Job ID = 14521599 SRX = SRX9399111 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6338066 spots for SRR12935392/SRR12935392.sra Written 6338066 spots for SRR12935392/SRR12935392.sra 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: 00:02:40 6338066 reads; of these: 6338066 (100.00%) were paired; of these: 428210 (6.76%) aligned concordantly 0 times 4072730 (64.26%) aligned concordantly exactly 1 time 1837126 (28.99%) aligned concordantly >1 times ---- 428210 pairs aligned concordantly 0 times; of these: 34465 (8.05%) aligned discordantly 1 time ---- 393745 pairs aligned 0 times concordantly or discordantly; of these: 787490 mates make up the pairs; of these: 647602 (82.24%) aligned 0 times 85219 (10.82%) aligned exactly 1 time 54669 (6.94%) aligned >1 times 94.89% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 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] 2002887 / 5939151 = 0.3372 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:16:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.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, 15 Jan 2022 21:16:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:16:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:16:44: 1000000 INFO @ Sat, 15 Jan 2022 21:16:49: 2000000 INFO @ Sat, 15 Jan 2022 21:16:54: 3000000 INFO @ Sat, 15 Jan 2022 21:16:58: 4000000 INFO @ Sat, 15 Jan 2022 21:17:03: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:17:08: 6000000 INFO @ Sat, 15 Jan 2022 21:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.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, 15 Jan 2022 21:17:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:17:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:17:13: 7000000 INFO @ Sat, 15 Jan 2022 21:17:14: 1000000 INFO @ Sat, 15 Jan 2022 21:17:18: 8000000 INFO @ Sat, 15 Jan 2022 21:17:18: 2000000 INFO @ Sat, 15 Jan 2022 21:17:18: #1 tag size is determined as 30 bps INFO @ Sat, 15 Jan 2022 21:17:18: #1 tag size = 30 INFO @ Sat, 15 Jan 2022 21:17:18: #1 total tags in treatment: 3910182 INFO @ Sat, 15 Jan 2022 21:17:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:17:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:17:18: #1 tags after filtering in treatment: 2587846 INFO @ Sat, 15 Jan 2022 21:17:18: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 21:17:18: #1 finished! INFO @ Sat, 15 Jan 2022 21:17:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:17:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:17:18: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 21:17:18: Too few paired peaks (31) 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, 15 Jan 2022 21:17:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.05_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/SRX9399111/SRX9399111.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:17:22: 3000000 INFO @ Sat, 15 Jan 2022 21:17:26: 4000000 INFO @ Sat, 15 Jan 2022 21:17:30: 5000000 INFO @ Sat, 15 Jan 2022 21:17:33: 6000000 INFO @ Sat, 15 Jan 2022 21:17:37: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:17:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.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, 15 Jan 2022 21:17:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:17:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:17:41: 8000000 INFO @ Sat, 15 Jan 2022 21:17:42: #1 tag size is determined as 30 bps INFO @ Sat, 15 Jan 2022 21:17:42: #1 tag size = 30 INFO @ Sat, 15 Jan 2022 21:17:42: #1 total tags in treatment: 3910182 INFO @ Sat, 15 Jan 2022 21:17:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:17:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:17:42: #1 tags after filtering in treatment: 2587846 INFO @ Sat, 15 Jan 2022 21:17:42: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 21:17:42: #1 finished! INFO @ Sat, 15 Jan 2022 21:17:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:17:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:17:42: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 21:17:42: Too few paired peaks (31) 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, 15 Jan 2022 21:17:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.10_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/SRX9399111/SRX9399111.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:17:44: 1000000 INFO @ Sat, 15 Jan 2022 21:17:49: 2000000 INFO @ Sat, 15 Jan 2022 21:17:54: 3000000 INFO @ Sat, 15 Jan 2022 21:17:58: 4000000 INFO @ Sat, 15 Jan 2022 21:18:03: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:18:08: 6000000 INFO @ Sat, 15 Jan 2022 21:18:13: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:18:17: 8000000 INFO @ Sat, 15 Jan 2022 21:18:17: #1 tag size is determined as 30 bps INFO @ Sat, 15 Jan 2022 21:18:17: #1 tag size = 30 INFO @ Sat, 15 Jan 2022 21:18:17: #1 total tags in treatment: 3910182 INFO @ Sat, 15 Jan 2022 21:18:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:18:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:18:18: #1 tags after filtering in treatment: 2587846 INFO @ Sat, 15 Jan 2022 21:18:18: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 21:18:18: #1 finished! INFO @ Sat, 15 Jan 2022 21:18:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:18:18: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 21:18:18: Too few paired peaks (31) 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, 15 Jan 2022 21:18:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399111/SRX9399111.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling