Job ID = 2011839 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:52:02 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 : 16,316,100 reads read : 32,632,200 reads written : 32,632,197 reads 0-length : 3 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 Warning: skipping mate #1 of read 'SRR8313287.88780 88780 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313287.88780 88780 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313287.1111678 1111678 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313287.1111678 1111678 length=1' because it was < 2 characters long Error, fewer reads in file specified with -1 than in file specified with -2 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_sort_core] merging from 16 files... [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] 10651948 / 15759798 = 0.6759 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 03:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.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 03:29:35: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:29:35: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:29:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.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 03:29:36: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:29:36: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:29:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.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 03:29:36: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:29:36: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:29:44: 1000000 INFO @ Sat, 06 Jul 2019 03:29:47: 1000000 INFO @ Sat, 06 Jul 2019 03:29:47: 1000000 INFO @ Sat, 06 Jul 2019 03:29:52: 2000000 INFO @ Sat, 06 Jul 2019 03:29:57: 2000000 INFO @ Sat, 06 Jul 2019 03:29:58: 2000000 INFO @ Sat, 06 Jul 2019 03:30:00: 3000000 INFO @ Sat, 06 Jul 2019 03:30:07: 4000000 INFO @ Sat, 06 Jul 2019 03:30:08: 3000000 INFO @ Sat, 06 Jul 2019 03:30:08: 3000000 INFO @ Sat, 06 Jul 2019 03:30:15: 5000000 INFO @ Sat, 06 Jul 2019 03:30:18: 4000000 INFO @ Sat, 06 Jul 2019 03:30:19: 4000000 INFO @ Sat, 06 Jul 2019 03:30:22: 6000000 INFO @ Sat, 06 Jul 2019 03:30:27: 5000000 INFO @ Sat, 06 Jul 2019 03:30:29: 5000000 INFO @ Sat, 06 Jul 2019 03:30:29: 7000000 INFO @ Sat, 06 Jul 2019 03:30:37: 8000000 INFO @ Sat, 06 Jul 2019 03:30:37: 6000000 INFO @ Sat, 06 Jul 2019 03:30:40: 6000000 INFO @ Sat, 06 Jul 2019 03:30:45: 9000000 INFO @ Sat, 06 Jul 2019 03:30:47: 7000000 INFO @ Sat, 06 Jul 2019 03:30:50: 7000000 INFO @ Sat, 06 Jul 2019 03:30:52: 10000000 INFO @ Sat, 06 Jul 2019 03:30:55: #1 tag size is determined as 73 bps INFO @ Sat, 06 Jul 2019 03:30:55: #1 tag size = 73 INFO @ Sat, 06 Jul 2019 03:30:55: #1 total tags in treatment: 5103896 INFO @ Sat, 06 Jul 2019 03:30:55: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:30:55: #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 03:30:55: #1 tags after filtering in treatment: 3067404 INFO @ Sat, 06 Jul 2019 03:30:55: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 06 Jul 2019 03:30:55: #1 finished! INFO @ Sat, 06 Jul 2019 03:30:55: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:30:56: #2 number of paired peaks: 29 WARNING @ Sat, 06 Jul 2019 03:30:56: Too few paired peaks (29) 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 03:30:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.20_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/SRX5126595/SRX5126595.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:30:57: 8000000 INFO @ Sat, 06 Jul 2019 03:31:01: 8000000 INFO @ Sat, 06 Jul 2019 03:31:07: 9000000 INFO @ Sat, 06 Jul 2019 03:31:12: 9000000 INFO @ Sat, 06 Jul 2019 03:31:17: 10000000 INFO @ Sat, 06 Jul 2019 03:31:21: #1 tag size is determined as 73 bps INFO @ Sat, 06 Jul 2019 03:31:21: #1 tag size = 73 INFO @ Sat, 06 Jul 2019 03:31:21: #1 total tags in treatment: 5103896 INFO @ Sat, 06 Jul 2019 03:31:21: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:31:21: #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 03:31:21: #1 tags after filtering in treatment: 3067404 INFO @ Sat, 06 Jul 2019 03:31:21: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 06 Jul 2019 03:31:21: #1 finished! INFO @ Sat, 06 Jul 2019 03:31:21: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:31:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:31:22: #2 number of paired peaks: 29 WARNING @ Sat, 06 Jul 2019 03:31:22: Too few paired peaks (29) 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 03:31:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.10_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/SRX5126595/SRX5126595.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:31:22: 10000000 INFO @ Sat, 06 Jul 2019 03:31:26: #1 tag size is determined as 73 bps INFO @ Sat, 06 Jul 2019 03:31:26: #1 tag size = 73 INFO @ Sat, 06 Jul 2019 03:31:26: #1 total tags in treatment: 5103896 INFO @ Sat, 06 Jul 2019 03:31:26: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:31:26: #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 03:31:26: #1 tags after filtering in treatment: 3067404 INFO @ Sat, 06 Jul 2019 03:31:26: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 06 Jul 2019 03:31:26: #1 finished! INFO @ Sat, 06 Jul 2019 03:31:26: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:31:27: #2 number of paired peaks: 29 WARNING @ Sat, 06 Jul 2019 03:31:27: Too few paired peaks (29) 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 03:31:27: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.05_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126595/SRX5126595.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。