Job ID = 10224087 SRX = SRX8952643 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14917969 spots for SRR12458243/SRR12458243.sra Written 14917969 spots for SRR12458243/SRR12458243.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: 00:04:28 14917969 reads; of these: 14917969 (100.00%) were paired; of these: 7868895 (52.75%) aligned concordantly 0 times 5954982 (39.92%) aligned concordantly exactly 1 time 1094092 (7.33%) aligned concordantly >1 times ---- 7868895 pairs aligned concordantly 0 times; of these: 531239 (6.75%) aligned discordantly 1 time ---- 7337656 pairs aligned 0 times concordantly or discordantly; of these: 14675312 mates make up the pairs; of these: 13472595 (91.80%) aligned 0 times 748196 (5.10%) aligned exactly 1 time 454521 (3.10%) aligned >1 times 54.84% overall alignment rate Time searching: 00:04:28 Overall time: 00:04:28 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] 1626320 / 7530021 = 0.2160 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 @ Fri, 16 Oct 2020 09:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.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 @ Fri, 16 Oct 2020 09:30:39: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:30:39: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:30:46: 1000000 INFO @ Fri, 16 Oct 2020 09:30:52: 2000000 INFO @ Fri, 16 Oct 2020 09:30:59: 3000000 INFO @ Fri, 16 Oct 2020 09:31:05: 4000000 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 @ Fri, 16 Oct 2020 09:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.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 @ Fri, 16 Oct 2020 09:31:09: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:31:09: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:31:12: 5000000 INFO @ Fri, 16 Oct 2020 09:31:16: 1000000 INFO @ Fri, 16 Oct 2020 09:31:20: 6000000 INFO @ Fri, 16 Oct 2020 09:31:22: 2000000 INFO @ Fri, 16 Oct 2020 09:31:27: 7000000 INFO @ Fri, 16 Oct 2020 09:31:29: 3000000 INFO @ Fri, 16 Oct 2020 09:31:34: 8000000 INFO @ Fri, 16 Oct 2020 09:31:35: 4000000 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 @ Fri, 16 Oct 2020 09:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.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 @ Fri, 16 Oct 2020 09:31:39: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:31:39: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:31:42: 5000000 INFO @ Fri, 16 Oct 2020 09:31:42: 9000000 INFO @ Fri, 16 Oct 2020 09:31:47: 1000000 INFO @ Fri, 16 Oct 2020 09:31:48: 6000000 INFO @ Fri, 16 Oct 2020 09:31:49: 10000000 INFO @ Fri, 16 Oct 2020 09:31:54: 2000000 INFO @ Fri, 16 Oct 2020 09:31:55: 7000000 INFO @ Fri, 16 Oct 2020 09:31:57: 11000000 INFO @ Fri, 16 Oct 2020 09:32:01: 8000000 INFO @ Fri, 16 Oct 2020 09:32:02: 3000000 INFO @ Fri, 16 Oct 2020 09:32:04: 12000000 INFO @ Fri, 16 Oct 2020 09:32:07: 9000000 INFO @ Fri, 16 Oct 2020 09:32:09: 4000000 INFO @ Fri, 16 Oct 2020 09:32:11: 13000000 INFO @ Fri, 16 Oct 2020 09:32:12: #1 tag size is determined as 45 bps INFO @ Fri, 16 Oct 2020 09:32:12: #1 tag size = 45 INFO @ Fri, 16 Oct 2020 09:32:12: #1 total tags in treatment: 5498427 INFO @ Fri, 16 Oct 2020 09:32:12: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:32:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:32:12: #1 tags after filtering in treatment: 4015288 INFO @ Fri, 16 Oct 2020 09:32:12: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 16 Oct 2020 09:32:12: #1 finished! INFO @ Fri, 16 Oct 2020 09:32:12: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:32:12: #2 number of paired peaks: 39 WARNING @ Fri, 16 Oct 2020 09:32:12: Too few paired peaks (39) 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 @ Fri, 16 Oct 2020 09:32:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.05_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/SRX8952643/SRX8952643.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:32:14: 10000000 INFO @ Fri, 16 Oct 2020 09:32:16: 5000000 INFO @ Fri, 16 Oct 2020 09:32:20: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:32:24: 6000000 INFO @ Fri, 16 Oct 2020 09:32:27: 12000000 INFO @ Fri, 16 Oct 2020 09:32:31: 7000000 INFO @ Fri, 16 Oct 2020 09:32:33: 13000000 INFO @ Fri, 16 Oct 2020 09:32:34: #1 tag size is determined as 45 bps INFO @ Fri, 16 Oct 2020 09:32:34: #1 tag size = 45 INFO @ Fri, 16 Oct 2020 09:32:34: #1 total tags in treatment: 5498427 INFO @ Fri, 16 Oct 2020 09:32:34: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:32:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:32:34: #1 tags after filtering in treatment: 4015288 INFO @ Fri, 16 Oct 2020 09:32:34: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 16 Oct 2020 09:32:34: #1 finished! INFO @ Fri, 16 Oct 2020 09:32:34: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:32:34: #2 number of paired peaks: 39 WARNING @ Fri, 16 Oct 2020 09:32:34: Too few paired peaks (39) 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 @ Fri, 16 Oct 2020 09:32:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.10_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/SRX8952643/SRX8952643.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:32:39: 8000000 INFO @ Fri, 16 Oct 2020 09:32:45: 9000000 INFO @ Fri, 16 Oct 2020 09:32:52: 10000000 INFO @ Fri, 16 Oct 2020 09:32:59: 11000000 INFO @ Fri, 16 Oct 2020 09:33:06: 12000000 INFO @ Fri, 16 Oct 2020 09:33:13: 13000000 INFO @ Fri, 16 Oct 2020 09:33:13: #1 tag size is determined as 45 bps INFO @ Fri, 16 Oct 2020 09:33:13: #1 tag size = 45 INFO @ Fri, 16 Oct 2020 09:33:13: #1 total tags in treatment: 5498427 INFO @ Fri, 16 Oct 2020 09:33:13: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:33:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:33:13: #1 tags after filtering in treatment: 4015288 INFO @ Fri, 16 Oct 2020 09:33:13: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 16 Oct 2020 09:33:13: #1 finished! INFO @ Fri, 16 Oct 2020 09:33:13: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:33:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:33:14: #2 number of paired peaks: 39 WARNING @ Fri, 16 Oct 2020 09:33:14: Too few paired peaks (39) 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 @ Fri, 16 Oct 2020 09:33:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.20_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/SRX8952643/SRX8952643.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952643/SRX8952643.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling