Job ID = 10224019 SRX = SRX8754208 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3506309 spots for SRR12246279/SRR12246279.sra Written 3506309 spots for SRR12246279/SRR12246279.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: 00:01:37 3506309 reads; of these: 3506309 (100.00%) were paired; of these: 121459 (3.46%) aligned concordantly 0 times 3105001 (88.55%) aligned concordantly exactly 1 time 279849 (7.98%) aligned concordantly >1 times ---- 121459 pairs aligned concordantly 0 times; of these: 25393 (20.91%) aligned discordantly 1 time ---- 96066 pairs aligned 0 times concordantly or discordantly; of these: 192132 mates make up the pairs; of these: 170662 (88.83%) aligned 0 times 14653 (7.63%) aligned exactly 1 time 6817 (3.55%) aligned >1 times 97.57% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 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] 56268 / 3409240 = 0.0165 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 09:11:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.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 09:11:52: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:11:52: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:11:57: 1000000 INFO @ Fri, 16 Oct 2020 09:12:02: 2000000 INFO @ Fri, 16 Oct 2020 09:12:06: 3000000 INFO @ Fri, 16 Oct 2020 09:12:11: 4000000 INFO @ Fri, 16 Oct 2020 09:12:15: 5000000 INFO @ Fri, 16 Oct 2020 09:12:20: 6000000 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 09:12:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.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 09:12:22: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:12:22: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:12:23: #1 tag size is determined as 38 bps INFO @ Fri, 16 Oct 2020 09:12:23: #1 tag size = 38 INFO @ Fri, 16 Oct 2020 09:12:23: #1 total tags in treatment: 3328672 INFO @ Fri, 16 Oct 2020 09:12:23: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:12:23: #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 09:12:23: #1 tags after filtering in treatment: 3019749 INFO @ Fri, 16 Oct 2020 09:12:23: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 16 Oct 2020 09:12:23: #1 finished! INFO @ Fri, 16 Oct 2020 09:12:23: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:12:23: #2 number of paired peaks: 6 WARNING @ Fri, 16 Oct 2020 09:12:23: Too few paired peaks (6) 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 09:12:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 7 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:12:27: 1000000 INFO @ Fri, 16 Oct 2020 09:12:32: 2000000 INFO @ Fri, 16 Oct 2020 09:12:36: 3000000 INFO @ Fri, 16 Oct 2020 09:12:41: 4000000 INFO @ Fri, 16 Oct 2020 09:12:45: 5000000 INFO @ Fri, 16 Oct 2020 09:12:50: 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 @ Fri, 16 Oct 2020 09:12:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.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 09:12:52: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:12:52: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:12:53: #1 tag size is determined as 38 bps INFO @ Fri, 16 Oct 2020 09:12:53: #1 tag size = 38 INFO @ Fri, 16 Oct 2020 09:12:53: #1 total tags in treatment: 3328672 INFO @ Fri, 16 Oct 2020 09:12:53: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:12:53: #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 09:12:53: #1 tags after filtering in treatment: 3019749 INFO @ Fri, 16 Oct 2020 09:12:53: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 16 Oct 2020 09:12:53: #1 finished! INFO @ Fri, 16 Oct 2020 09:12:53: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:12:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:12:53: #2 number of paired peaks: 6 WARNING @ Fri, 16 Oct 2020 09:12:53: Too few paired peaks (6) 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 09:12:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.10_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/SRX8754208/SRX8754208.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:12:57: 1000000 INFO @ Fri, 16 Oct 2020 09:13:02: 2000000 INFO @ Fri, 16 Oct 2020 09:13:07: 3000000 INFO @ Fri, 16 Oct 2020 09:13:11: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:13:16: 5000000 INFO @ Fri, 16 Oct 2020 09:13:20: 6000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:13:24: #1 tag size is determined as 38 bps INFO @ Fri, 16 Oct 2020 09:13:24: #1 tag size = 38 INFO @ Fri, 16 Oct 2020 09:13:24: #1 total tags in treatment: 3328672 INFO @ Fri, 16 Oct 2020 09:13:24: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:13:24: #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 09:13:24: #1 tags after filtering in treatment: 3019749 INFO @ Fri, 16 Oct 2020 09:13:24: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 16 Oct 2020 09:13:24: #1 finished! INFO @ Fri, 16 Oct 2020 09:13:24: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:13:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:13:24: #2 number of paired peaks: 6 WARNING @ Fri, 16 Oct 2020 09:13:24: Too few paired peaks (6) 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 09:13:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.20_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/SRX8754208/SRX8754208.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754208/SRX8754208.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling