Job ID = 14521642 SRX = SRX9399134 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8085398 spots for SRR12935415/SRR12935415.sra Written 8085398 spots for SRR12935415/SRR12935415.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: 00:03:27 8085398 reads; of these: 8085398 (100.00%) were paired; of these: 1537737 (19.02%) aligned concordantly 0 times 5288384 (65.41%) aligned concordantly exactly 1 time 1259277 (15.57%) aligned concordantly >1 times ---- 1537737 pairs aligned concordantly 0 times; of these: 283311 (18.42%) aligned discordantly 1 time ---- 1254426 pairs aligned 0 times concordantly or discordantly; of these: 2508852 mates make up the pairs; of these: 1941076 (77.37%) aligned 0 times 373126 (14.87%) aligned exactly 1 time 194650 (7.76%) aligned >1 times 88.00% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 1676395 / 6804875 = 0.2464 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 21:27:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.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 21:27:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:27:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:27:37: 1000000 INFO @ Sat, 15 Jan 2022 21:27:42: 2000000 INFO @ Sat, 15 Jan 2022 21:27:47: 3000000 INFO @ Sat, 15 Jan 2022 21:27:51: 4000000 INFO @ Sat, 15 Jan 2022 21:27:56: 5000000 INFO @ Sat, 15 Jan 2022 21:28:00: 6000000 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 21:28:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.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 21:28:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:28:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:28:06: 7000000 INFO @ Sat, 15 Jan 2022 21:28:09: 1000000 INFO @ Sat, 15 Jan 2022 21:28:11: 8000000 INFO @ Sat, 15 Jan 2022 21:28:16: 2000000 INFO @ Sat, 15 Jan 2022 21:28:17: 9000000 INFO @ Sat, 15 Jan 2022 21:28:22: 10000000 INFO @ Sat, 15 Jan 2022 21:28:22: 3000000 INFO @ Sat, 15 Jan 2022 21:28:27: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:28:27: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:28:27: #1 total tags in treatment: 4904584 INFO @ Sat, 15 Jan 2022 21:28:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:28:27: #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 21:28:27: #1 tags after filtering in treatment: 3205944 INFO @ Sat, 15 Jan 2022 21:28:27: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 21:28:27: #1 finished! INFO @ Sat, 15 Jan 2022 21:28:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:28:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:28:28: #2 number of paired peaks: 27 WARNING @ Sat, 15 Jan 2022 21:28:28: 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 21:28:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.05_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/SRX9399134/SRX9399134.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:28:29: 4000000 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 21:28:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.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 21:28:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:28:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:28:35: 5000000 INFO @ Sat, 15 Jan 2022 21:28:38: 1000000 INFO @ Sat, 15 Jan 2022 21:28:42: 6000000 INFO @ Sat, 15 Jan 2022 21:28:44: 2000000 INFO @ Sat, 15 Jan 2022 21:28:48: 7000000 INFO @ Sat, 15 Jan 2022 21:28:50: 3000000 INFO @ Sat, 15 Jan 2022 21:28:55: 8000000 INFO @ Sat, 15 Jan 2022 21:28:56: 4000000 INFO @ Sat, 15 Jan 2022 21:29:01: 5000000 INFO @ Sat, 15 Jan 2022 21:29:02: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:29:07: 6000000 INFO @ Sat, 15 Jan 2022 21:29:09: 10000000 INFO @ Sat, 15 Jan 2022 21:29:13: 7000000 INFO @ Sat, 15 Jan 2022 21:29:14: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:29:14: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:29:14: #1 total tags in treatment: 4904584 INFO @ Sat, 15 Jan 2022 21:29:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:29:14: #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 21:29:14: #1 tags after filtering in treatment: 3205944 INFO @ Sat, 15 Jan 2022 21:29:14: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 21:29:14: #1 finished! INFO @ Sat, 15 Jan 2022 21:29:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:29:15: #2 number of paired peaks: 27 WARNING @ Sat, 15 Jan 2022 21:29:15: 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 21:29:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.10_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/SRX9399134/SRX9399134.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:29:18: 8000000 INFO @ Sat, 15 Jan 2022 21:29:24: 9000000 INFO @ Sat, 15 Jan 2022 21:29:29: 10000000 INFO @ Sat, 15 Jan 2022 21:29:34: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:29:34: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:29:34: #1 total tags in treatment: 4904584 INFO @ Sat, 15 Jan 2022 21:29:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:29:34: #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 21:29:34: #1 tags after filtering in treatment: 3205944 INFO @ Sat, 15 Jan 2022 21:29:34: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 21:29:34: #1 finished! INFO @ Sat, 15 Jan 2022 21:29:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:29:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:29:34: #2 number of paired peaks: 27 WARNING @ Sat, 15 Jan 2022 21:29:34: 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 21:29:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.20_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/SRX9399134/SRX9399134.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399134/SRX9399134.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling