1 finished! INFO @ Tue, 10 Dec 2019 14:03:20: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:03:20: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:03:20: 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 14:03:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.10_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/SRX5486254/SRX5486254.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:03:21: 5000000 INFO @ Tue, 10 Dec 2019 14:03:32: 6000000 INFO @ Tue, 10 Dec 2019 14:03:42: 7000000 INFO @ Tue, 10 Dec 2019 14:03:50: 8000000 INFO @ Tue, 10 Dec 2019 14:03:51: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 14:03:51: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 14:03:51: #1 total tags in treatment: 8092397 INFO @ Tue, 10 Dec 2019 14:03:51: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:03:51: #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 14:03:51: #1 tags after filtering in treatment: 8092397 INFO @ Tue, 10 Dec 2019 14:03:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:03:51: #1 finished! INFO @ Tue, 10 Dec 2019 14:03:51: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:03:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:03:52: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:03:52: 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 14:03:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.20_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/SRX5486254/SRX5486254.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486254/SRX5486254.20_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。