Job ID = 2010918 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 20,497,978 reads read : 40,995,956 reads written : 40,995,956 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1105630.sra.cache’: 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: 00:24:58 20497978 reads; of these: 20497978 (100.00%) were paired; of these: 2120272 (10.34%) aligned concordantly 0 times 16236875 (79.21%) aligned concordantly exactly 1 time 2140831 (10.44%) aligned concordantly >1 times ---- 2120272 pairs aligned concordantly 0 times; of these: 409408 (19.31%) aligned discordantly 1 time ---- 1710864 pairs aligned 0 times concordantly or discordantly; of these: 3421728 mates make up the pairs; of these: 2751154 (80.40%) aligned 0 times 437732 (12.79%) aligned exactly 1 time 232842 (6.80%) aligned >1 times 93.29% overall alignment rate Time searching: 00:24:58 Overall time: 00:24:58 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] 4455504 / 18732208 = 0.2379 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 02:02:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.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 02:02:02: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:02:02: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:02:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.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 02:02:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:02:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:02:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.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 02:02:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:02:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:02:14: 1000000 INFO @ Sat, 06 Jul 2019 02:02:14: 1000000 INFO @ Sat, 06 Jul 2019 02:02:18: 1000000 INFO @ Sat, 06 Jul 2019 02:02:25: 2000000 INFO @ Sat, 06 Jul 2019 02:02:26: 2000000 INFO @ Sat, 06 Jul 2019 02:02:33: 2000000 INFO @ Sat, 06 Jul 2019 02:02:35: 3000000 INFO @ Sat, 06 Jul 2019 02:02:36: 3000000 INFO @ Sat, 06 Jul 2019 02:02:45: 4000000 INFO @ Sat, 06 Jul 2019 02:02:47: 4000000 INFO @ Sat, 06 Jul 2019 02:02:47: 3000000 INFO @ Sat, 06 Jul 2019 02:02:55: 5000000 INFO @ Sat, 06 Jul 2019 02:02:57: 5000000 INFO @ Sat, 06 Jul 2019 02:03:01: 4000000 INFO @ Sat, 06 Jul 2019 02:03:05: 6000000 INFO @ Sat, 06 Jul 2019 02:03:08: 6000000 INFO @ Sat, 06 Jul 2019 02:03:14: 5000000 INFO @ Sat, 06 Jul 2019 02:03:15: 7000000 INFO @ Sat, 06 Jul 2019 02:03:19: 7000000 INFO @ Sat, 06 Jul 2019 02:03:25: 8000000 INFO @ Sat, 06 Jul 2019 02:03:27: 6000000 INFO @ Sat, 06 Jul 2019 02:03:29: 8000000 INFO @ Sat, 06 Jul 2019 02:03:35: 9000000 INFO @ Sat, 06 Jul 2019 02:03:39: 7000000 INFO @ Sat, 06 Jul 2019 02:03:40: 9000000 INFO @ Sat, 06 Jul 2019 02:03:46: 10000000 INFO @ Sat, 06 Jul 2019 02:03:50: 10000000 INFO @ Sat, 06 Jul 2019 02:03:52: 8000000 INFO @ Sat, 06 Jul 2019 02:03:56: 11000000 INFO @ Sat, 06 Jul 2019 02:04:01: 11000000 INFO @ Sat, 06 Jul 2019 02:04:04: 9000000 INFO @ Sat, 06 Jul 2019 02:04:07: 12000000 INFO @ Sat, 06 Jul 2019 02:04:11: 12000000 INFO @ Sat, 06 Jul 2019 02:04:16: 13000000 INFO @ Sat, 06 Jul 2019 02:04:16: 10000000 INFO @ Sat, 06 Jul 2019 02:04:21: 13000000 INFO @ Sat, 06 Jul 2019 02:04:27: 14000000 INFO @ Sat, 06 Jul 2019 02:04:29: 11000000 INFO @ Sat, 06 Jul 2019 02:04:32: 14000000 INFO @ Sat, 06 Jul 2019 02:04:37: 15000000 INFO @ Sat, 06 Jul 2019 02:04:41: 12000000 INFO @ Sat, 06 Jul 2019 02:04:42: 15000000 INFO @ Sat, 06 Jul 2019 02:04:47: 16000000 INFO @ Sat, 06 Jul 2019 02:04:53: 16000000 INFO @ Sat, 06 Jul 2019 02:04:53: 13000000 INFO @ Sat, 06 Jul 2019 02:04:56: 17000000 INFO @ Sat, 06 Jul 2019 02:05:02: 17000000 INFO @ Sat, 06 Jul 2019 02:05:06: 18000000 INFO @ Sat, 06 Jul 2019 02:05:06: 14000000 INFO @ Sat, 06 Jul 2019 02:05:12: 18000000 INFO @ Sat, 06 Jul 2019 02:05:15: 19000000 INFO @ Sat, 06 Jul 2019 02:05:20: 15000000 INFO @ Sat, 06 Jul 2019 02:05:22: 19000000 INFO @ Sat, 06 Jul 2019 02:05:25: 20000000 INFO @ Sat, 06 Jul 2019 02:05:32: 20000000 INFO @ Sat, 06 Jul 2019 02:05:33: 16000000 INFO @ Sat, 06 Jul 2019 02:05:36: 21000000 INFO @ Sat, 06 Jul 2019 02:05:42: 21000000 INFO @ Sat, 06 Jul 2019 02:05:45: 17000000 INFO @ Sat, 06 Jul 2019 02:05:45: 22000000 BedGraph に変換しました。 INFO @ Sat, 06 Jul 2019 02:05:52: 22000000 INFO @ Sat, 06 Jul 2019 02:05:54: 23000000 INFO @ Sat, 06 Jul 2019 02:05:56: 18000000 INFO @ Sat, 06 Jul 2019 02:06:02: 23000000 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:06:04: 24000000 INFO @ Sat, 06 Jul 2019 02:06:07: 19000000 INFO @ Sat, 06 Jul 2019 02:06:11: 24000000 INFO @ Sat, 06 Jul 2019 02:06:13: 25000000 INFO @ Sat, 06 Jul 2019 02:06:19: 20000000 INFO @ Sat, 06 Jul 2019 02:06:21: 25000000 INFO @ Sat, 06 Jul 2019 02:06:23: 26000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 02:06:30: 21000000 INFO @ Sat, 06 Jul 2019 02:06:32: 26000000 INFO @ Sat, 06 Jul 2019 02:06:33: 27000000 INFO @ Sat, 06 Jul 2019 02:06:41: 22000000 INFO @ Sat, 06 Jul 2019 02:06:42: 27000000 INFO @ Sat, 06 Jul 2019 02:06:42: 28000000 INFO @ Sat, 06 Jul 2019 02:06:51: 23000000 INFO @ Sat, 06 Jul 2019 02:06:51: 29000000 INFO @ Sat, 06 Jul 2019 02:06:52: 28000000 INFO @ Sat, 06 Jul 2019 02:06:55: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 02:06:55: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 02:06:55: #1 total tags in treatment: 14042816 INFO @ Sat, 06 Jul 2019 02:06:55: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:06:55: #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 02:06:55: #1 tags after filtering in treatment: 9048502 INFO @ Sat, 06 Jul 2019 02:06:55: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 02:06:55: #1 finished! INFO @ Sat, 06 Jul 2019 02:06:55: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:06:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:06:56: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:06:56: 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 02:06:56: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:07:01: 29000000 INFO @ Sat, 06 Jul 2019 02:07:01: 24000000 INFO @ Sat, 06 Jul 2019 02:07:05: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 02:07:05: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 02:07:05: #1 total tags in treatment: 14042816 INFO @ Sat, 06 Jul 2019 02:07:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:07:05: #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 02:07:05: #1 tags after filtering in treatment: 9048502 INFO @ Sat, 06 Jul 2019 02:07:05: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 02:07:05: #1 finished! INFO @ Sat, 06 Jul 2019 02:07:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:07:06: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:07:06: 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 02:07:06: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:07:11: 25000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.05_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/SRX424389/SRX424389.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.05_peaks.narrowPeak’: No such file or directory pass1 - making usageList (0 chroms): 2 millis CompletedMACS2peakCalling needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:07:22: 26000000 INFO @ Sat, 06 Jul 2019 02:07:32: 27000000 INFO @ Sat, 06 Jul 2019 02:07:42: 28000000 INFO @ Sat, 06 Jul 2019 02:07:53: 29000000 INFO @ Sat, 06 Jul 2019 02:07:56: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 02:07:56: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 02:07:56: #1 total tags in treatment: 14042816 INFO @ Sat, 06 Jul 2019 02:07:56: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:07:56: #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 02:07:56: #1 tags after filtering in treatment: 9048502 INFO @ Sat, 06 Jul 2019 02:07:56: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 02:07:56: #1 finished! INFO @ Sat, 06 Jul 2019 02:07:56: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:07:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:07:57: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:07:57: 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 02:07:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.20_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/SRX424389/SRX424389.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424389/SRX424389.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling