Job ID = 2011654 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,229,620 reads read : 20,459,240 reads written : 20,459,240 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1146722.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: 00:07:06 10229620 reads; of these: 10229620 (100.00%) were paired; of these: 1949764 (19.06%) aligned concordantly 0 times 7206375 (70.45%) aligned concordantly exactly 1 time 1073481 (10.49%) aligned concordantly >1 times ---- 1949764 pairs aligned concordantly 0 times; of these: 226661 (11.63%) aligned discordantly 1 time ---- 1723103 pairs aligned 0 times concordantly or discordantly; of these: 3446206 mates make up the pairs; of these: 3191579 (92.61%) aligned 0 times 154088 (4.47%) aligned exactly 1 time 100539 (2.92%) aligned >1 times 84.40% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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 8 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] 2745383 / 8400242 = 0.3268 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 02:04:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.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 02:04:01: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:04:01: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:04:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.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 02:04:02: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:04:02: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:04:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.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 02:04:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:04:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:04:09: 1000000 INFO @ Sat, 06 Jul 2019 02:04:11: 1000000 INFO @ Sat, 06 Jul 2019 02:04:11: 1000000 INFO @ Sat, 06 Jul 2019 02:04:16: 2000000 INFO @ Sat, 06 Jul 2019 02:04:20: 2000000 INFO @ Sat, 06 Jul 2019 02:04:21: 2000000 INFO @ Sat, 06 Jul 2019 02:04:22: 3000000 INFO @ Sat, 06 Jul 2019 02:04:28: 3000000 INFO @ Sat, 06 Jul 2019 02:04:29: 4000000 INFO @ Sat, 06 Jul 2019 02:04:31: 3000000 INFO @ Sat, 06 Jul 2019 02:04:36: 5000000 INFO @ Sat, 06 Jul 2019 02:04:37: 4000000 INFO @ Sat, 06 Jul 2019 02:04:41: 4000000 INFO @ Sat, 06 Jul 2019 02:04:42: 6000000 INFO @ Sat, 06 Jul 2019 02:04:45: 5000000 INFO @ Sat, 06 Jul 2019 02:04:49: 7000000 INFO @ Sat, 06 Jul 2019 02:04:50: 5000000 INFO @ Sat, 06 Jul 2019 02:04:53: 6000000 INFO @ Sat, 06 Jul 2019 02:04:56: 8000000 INFO @ Sat, 06 Jul 2019 02:05:00: 6000000 INFO @ Sat, 06 Jul 2019 02:05:02: 7000000 INFO @ Sat, 06 Jul 2019 02:05:02: 9000000 INFO @ Sat, 06 Jul 2019 02:05:09: 10000000 INFO @ Sat, 06 Jul 2019 02:05:10: 8000000 INFO @ Sat, 06 Jul 2019 02:05:10: 7000000 INFO @ Sat, 06 Jul 2019 02:05:15: 11000000 INFO @ Sat, 06 Jul 2019 02:05:18: 9000000 INFO @ Sat, 06 Jul 2019 02:05:20: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:05:20: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:05:20: #1 total tags in treatment: 5567927 INFO @ Sat, 06 Jul 2019 02:05:20: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:05:20: #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 02:05:20: 8000000 INFO @ Sat, 06 Jul 2019 02:05:20: #1 tags after filtering in treatment: 4552276 INFO @ Sat, 06 Jul 2019 02:05:20: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 06 Jul 2019 02:05:20: #1 finished! INFO @ Sat, 06 Jul 2019 02:05:20: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:05:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:05:21: #2 number of paired peaks: 29 WARNING @ Sat, 06 Jul 2019 02:05:21: 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 02:05:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.10_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/SRX455432/SRX455432.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:05:27: 10000000 INFO @ Sat, 06 Jul 2019 02:05:30: 9000000 INFO @ Sat, 06 Jul 2019 02:05:35: 11000000 INFO @ Sat, 06 Jul 2019 02:05:40: 10000000 INFO @ Sat, 06 Jul 2019 02:05:41: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:05:41: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:05:41: #1 total tags in treatment: 5567927 INFO @ Sat, 06 Jul 2019 02:05:41: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:05:41: #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 02:05:41: #1 tags after filtering in treatment: 4552276 INFO @ Sat, 06 Jul 2019 02:05:41: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 06 Jul 2019 02:05:41: #1 finished! INFO @ Sat, 06 Jul 2019 02:05:41: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:05:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:05:41: #2 number of paired peaks: 29 WARNING @ Sat, 06 Jul 2019 02:05:41: 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 02:05:41: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:05:48: 11000000 INFO @ Sat, 06 Jul 2019 02:05:55: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:05:55: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:05:55: #1 total tags in treatment: 5567927 INFO @ Sat, 06 Jul 2019 02:05:55: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:05:55: #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 02:05:55: #1 tags after filtering in treatment: 4552276 INFO @ Sat, 06 Jul 2019 02:05:55: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 06 Jul 2019 02:05:55: #1 finished! INFO @ Sat, 06 Jul 2019 02:05:55: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:05:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:05:55: #2 number of paired peaks: 29 WARNING @ Sat, 06 Jul 2019 02:05:55: 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 02:05:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.20_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.05_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/SRX455432/SRX455432.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455432/SRX455432.05_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。