Job ID = 5791738 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,270,833 reads read : 10,541,666 reads written : 10,541,666 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: 00:02:23 5270833 reads; of these: 5270833 (100.00%) were paired; of these: 156614 (2.97%) aligned concordantly 0 times 4440973 (84.26%) aligned concordantly exactly 1 time 673246 (12.77%) aligned concordantly >1 times ---- 156614 pairs aligned concordantly 0 times; of these: 14413 (9.20%) aligned discordantly 1 time ---- 142201 pairs aligned 0 times concordantly or discordantly; of these: 284402 mates make up the pairs; of these: 253215 (89.03%) aligned 0 times 21852 (7.68%) aligned exactly 1 time 9335 (3.28%) aligned >1 times 97.60% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 143309 / 5125938 = 0.0280 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:44:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.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 @ Wed, 22 Apr 2020 10:44:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:44:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:45:04: 1000000 INFO @ Wed, 22 Apr 2020 10:45:09: 2000000 INFO @ Wed, 22 Apr 2020 10:45:14: 3000000 INFO @ Wed, 22 Apr 2020 10:45:18: 4000000 INFO @ Wed, 22 Apr 2020 10:45:23: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:45:28: 6000000 INFO @ Wed, 22 Apr 2020 10:45:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.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 @ Wed, 22 Apr 2020 10:45:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:45:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:45:33: 7000000 INFO @ Wed, 22 Apr 2020 10:45:34: 1000000 INFO @ Wed, 22 Apr 2020 10:45:37: 8000000 INFO @ Wed, 22 Apr 2020 10:45:39: 2000000 INFO @ Wed, 22 Apr 2020 10:45:42: 9000000 INFO @ Wed, 22 Apr 2020 10:45:43: 3000000 INFO @ Wed, 22 Apr 2020 10:45:47: 10000000 INFO @ Wed, 22 Apr 2020 10:45:47: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 10:45:47: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 10:45:47: #1 total tags in treatment: 4971057 INFO @ Wed, 22 Apr 2020 10:45:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:45:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:45:47: #1 tags after filtering in treatment: 4117303 INFO @ Wed, 22 Apr 2020 10:45:47: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 10:45:47: #1 finished! INFO @ Wed, 22 Apr 2020 10:45:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:45:47: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 10:45:47: Too few paired peaks (28) 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 @ Wed, 22 Apr 2020 10:45:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.05_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/SRX7741024/SRX7741024.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:45:48: 4000000 INFO @ Wed, 22 Apr 2020 10:45:53: 5000000 INFO @ Wed, 22 Apr 2020 10:45:57: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:45:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.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 @ Wed, 22 Apr 2020 10:45:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:45:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:46:02: 7000000 INFO @ Wed, 22 Apr 2020 10:46:04: 1000000 INFO @ Wed, 22 Apr 2020 10:46:06: 8000000 INFO @ Wed, 22 Apr 2020 10:46:09: 2000000 INFO @ Wed, 22 Apr 2020 10:46:11: 9000000 INFO @ Wed, 22 Apr 2020 10:46:14: 3000000 INFO @ Wed, 22 Apr 2020 10:46:16: 10000000 INFO @ Wed, 22 Apr 2020 10:46:16: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 10:46:16: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 10:46:16: #1 total tags in treatment: 4971057 INFO @ Wed, 22 Apr 2020 10:46:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:46:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:46:16: #1 tags after filtering in treatment: 4117303 INFO @ Wed, 22 Apr 2020 10:46:16: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 10:46:16: #1 finished! INFO @ Wed, 22 Apr 2020 10:46:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:46:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:46:16: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 10:46:16: Too few paired peaks (28) 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 @ Wed, 22 Apr 2020 10:46:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.10_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/SRX7741024/SRX7741024.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:46:19: 4000000 INFO @ Wed, 22 Apr 2020 10:46:24: 5000000 INFO @ Wed, 22 Apr 2020 10:46:29: 6000000 INFO @ Wed, 22 Apr 2020 10:46:34: 7000000 INFO @ Wed, 22 Apr 2020 10:46:38: 8000000 INFO @ Wed, 22 Apr 2020 10:46:43: 9000000 INFO @ Wed, 22 Apr 2020 10:46:48: 10000000 INFO @ Wed, 22 Apr 2020 10:46:48: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 10:46:48: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 10:46:48: #1 total tags in treatment: 4971057 INFO @ Wed, 22 Apr 2020 10:46:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:46:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:46:48: #1 tags after filtering in treatment: 4117303 INFO @ Wed, 22 Apr 2020 10:46:48: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 10:46:48: #1 finished! INFO @ Wed, 22 Apr 2020 10:46:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:46:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:46:49: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 10:46:49: Too few paired peaks (28) 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 @ Wed, 22 Apr 2020 10:46:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.20_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/SRX7741024/SRX7741024.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741024/SRX7741024.20_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。