Job ID = 2011854 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:55:12 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 : 14,978,772 reads read : 29,957,544 reads written : 29,957,540 reads 0-length : 4 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 'SRR8313301.9263520 9263520 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313301.9263520 9263520 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313301.12641614 12641614 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313301.12641614 12641614 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313301.13905401 13905401 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313301.13905401 13905401 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 12 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] 6860926 / 14393481 = 0.4767 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 03:30:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.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 03:30:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:30:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.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 03:30:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:30:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:30:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.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 03:30:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:30:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:30:14: 1000000 INFO @ Sat, 06 Jul 2019 03:30:15: 1000000 INFO @ Sat, 06 Jul 2019 03:30:16: 1000000 INFO @ Sat, 06 Jul 2019 03:30:24: 2000000 INFO @ Sat, 06 Jul 2019 03:30:25: 2000000 INFO @ Sat, 06 Jul 2019 03:30:26: 2000000 INFO @ Sat, 06 Jul 2019 03:30:34: 3000000 INFO @ Sat, 06 Jul 2019 03:30:35: 3000000 INFO @ Sat, 06 Jul 2019 03:30:35: 3000000 INFO @ Sat, 06 Jul 2019 03:30:43: 4000000 INFO @ Sat, 06 Jul 2019 03:30:44: 4000000 INFO @ Sat, 06 Jul 2019 03:30:45: 4000000 INFO @ Sat, 06 Jul 2019 03:30:53: 5000000 INFO @ Sat, 06 Jul 2019 03:30:54: 5000000 INFO @ Sat, 06 Jul 2019 03:30:54: 5000000 INFO @ Sat, 06 Jul 2019 03:31:02: 6000000 INFO @ Sat, 06 Jul 2019 03:31:02: 6000000 INFO @ Sat, 06 Jul 2019 03:31:02: 6000000 INFO @ Sat, 06 Jul 2019 03:31:11: 7000000 INFO @ Sat, 06 Jul 2019 03:31:11: 7000000 INFO @ Sat, 06 Jul 2019 03:31:11: 7000000 INFO @ Sat, 06 Jul 2019 03:31:20: 8000000 INFO @ Sat, 06 Jul 2019 03:31:20: 8000000 INFO @ Sat, 06 Jul 2019 03:31:20: 8000000 INFO @ Sat, 06 Jul 2019 03:31:29: 9000000 INFO @ Sat, 06 Jul 2019 03:31:29: 9000000 INFO @ Sat, 06 Jul 2019 03:31:30: 9000000 INFO @ Sat, 06 Jul 2019 03:31:39: 10000000 INFO @ Sat, 06 Jul 2019 03:31:39: 10000000 INFO @ Sat, 06 Jul 2019 03:31:41: 10000000 INFO @ Sat, 06 Jul 2019 03:31:48: 11000000 INFO @ Sat, 06 Jul 2019 03:31:48: 11000000 INFO @ Sat, 06 Jul 2019 03:31:51: 11000000 INFO @ Sat, 06 Jul 2019 03:31:57: 12000000 INFO @ Sat, 06 Jul 2019 03:31:57: 12000000 INFO @ Sat, 06 Jul 2019 03:32:01: 12000000 INFO @ Sat, 06 Jul 2019 03:32:05: 13000000 INFO @ Sat, 06 Jul 2019 03:32:06: 13000000 INFO @ Sat, 06 Jul 2019 03:32:11: 13000000 INFO @ Sat, 06 Jul 2019 03:32:14: 14000000 INFO @ Sat, 06 Jul 2019 03:32:15: 14000000 INFO @ Sat, 06 Jul 2019 03:32:20: 14000000 INFO @ Sat, 06 Jul 2019 03:32:23: 15000000 INFO @ Sat, 06 Jul 2019 03:32:24: 15000000 INFO @ Sat, 06 Jul 2019 03:32:25: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 03:32:25: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 03:32:25: #1 total tags in treatment: 7493159 INFO @ Sat, 06 Jul 2019 03:32:25: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:32:25: #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 03:32:26: #1 tags after filtering in treatment: 5518531 INFO @ Sat, 06 Jul 2019 03:32:26: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:32:26: #1 finished! INFO @ Sat, 06 Jul 2019 03:32:26: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:32:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:32:26: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:32:26: 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 @ Sat, 06 Jul 2019 03:32:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.20_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/SRX5126609/SRX5126609.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:32:26: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 03:32:26: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 03:32:26: #1 total tags in treatment: 7493159 INFO @ Sat, 06 Jul 2019 03:32:26: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:32:26: #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 03:32:27: #1 tags after filtering in treatment: 5518531 INFO @ Sat, 06 Jul 2019 03:32:27: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:32:27: #1 finished! INFO @ Sat, 06 Jul 2019 03:32:27: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:32:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:32:27: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:32:27: 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 @ Sat, 06 Jul 2019 03:32:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.10_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/SRX5126609/SRX5126609.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:32:29: 15000000 INFO @ Sat, 06 Jul 2019 03:32:32: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 03:32:32: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 03:32:32: #1 total tags in treatment: 7493159 INFO @ Sat, 06 Jul 2019 03:32:32: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:32:32: #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 03:32:32: #1 tags after filtering in treatment: 5518531 INFO @ Sat, 06 Jul 2019 03:32:32: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:32:32: #1 finished! INFO @ Sat, 06 Jul 2019 03:32:32: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:32:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:32:33: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:32:33: 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 @ Sat, 06 Jul 2019 03:32:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.05_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/SRX5126609/SRX5126609.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126609/SRX5126609.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。