Job ID = 14519691 SRX = SRX9067179 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3846359 spots for SRR12580332/SRR12580332.sra Written 3846359 spots for SRR12580332/SRR12580332.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: 00:02:13 3846359 reads; of these: 3846359 (100.00%) were paired; of these: 407919 (10.61%) aligned concordantly 0 times 3124046 (81.22%) aligned concordantly exactly 1 time 314394 (8.17%) aligned concordantly >1 times ---- 407919 pairs aligned concordantly 0 times; of these: 104803 (25.69%) aligned discordantly 1 time ---- 303116 pairs aligned 0 times concordantly or discordantly; of these: 606232 mates make up the pairs; of these: 408171 (67.33%) aligned 0 times 161504 (26.64%) aligned exactly 1 time 36557 (6.03%) aligned >1 times 94.69% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 284763 / 3484861 = 0.0817 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 17:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.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 17:29:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:29:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:29:44: 1000000 INFO @ Sat, 15 Jan 2022 17:29:50: 2000000 INFO @ Sat, 15 Jan 2022 17:29:55: 3000000 INFO @ Sat, 15 Jan 2022 17:30:00: 4000000 INFO @ Sat, 15 Jan 2022 17:30:06: 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 17:30:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.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 17:30:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:30:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:30:11: 6000000 INFO @ Sat, 15 Jan 2022 17:30:14: 1000000 INFO @ Sat, 15 Jan 2022 17:30:14: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 17:30:14: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 17:30:14: #1 total tags in treatment: 3155164 INFO @ Sat, 15 Jan 2022 17:30:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:30:14: #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 17:30:14: #1 tags after filtering in treatment: 2345603 INFO @ Sat, 15 Jan 2022 17:30:14: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 17:30:14: #1 finished! INFO @ Sat, 15 Jan 2022 17:30:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:30:14: #2 number of paired peaks: 11 WARNING @ Sat, 15 Jan 2022 17:30:14: Too few paired peaks (11) 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 17:30:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.05_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/SRX9067179/SRX9067179.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:30:19: 2000000 INFO @ Sat, 15 Jan 2022 17:30:23: 3000000 INFO @ Sat, 15 Jan 2022 17:30:28: 4000000 INFO @ Sat, 15 Jan 2022 17:30:32: 5000000 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 17:30:37: 6000000 INFO @ Sat, 15 Jan 2022 17:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.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 17:30:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:30:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:30:40: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 17:30:40: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 17:30:40: #1 total tags in treatment: 3155164 INFO @ Sat, 15 Jan 2022 17:30:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:30:40: #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 17:30:40: #1 tags after filtering in treatment: 2345603 INFO @ Sat, 15 Jan 2022 17:30:40: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 17:30:40: #1 finished! INFO @ Sat, 15 Jan 2022 17:30:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:30:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:30:40: #2 number of paired peaks: 11 WARNING @ Sat, 15 Jan 2022 17:30:40: Too few paired peaks (11) 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 17:30:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.10_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/SRX9067179/SRX9067179.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:30:43: 1000000 INFO @ Sat, 15 Jan 2022 17:30:48: 2000000 INFO @ Sat, 15 Jan 2022 17:30:53: 3000000 INFO @ Sat, 15 Jan 2022 17:30:57: 4000000 INFO @ Sat, 15 Jan 2022 17:31:02: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:31:06: 6000000 INFO @ Sat, 15 Jan 2022 17:31:10: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 17:31:10: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 17:31:10: #1 total tags in treatment: 3155164 INFO @ Sat, 15 Jan 2022 17:31:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:31:10: #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 17:31:10: #1 tags after filtering in treatment: 2345603 INFO @ Sat, 15 Jan 2022 17:31:10: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 17:31:10: #1 finished! INFO @ Sat, 15 Jan 2022 17:31:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:31:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:31:10: #2 number of paired peaks: 11 WARNING @ Sat, 15 Jan 2022 17:31:10: Too few paired peaks (11) 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 17:31:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.20_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/SRX9067179/SRX9067179.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067179/SRX9067179.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。