Job ID = 2010749 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,537,437 reads read : 27,074,874 reads written : 27,074,874 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 Multiseed full-index search: 00:12:35 13537437 reads; of these: 13537437 (100.00%) were paired; of these: 1871785 (13.83%) aligned concordantly 0 times 10214262 (75.45%) aligned concordantly exactly 1 time 1451390 (10.72%) aligned concordantly >1 times ---- 1871785 pairs aligned concordantly 0 times; of these: 174391 (9.32%) aligned discordantly 1 time ---- 1697394 pairs aligned 0 times concordantly or discordantly; of these: 3394788 mates make up the pairs; of these: 2850263 (83.96%) aligned 0 times 397228 (11.70%) aligned exactly 1 time 147297 (4.34%) aligned >1 times 89.47% overall alignment rate Time searching: 00:12:35 Overall time: 00:12:35 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] 246283 / 11805730 = 0.0209 in library ' ' 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 00:58:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.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 00:58:28: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:58:28: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.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 00:58:29: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:58:29: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:58:37: 1000000 INFO @ Sat, 06 Jul 2019 00:58:42: 1000000 INFO @ Sat, 06 Jul 2019 00:58:45: 2000000 INFO @ Sat, 06 Jul 2019 00:58:54: 3000000 INFO @ Sat, 06 Jul 2019 00:58:54: 2000000 INFO @ Sat, 06 Jul 2019 00:59:02: 4000000 INFO @ Sat, 06 Jul 2019 00:59:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.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 00:59:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:59:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:59:06: 3000000 INFO @ Sat, 06 Jul 2019 00:59:11: 5000000 INFO @ Sat, 06 Jul 2019 00:59:17: 1000000 INFO @ Sat, 06 Jul 2019 00:59:19: 4000000 INFO @ Sat, 06 Jul 2019 00:59:20: 6000000 INFO @ Sat, 06 Jul 2019 00:59:28: 7000000 INFO @ Sat, 06 Jul 2019 00:59:32: 2000000 INFO @ Sat, 06 Jul 2019 00:59:32: 5000000 INFO @ Sat, 06 Jul 2019 00:59:37: 8000000 INFO @ Sat, 06 Jul 2019 00:59:45: 6000000 INFO @ Sat, 06 Jul 2019 00:59:45: 9000000 INFO @ Sat, 06 Jul 2019 00:59:46: 3000000 INFO @ Sat, 06 Jul 2019 00:59:54: 10000000 INFO @ Sat, 06 Jul 2019 00:59:58: 7000000 INFO @ Sat, 06 Jul 2019 01:00:00: 4000000 INFO @ Sat, 06 Jul 2019 01:00:03: 11000000 INFO @ Sat, 06 Jul 2019 01:00:10: 8000000 INFO @ Sat, 06 Jul 2019 01:00:12: 12000000 INFO @ Sat, 06 Jul 2019 01:00:14: 5000000 INFO @ Sat, 06 Jul 2019 01:00:20: 13000000 INFO @ Sat, 06 Jul 2019 01:00:23: 9000000 INFO @ Sat, 06 Jul 2019 01:00:28: 6000000 INFO @ Sat, 06 Jul 2019 01:00:29: 14000000 INFO @ Sat, 06 Jul 2019 01:00:36: 10000000 INFO @ Sat, 06 Jul 2019 01:00:38: 15000000 INFO @ Sat, 06 Jul 2019 01:00:42: 7000000 INFO @ Sat, 06 Jul 2019 01:00:46: 16000000 INFO @ Sat, 06 Jul 2019 01:00:49: 11000000 INFO @ Sat, 06 Jul 2019 01:00:55: 17000000 INFO @ Sat, 06 Jul 2019 01:00:56: 8000000 INFO @ Sat, 06 Jul 2019 01:01:02: 12000000 INFO @ Sat, 06 Jul 2019 01:01:04: 18000000 INFO @ Sat, 06 Jul 2019 01:01:10: 9000000 INFO @ Sat, 06 Jul 2019 01:01:12: 19000000 INFO @ Sat, 06 Jul 2019 01:01:14: 13000000 INFO @ Sat, 06 Jul 2019 01:01:21: 20000000 INFO @ Sat, 06 Jul 2019 01:01:24: 10000000 INFO @ Sat, 06 Jul 2019 01:01:27: 14000000 INFO @ Sat, 06 Jul 2019 01:01:30: 21000000 INFO @ Sat, 06 Jul 2019 01:01:38: 22000000 INFO @ Sat, 06 Jul 2019 01:01:39: 11000000 INFO @ Sat, 06 Jul 2019 01:01:40: 15000000 INFO @ Sat, 06 Jul 2019 01:01:47: 23000000 INFO @ Sat, 06 Jul 2019 01:01:53: 12000000 INFO @ Sat, 06 Jul 2019 01:01:53: 16000000 INFO @ Sat, 06 Jul 2019 01:01:54: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 01:01:54: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 01:01:54: #1 total tags in treatment: 11420859 INFO @ Sat, 06 Jul 2019 01:01:54: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:01:54: #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 01:01:54: #1 tags after filtering in treatment: 8373387 INFO @ Sat, 06 Jul 2019 01:01:54: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 06 Jul 2019 01:01:54: #1 finished! INFO @ Sat, 06 Jul 2019 01:01:54: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:01:55: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:01:55: 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 01:01:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.05_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/SRX386929/SRX386929.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:02:06: 17000000 INFO @ Sat, 06 Jul 2019 01:02:06: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 01:02:18: 18000000 INFO @ Sat, 06 Jul 2019 01:02:20: 14000000 INFO @ Sat, 06 Jul 2019 01:02:31: 19000000 INFO @ Sat, 06 Jul 2019 01:02:34: 15000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 01:02:44: 20000000 INFO @ Sat, 06 Jul 2019 01:02:48: 16000000 INFO @ Sat, 06 Jul 2019 01:02:56: 21000000 INFO @ Sat, 06 Jul 2019 01:03:02: 17000000 INFO @ Sat, 06 Jul 2019 01:03:09: 22000000 INFO @ Sat, 06 Jul 2019 01:03:16: 18000000 INFO @ Sat, 06 Jul 2019 01:03:21: 23000000 INFO @ Sat, 06 Jul 2019 01:03:30: 19000000 INFO @ Sat, 06 Jul 2019 01:03:31: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 01:03:31: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 01:03:31: #1 total tags in treatment: 11420859 INFO @ Sat, 06 Jul 2019 01:03:31: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:03:31: #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 01:03:31: #1 tags after filtering in treatment: 8373387 INFO @ Sat, 06 Jul 2019 01:03:31: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 06 Jul 2019 01:03:31: #1 finished! INFO @ Sat, 06 Jul 2019 01:03:31: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:03:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:03:32: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:03:32: 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 01:03:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.10_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/SRX386929/SRX386929.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:03:43: 20000000 INFO @ Sat, 06 Jul 2019 01:03:55: 21000000 INFO @ Sat, 06 Jul 2019 01:04:06: 22000000 INFO @ Sat, 06 Jul 2019 01:04:17: 23000000 INFO @ Sat, 06 Jul 2019 01:04:26: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 01:04:26: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 01:04:26: #1 total tags in treatment: 11420859 INFO @ Sat, 06 Jul 2019 01:04:26: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:04:26: #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 01:04:26: #1 tags after filtering in treatment: 8373387 INFO @ Sat, 06 Jul 2019 01:04:26: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 06 Jul 2019 01:04:26: #1 finished! INFO @ Sat, 06 Jul 2019 01:04:26: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:04:27: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:04:27: 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 01:04:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.20_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/SRX386929/SRX386929.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386929/SRX386929.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling