Job ID = 2011847 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,502,329 reads read : 27,004,658 reads written : 27,003,572 reads 0-length : 1,086 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 'SRR8313294.486873 486873 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.486873 486873 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.545705 545705 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.545705 545705 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.1400122 1400122 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.1400122 1400122 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.1419374 1419374 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.1419374 1419374 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.1466826 1466826 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.1466826 1466826 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.1636032 1636032 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.1636032 1636032 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.1988666 1988666 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.1988666 1988666 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.2110662 2110662 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.2110662 2110662 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.2134273 2134273 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.2134273 2134273 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.2150892 2150892 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.2150892 2150892 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.3131157 3131157 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.3131157 3131157 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.3641838 3641838 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.3641838 3641838 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.3652955 3652955 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.3652955 3652955 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.3951026 3951026 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.3951026 3951026 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.4381655 4381655 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.4381655 4381655 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.4553252 4553252 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.4553252 4553252 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.4715915 4715915 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.4715915 4715915 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.4975666 4975666 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.4975666 4975666 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.5226653 5226653 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.5226653 5226653 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.5827612 5827612 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.5827612 5827612 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.5994174 5994174 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.5994174 5994174 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.6570095 6570095 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.6570095 6570095 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.7339608 7339608 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.7339608 7339608 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.7623456 7623456 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.7623456 7623456 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.7734904 7734904 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.7734904 7734904 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.7940513 7940513 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.7940513 7940513 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.8128399 8128399 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.8128399 8128399 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.8692912 8692912 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.8692912 8692912 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.8740540 8740540 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.8740540 8740540 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.8761943 8761943 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.8761943 8761943 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.9189152 9189152 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.9189152 9189152 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.9659435 9659435 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.9659435 9659435 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.9768919 9768919 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.9768919 9768919 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.9840782 9840782 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.9840782 9840782 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.10046278 10046278 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.10046278 10046278 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.10986527 10986527 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.10986527 10986527 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.11073798 11073798 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.11073798 11073798 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.11258056 11258056 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.11258056 11258056 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.11279860 11279860 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.11279860 11279860 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.11331960 11331960 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.11331960 11331960 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.11333426 11333426 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.11333426 11333426 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.11340152 11340152 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.11340152 11340152 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.11687387 11687387 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.11687387 11687387 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.11874647 11874647 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.11874647 11874647 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.11956806 11956806 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.11956806 11956806 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.12977540 12977540 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.12977540 12977540 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.13037176 13037176 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.13037176 13037176 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313294.13259333 13259333 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313294.13259333 13259333 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] 8589384 / 12320613 = 0.6972 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 03:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.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 03:22:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:22:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:22:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.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 03:22:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:22:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:22:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.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 03:22:07: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:22:07: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:22:15: 1000000 INFO @ Sat, 06 Jul 2019 03:22:16: 1000000 INFO @ Sat, 06 Jul 2019 03:22:16: 1000000 INFO @ Sat, 06 Jul 2019 03:22:22: 2000000 INFO @ Sat, 06 Jul 2019 03:22:25: 2000000 INFO @ Sat, 06 Jul 2019 03:22:26: 2000000 INFO @ Sat, 06 Jul 2019 03:22:29: 3000000 INFO @ Sat, 06 Jul 2019 03:22:33: 3000000 INFO @ Sat, 06 Jul 2019 03:22:36: 3000000 INFO @ Sat, 06 Jul 2019 03:22:36: 4000000 INFO @ Sat, 06 Jul 2019 03:22:42: 4000000 INFO @ Sat, 06 Jul 2019 03:22:43: 5000000 INFO @ Sat, 06 Jul 2019 03:22:46: 4000000 INFO @ Sat, 06 Jul 2019 03:22:50: 5000000 INFO @ Sat, 06 Jul 2019 03:22:50: 6000000 INFO @ Sat, 06 Jul 2019 03:22:56: 5000000 INFO @ Sat, 06 Jul 2019 03:22:57: 7000000 INFO @ Sat, 06 Jul 2019 03:22:58: 6000000 INFO @ Sat, 06 Jul 2019 03:23:03: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:23:03: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:23:03: #1 total tags in treatment: 3702013 INFO @ Sat, 06 Jul 2019 03:23:03: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:23:03: #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 03:23:03: #1 tags after filtering in treatment: 2769853 INFO @ Sat, 06 Jul 2019 03:23:03: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 03:23:03: #1 finished! INFO @ Sat, 06 Jul 2019 03:23:03: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:23:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:23:03: #2 number of paired peaks: 30 WARNING @ Sat, 06 Jul 2019 03:23:03: Too few paired peaks (30) 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 03:23:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.20_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/SRX5126602/SRX5126602.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:23:05: 6000000 INFO @ Sat, 06 Jul 2019 03:23:07: 7000000 INFO @ Sat, 06 Jul 2019 03:23:14: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:23:14: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:23:14: #1 total tags in treatment: 3702013 INFO @ Sat, 06 Jul 2019 03:23:14: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:23:14: #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 03:23:14: #1 tags after filtering in treatment: 2769853 INFO @ Sat, 06 Jul 2019 03:23:14: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 03:23:14: #1 finished! INFO @ Sat, 06 Jul 2019 03:23:14: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:23:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:23:14: #2 number of paired peaks: 30 WARNING @ Sat, 06 Jul 2019 03:23:14: Too few paired peaks (30) 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 03:23:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.10_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/SRX5126602/SRX5126602.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:23:15: 7000000 INFO @ Sat, 06 Jul 2019 03:23:22: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:23:22: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:23:22: #1 total tags in treatment: 3702013 INFO @ Sat, 06 Jul 2019 03:23:22: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:23:22: #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 03:23:22: #1 tags after filtering in treatment: 2769853 INFO @ Sat, 06 Jul 2019 03:23:22: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 03:23:22: #1 finished! INFO @ Sat, 06 Jul 2019 03:23:22: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:23:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:23:22: #2 number of paired peaks: 30 WARNING @ Sat, 06 Jul 2019 03:23:22: Too few paired peaks (30) 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 03:23:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.05_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/SRX5126602/SRX5126602.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126602/SRX5126602.05_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。