Job ID = 2010995 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,070,223 reads read : 20,140,446 reads written : 20,140,446 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: 00:05:27 10070223 reads; of these: 10070223 (100.00%) were paired; of these: 4636661 (46.04%) aligned concordantly 0 times 5219261 (51.83%) aligned concordantly exactly 1 time 214301 (2.13%) aligned concordantly >1 times ---- 4636661 pairs aligned concordantly 0 times; of these: 29893 (0.64%) aligned discordantly 1 time ---- 4606768 pairs aligned 0 times concordantly or discordantly; of these: 9213536 mates make up the pairs; of these: 5025018 (54.54%) aligned 0 times 3996433 (43.38%) aligned exactly 1 time 192085 (2.08%) aligned >1 times 75.05% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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_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] 246951 / 5462232 = 0.0452 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 01:48:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.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 01:48:34: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:48:34: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.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 01:48:35: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:48:35: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:48:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.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 01:48:38: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:48:38: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:48:42: 1000000 INFO @ Sat, 06 Jul 2019 01:48:45: 1000000 INFO @ Sat, 06 Jul 2019 01:48:48: 1000000 INFO @ Sat, 06 Jul 2019 01:48:50: 2000000 INFO @ Sat, 06 Jul 2019 01:48:56: 2000000 INFO @ Sat, 06 Jul 2019 01:48:59: 3000000 INFO @ Sat, 06 Jul 2019 01:48:59: 2000000 INFO @ Sat, 06 Jul 2019 01:49:07: 4000000 INFO @ Sat, 06 Jul 2019 01:49:07: 3000000 INFO @ Sat, 06 Jul 2019 01:49:11: 3000000 INFO @ Sat, 06 Jul 2019 01:49:15: 5000000 INFO @ Sat, 06 Jul 2019 01:49:19: 4000000 INFO @ Sat, 06 Jul 2019 01:49:23: 6000000 INFO @ Sat, 06 Jul 2019 01:49:23: 4000000 INFO @ Sat, 06 Jul 2019 01:49:30: 7000000 INFO @ Sat, 06 Jul 2019 01:49:30: 5000000 INFO @ Sat, 06 Jul 2019 01:49:34: 5000000 INFO @ Sat, 06 Jul 2019 01:49:39: 8000000 INFO @ Sat, 06 Jul 2019 01:49:42: 6000000 INFO @ Sat, 06 Jul 2019 01:49:46: 6000000 INFO @ Sat, 06 Jul 2019 01:49:47: 9000000 INFO @ Sat, 06 Jul 2019 01:49:53: 7000000 INFO @ Sat, 06 Jul 2019 01:49:55: 10000000 INFO @ Sat, 06 Jul 2019 01:49:57: 7000000 INFO @ Sat, 06 Jul 2019 01:50:02: 11000000 INFO @ Sat, 06 Jul 2019 01:50:04: 8000000 INFO @ Sat, 06 Jul 2019 01:50:07: 8000000 INFO @ Sat, 06 Jul 2019 01:50:10: 12000000 INFO @ Sat, 06 Jul 2019 01:50:15: 9000000 INFO @ Sat, 06 Jul 2019 01:50:18: 13000000 INFO @ Sat, 06 Jul 2019 01:50:18: 9000000 INFO @ Sat, 06 Jul 2019 01:50:26: 14000000 INFO @ Sat, 06 Jul 2019 01:50:26: 10000000 INFO @ Sat, 06 Jul 2019 01:50:30: 10000000 INFO @ Sat, 06 Jul 2019 01:50:30: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:50:30: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:50:30: #1 total tags in treatment: 5186850 INFO @ Sat, 06 Jul 2019 01:50:30: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:50:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 01:50:31: #1 tags after filtering in treatment: 3026940 INFO @ Sat, 06 Jul 2019 01:50:31: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 01:50:31: #1 finished! INFO @ Sat, 06 Jul 2019 01:50:31: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:50:31: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:50:31: 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 01:50:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.05_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/SRX4342941/SRX4342941.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:50:37: 11000000 INFO @ Sat, 06 Jul 2019 01:50:41: 11000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 01:50:47: 12000000 INFO @ Sat, 06 Jul 2019 01:50:51: 12000000 INFO @ Sat, 06 Jul 2019 01:50:58: 13000000 INFO @ Sat, 06 Jul 2019 01:51:02: 13000000 INFO @ Sat, 06 Jul 2019 01:51:09: 14000000 INFO @ Sat, 06 Jul 2019 01:51:13: 14000000 INFO @ Sat, 06 Jul 2019 01:51:16: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:51:16: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:51:16: #1 total tags in treatment: 5186850 INFO @ Sat, 06 Jul 2019 01:51:16: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:51:16: #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 01:51:16: #1 tags after filtering in treatment: 3026940 INFO @ Sat, 06 Jul 2019 01:51:16: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 01:51:16: #1 finished! INFO @ Sat, 06 Jul 2019 01:51:16: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:51:16: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:51:16: 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 01:51:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.10_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/SRX4342941/SRX4342941.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:51:19: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:51:19: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:51:19: #1 total tags in treatment: 5186850 INFO @ Sat, 06 Jul 2019 01:51:19: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:51:19: #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 01:51:19: #1 tags after filtering in treatment: 3026940 INFO @ Sat, 06 Jul 2019 01:51:19: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 01:51:19: #1 finished! INFO @ Sat, 06 Jul 2019 01:51:19: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:51:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:51:19: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:51:19: 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 01:51:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.20_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/SRX4342941/SRX4342941.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342941/SRX4342941.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling