Job ID = 10224045 SRX = SRX8926530 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4778434 spots for SRR12430721/SRR12430721.sra Written 4778434 spots for SRR12430721/SRR12430721.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: 00:01:53 4778434 reads; of these: 4778434 (100.00%) were paired; of these: 1558286 (32.61%) aligned concordantly 0 times 2573766 (53.86%) aligned concordantly exactly 1 time 646382 (13.53%) aligned concordantly >1 times ---- 1558286 pairs aligned concordantly 0 times; of these: 13395 (0.86%) aligned discordantly 1 time ---- 1544891 pairs aligned 0 times concordantly or discordantly; of these: 3089782 mates make up the pairs; of these: 3045679 (98.57%) aligned 0 times 25710 (0.83%) aligned exactly 1 time 18393 (0.60%) aligned >1 times 68.13% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 476584 / 3232886 = 0.1474 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 09:16:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.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 09:16:29: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:16:29: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:16:34: 1000000 INFO @ Fri, 16 Oct 2020 09:16:40: 2000000 INFO @ Fri, 16 Oct 2020 09:16:45: 3000000 INFO @ Fri, 16 Oct 2020 09:16:50: 4000000 INFO @ Fri, 16 Oct 2020 09:16:55: 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 @ Fri, 16 Oct 2020 09:16:58: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:16:58: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:16:58: #1 total tags in treatment: 2743892 INFO @ Fri, 16 Oct 2020 09:16:58: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:16:58: #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 09:16:58: #1 tags after filtering in treatment: 2235169 INFO @ Fri, 16 Oct 2020 09:16:58: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 16 Oct 2020 09:16:58: #1 finished! INFO @ Fri, 16 Oct 2020 09:16:58: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:16:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:16:58: #2 number of paired peaks: 46 WARNING @ Fri, 16 Oct 2020 09:16:58: Too few paired peaks (46) 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 09:16:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.05_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/SRX8926530/SRX8926530.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.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 09:17:01: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:17:01: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:17:06: 1000000 INFO @ Fri, 16 Oct 2020 09:17:11: 2000000 INFO @ Fri, 16 Oct 2020 09:17:16: 3000000 INFO @ Fri, 16 Oct 2020 09:17:21: 4000000 INFO @ Fri, 16 Oct 2020 09:17:27: 5000000 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 09:17:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.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 09:17:29: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:17:29: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:17:29: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:17:29: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:17:29: #1 total tags in treatment: 2743892 INFO @ Fri, 16 Oct 2020 09:17:29: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:17:29: #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 09:17:30: #1 tags after filtering in treatment: 2235169 INFO @ Fri, 16 Oct 2020 09:17:30: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 16 Oct 2020 09:17:30: #1 finished! INFO @ Fri, 16 Oct 2020 09:17:30: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:17:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:17:30: #2 number of paired peaks: 46 WARNING @ Fri, 16 Oct 2020 09:17:30: Too few paired peaks (46) 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 09:17:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.10_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/SRX8926530/SRX8926530.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:17:35: 1000000 INFO @ Fri, 16 Oct 2020 09:17:41: 2000000 INFO @ Fri, 16 Oct 2020 09:17:46: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:17:52: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:17:58: 5000000 INFO @ Fri, 16 Oct 2020 09:18:01: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:18:01: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:18:01: #1 total tags in treatment: 2743892 INFO @ Fri, 16 Oct 2020 09:18:01: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:18:01: #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 09:18:01: #1 tags after filtering in treatment: 2235169 INFO @ Fri, 16 Oct 2020 09:18:01: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 16 Oct 2020 09:18:01: #1 finished! INFO @ Fri, 16 Oct 2020 09:18:01: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:18:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:18:01: #2 number of paired peaks: 46 WARNING @ Fri, 16 Oct 2020 09:18:01: Too few paired peaks (46) 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 09:18:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.20_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/SRX8926530/SRX8926530.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8926530/SRX8926530.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling