Job ID = 2010989 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T16:32:40 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 : 6,999,492 reads read : 13,998,984 reads written : 10,136,020 reads 0-length : 3,862,964 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 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 48995 / 1714490 = 0.0286 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 06 Jul 2019 01:39:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.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, 06 Jul 2019 01:39:34: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:39:34: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:39:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.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, 06 Jul 2019 01:39:35: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:39:35: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:39:41: 1000000 INFO @ Sat, 06 Jul 2019 01:39:43: 1000000 INFO @ Sat, 06 Jul 2019 01:39:48: 2000000 INFO @ Sat, 06 Jul 2019 01:39:51: 2000000 INFO @ Sat, 06 Jul 2019 01:39:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.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, 06 Jul 2019 01:39:54: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:39:54: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:39:56: 3000000 INFO @ Sat, 06 Jul 2019 01:40:00: 3000000 INFO @ Sat, 06 Jul 2019 01:40:02: 1000000 INFO @ Sat, 06 Jul 2019 01:40:03: 4000000 INFO @ Sat, 06 Jul 2019 01:40:07: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:40:07: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:40:07: #1 total tags in treatment: 1658036 INFO @ Sat, 06 Jul 2019 01:40:07: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:40:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:40:07: #1 tags after filtering in treatment: 1351754 INFO @ Sat, 06 Jul 2019 01:40:07: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 06 Jul 2019 01:40:07: #1 finished! INFO @ Sat, 06 Jul 2019 01:40:07: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:40:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:40:08: #2 number of paired peaks: 27 WARNING @ Sat, 06 Jul 2019 01:40:08: Too few paired peaks (27) 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, 06 Jul 2019 01:40:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.05_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/SRX4342935/SRX4342935.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:40:08: 4000000 INFO @ Sat, 06 Jul 2019 01:40:10: 2000000 INFO @ Sat, 06 Jul 2019 01:40:12: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:40:12: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:40:12: #1 total tags in treatment: 1658036 INFO @ Sat, 06 Jul 2019 01:40:12: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:40:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:40:13: #1 tags after filtering in treatment: 1351754 INFO @ Sat, 06 Jul 2019 01:40:13: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 06 Jul 2019 01:40:13: #1 finished! INFO @ Sat, 06 Jul 2019 01:40:13: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:40:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:40:13: #2 number of paired peaks: 27 WARNING @ Sat, 06 Jul 2019 01:40:13: Too few paired peaks (27) 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, 06 Jul 2019 01:40:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.10_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/SRX4342935/SRX4342935.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:40:16: 3000000 INFO @ Sat, 06 Jul 2019 01:40:23: 4000000 INFO @ Sat, 06 Jul 2019 01:40:27: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:40:27: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:40:27: #1 total tags in treatment: 1658036 INFO @ Sat, 06 Jul 2019 01:40:27: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:40:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:40:27: #1 tags after filtering in treatment: 1351754 INFO @ Sat, 06 Jul 2019 01:40:27: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 06 Jul 2019 01:40:27: #1 finished! INFO @ Sat, 06 Jul 2019 01:40:27: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:40:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:40:27: #2 number of paired peaks: 27 WARNING @ Sat, 06 Jul 2019 01:40:27: Too few paired peaks (27) 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, 06 Jul 2019 01:40:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.20_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/SRX4342935/SRX4342935.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342935/SRX4342935.20_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。