Job ID = 14521629 SRX = SRX9399011 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5278402 spots for SRR12935293/SRR12935293.sra Written 5278402 spots for SRR12935293/SRR12935293.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: 00:03:17 5278402 reads; of these: 5278402 (100.00%) were paired; of these: 865121 (16.39%) aligned concordantly 0 times 3685082 (69.81%) aligned concordantly exactly 1 time 728199 (13.80%) aligned concordantly >1 times ---- 865121 pairs aligned concordantly 0 times; of these: 189568 (21.91%) aligned discordantly 1 time ---- 675553 pairs aligned 0 times concordantly or discordantly; of these: 1351106 mates make up the pairs; of these: 1001579 (74.13%) aligned 0 times 237950 (17.61%) aligned exactly 1 time 111577 (8.26%) aligned >1 times 90.51% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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] 479383 / 4492551 = 0.1067 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 21:21:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.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 21:21:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:21:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:22:00: 1000000 INFO @ Sat, 15 Jan 2022 21:22:06: 2000000 INFO @ Sat, 15 Jan 2022 21:22:12: 3000000 INFO @ Sat, 15 Jan 2022 21:22:19: 4000000 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 21:22:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.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 21:22:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:22:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:22:25: 5000000 INFO @ Sat, 15 Jan 2022 21:22:30: 1000000 INFO @ Sat, 15 Jan 2022 21:22:33: 6000000 INFO @ Sat, 15 Jan 2022 21:22:36: 2000000 INFO @ Sat, 15 Jan 2022 21:22:39: 7000000 INFO @ Sat, 15 Jan 2022 21:22:43: 3000000 INFO @ Sat, 15 Jan 2022 21:22:46: 8000000 INFO @ Sat, 15 Jan 2022 21:22:50: 4000000 INFO @ Sat, 15 Jan 2022 21:22:50: #1 tag size is determined as 35 bps INFO @ Sat, 15 Jan 2022 21:22:50: #1 tag size = 35 INFO @ Sat, 15 Jan 2022 21:22:50: #1 total tags in treatment: 3935660 INFO @ Sat, 15 Jan 2022 21:22:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:22:50: #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 21:22:50: #1 tags after filtering in treatment: 2739035 INFO @ Sat, 15 Jan 2022 21:22:50: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 21:22:50: #1 finished! INFO @ Sat, 15 Jan 2022 21:22:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:22:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:22:50: #2 number of paired peaks: 27 WARNING @ Sat, 15 Jan 2022 21:22:50: Too few paired peaks (27) 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 21:22:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.05_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/SRX9399011/SRX9399011.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 21:22:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.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 21:22:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:22:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:22:57: 5000000 INFO @ Sat, 15 Jan 2022 21:23:00: 1000000 INFO @ Sat, 15 Jan 2022 21:23:04: 6000000 INFO @ Sat, 15 Jan 2022 21:23:08: 2000000 INFO @ Sat, 15 Jan 2022 21:23:11: 7000000 INFO @ Sat, 15 Jan 2022 21:23:14: 3000000 INFO @ Sat, 15 Jan 2022 21:23:18: 8000000 INFO @ Sat, 15 Jan 2022 21:23:21: 4000000 INFO @ Sat, 15 Jan 2022 21:23:22: #1 tag size is determined as 35 bps INFO @ Sat, 15 Jan 2022 21:23:22: #1 tag size = 35 INFO @ Sat, 15 Jan 2022 21:23:22: #1 total tags in treatment: 3935660 INFO @ Sat, 15 Jan 2022 21:23:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:23:22: #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 21:23:22: #1 tags after filtering in treatment: 2739035 INFO @ Sat, 15 Jan 2022 21:23:22: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 21:23:22: #1 finished! INFO @ Sat, 15 Jan 2022 21:23:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:23:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:23:22: #2 number of paired peaks: 27 WARNING @ Sat, 15 Jan 2022 21:23:22: Too few paired peaks (27) 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 21:23:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.10_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/SRX9399011/SRX9399011.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:23:27: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:23:33: 6000000 INFO @ Sat, 15 Jan 2022 21:23:39: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:23:46: 8000000 INFO @ Sat, 15 Jan 2022 21:23:49: #1 tag size is determined as 35 bps INFO @ Sat, 15 Jan 2022 21:23:49: #1 tag size = 35 INFO @ Sat, 15 Jan 2022 21:23:49: #1 total tags in treatment: 3935660 INFO @ Sat, 15 Jan 2022 21:23:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:23:49: #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 21:23:49: #1 tags after filtering in treatment: 2739035 INFO @ Sat, 15 Jan 2022 21:23:49: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 21:23:49: #1 finished! INFO @ Sat, 15 Jan 2022 21:23:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:23:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:23:50: #2 number of paired peaks: 27 WARNING @ Sat, 15 Jan 2022 21:23:50: Too few paired peaks (27) 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 21:23:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.20_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/SRX9399011/SRX9399011.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399011/SRX9399011.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling