Job ID = 2010993 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,342,914 reads read : 8,685,828 reads written : 8,685,828 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: 00:02:25 4342914 reads; of these: 4342914 (100.00%) were paired; of these: 2634374 (60.66%) aligned concordantly 0 times 1464606 (33.72%) aligned concordantly exactly 1 time 243934 (5.62%) aligned concordantly >1 times ---- 2634374 pairs aligned concordantly 0 times; of these: 7366 (0.28%) aligned discordantly 1 time ---- 2627008 pairs aligned 0 times concordantly or discordantly; of these: 5254016 mates make up the pairs; of these: 3425111 (65.19%) aligned 0 times 1528346 (29.09%) aligned exactly 1 time 300559 (5.72%) aligned >1 times 60.57% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 230396 / 1715445 = 0.1343 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 01:39:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.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 01:39:21: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:39:21: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:39:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.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 01:39:22: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:39:22: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:39:29: 1000000 INFO @ Sat, 06 Jul 2019 01:39:30: 1000000 INFO @ Sat, 06 Jul 2019 01:39:36: 2000000 INFO @ Sat, 06 Jul 2019 01:39:40: 2000000 INFO @ Sat, 06 Jul 2019 01:39:42: 3000000 INFO @ Sat, 06 Jul 2019 01:39:48: 4000000 INFO @ Sat, 06 Jul 2019 01:39:49: 3000000 INFO @ Sat, 06 Jul 2019 01:39:54: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:39:54: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:39:54: #1 total tags in treatment: 1478414 INFO @ Sat, 06 Jul 2019 01:39:54: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:39:54: #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 01:39:54: #1 tags after filtering in treatment: 1137493 INFO @ Sat, 06 Jul 2019 01:39:54: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 01:39:54: #1 finished! INFO @ Sat, 06 Jul 2019 01:39:54: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:39:54: #2 number of paired peaks: 26 WARNING @ Sat, 06 Jul 2019 01:39:54: 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 @ Sat, 06 Jul 2019 01:39:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.10_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/SRX4342939/SRX4342939.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:39:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.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 01:39:54: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:39:54: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:39:58: 4000000 INFO @ Sat, 06 Jul 2019 01:40:02: 1000000 INFO @ Sat, 06 Jul 2019 01:40:05: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:40:05: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:40:05: #1 total tags in treatment: 1478414 INFO @ Sat, 06 Jul 2019 01:40:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:40:05: #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 01:40:05: #1 tags after filtering in treatment: 1137493 INFO @ Sat, 06 Jul 2019 01:40:05: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 01:40:05: #1 finished! INFO @ Sat, 06 Jul 2019 01:40:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:40:05: #2 number of paired peaks: 26 WARNING @ Sat, 06 Jul 2019 01:40:05: 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 @ Sat, 06 Jul 2019 01:40:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.05_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/SRX4342939/SRX4342939.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:40:09: 2000000 INFO @ Sat, 06 Jul 2019 01:40:16: 3000000 INFO @ Sat, 06 Jul 2019 01:40:24: 4000000 INFO @ Sat, 06 Jul 2019 01:40:29: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:40:29: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:40:29: #1 total tags in treatment: 1478414 INFO @ Sat, 06 Jul 2019 01:40:29: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:40:29: #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 01:40:29: #1 tags after filtering in treatment: 1137493 INFO @ Sat, 06 Jul 2019 01:40:29: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 01:40:29: #1 finished! INFO @ Sat, 06 Jul 2019 01:40:29: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:40:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:40:29: #2 number of paired peaks: 26 WARNING @ Sat, 06 Jul 2019 01:40:29: 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 @ Sat, 06 Jul 2019 01:40:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.20_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/SRX4342939/SRX4342939.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342939/SRX4342939.20_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。