Job ID = 4289010 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,522,709 reads read : 13,045,418 reads written : 13,045,418 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: 00:06:43 6522709 reads; of these: 6522709 (100.00%) were paired; of these: 735662 (11.28%) aligned concordantly 0 times 5307544 (81.37%) aligned concordantly exactly 1 time 479503 (7.35%) aligned concordantly >1 times ---- 735662 pairs aligned concordantly 0 times; of these: 219009 (29.77%) aligned discordantly 1 time ---- 516653 pairs aligned 0 times concordantly or discordantly; of these: 1033306 mates make up the pairs; of these: 900441 (87.14%) aligned 0 times 85121 (8.24%) aligned exactly 1 time 47744 (4.62%) aligned >1 times 93.10% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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] 1474462 / 6005089 = 0.2455 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:25:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.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 @ Tue, 10 Dec 2019 13:25:40: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:25:40: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:25:49: 1000000 INFO @ Tue, 10 Dec 2019 13:25:59: 2000000 INFO @ Tue, 10 Dec 2019 13:26:09: 3000000 INFO @ Tue, 10 Dec 2019 13:26:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.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 @ Tue, 10 Dec 2019 13:26:10: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:26:10: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:26:19: 4000000 INFO @ Tue, 10 Dec 2019 13:26:23: 1000000 INFO @ Tue, 10 Dec 2019 13:26:30: 5000000 INFO @ Tue, 10 Dec 2019 13:26:36: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:26:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.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 @ Tue, 10 Dec 2019 13:26:40: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:26:40: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:26:40: 6000000 INFO @ Tue, 10 Dec 2019 13:26:50: 3000000 INFO @ Tue, 10 Dec 2019 13:26:51: 7000000 INFO @ Tue, 10 Dec 2019 13:26:55: 1000000 INFO @ Tue, 10 Dec 2019 13:27:01: 8000000 INFO @ Tue, 10 Dec 2019 13:27:06: 4000000 INFO @ Tue, 10 Dec 2019 13:27:10: 2000000 INFO @ Tue, 10 Dec 2019 13:27:12: 9000000 INFO @ Tue, 10 Dec 2019 13:27:14: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:27:14: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:27:14: #1 total tags in treatment: 4320339 INFO @ Tue, 10 Dec 2019 13:27:14: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:27:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:27:14: #1 tags after filtering in treatment: 3679120 INFO @ Tue, 10 Dec 2019 13:27:14: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 10 Dec 2019 13:27:14: #1 finished! INFO @ Tue, 10 Dec 2019 13:27:14: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:27:15: #2 number of paired peaks: 26 WARNING @ Tue, 10 Dec 2019 13:27:15: Too few paired peaks (26) 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 @ Tue, 10 Dec 2019 13:27:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.05_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/SRX3205547/SRX3205547.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:27:20: 5000000 INFO @ Tue, 10 Dec 2019 13:27:25: 3000000 INFO @ Tue, 10 Dec 2019 13:27:35: 6000000 INFO @ Tue, 10 Dec 2019 13:27:40: 4000000 INFO @ Tue, 10 Dec 2019 13:27:50: 7000000 INFO @ Tue, 10 Dec 2019 13:27:55: 5000000 INFO @ Tue, 10 Dec 2019 13:28:04: 8000000 INFO @ Tue, 10 Dec 2019 13:28:10: 6000000 INFO @ Tue, 10 Dec 2019 13:28:19: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 13:28:21: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:28:21: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:28:21: #1 total tags in treatment: 4320339 INFO @ Tue, 10 Dec 2019 13:28:21: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:28:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:28:21: #1 tags after filtering in treatment: 3679120 INFO @ Tue, 10 Dec 2019 13:28:21: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 10 Dec 2019 13:28:21: #1 finished! INFO @ Tue, 10 Dec 2019 13:28:21: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:28:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:28:22: #2 number of paired peaks: 26 WARNING @ Tue, 10 Dec 2019 13:28:22: Too few paired peaks (26) 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 @ Tue, 10 Dec 2019 13:28:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.10_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/SRX3205547/SRX3205547.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:28:24: 7000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 13:28:37: 8000000 INFO @ Tue, 10 Dec 2019 13:28:50: 9000000 INFO @ Tue, 10 Dec 2019 13:28:52: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:28:52: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:28:52: #1 total tags in treatment: 4320339 INFO @ Tue, 10 Dec 2019 13:28:52: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:28:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:28:52: #1 tags after filtering in treatment: 3679120 INFO @ Tue, 10 Dec 2019 13:28:52: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 10 Dec 2019 13:28:52: #1 finished! INFO @ Tue, 10 Dec 2019 13:28:52: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:28:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:28:52: #2 number of paired peaks: 26 WARNING @ Tue, 10 Dec 2019 13:28:52: Too few paired peaks (26) 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 @ Tue, 10 Dec 2019 13:28:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.20_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/SRX3205547/SRX3205547.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205547/SRX3205547.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling