Job ID = 14521008 SRX = SRX9397554 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6627116 spots for SRR12933797/SRR12933797.sra Written 6627116 spots for SRR12933797/SRR12933797.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: 00:02:53 6627116 reads; of these: 6627116 (100.00%) were paired; of these: 2515864 (37.96%) aligned concordantly 0 times 3245257 (48.97%) aligned concordantly exactly 1 time 865995 (13.07%) aligned concordantly >1 times ---- 2515864 pairs aligned concordantly 0 times; of these: 55493 (2.21%) aligned discordantly 1 time ---- 2460371 pairs aligned 0 times concordantly or discordantly; of these: 4920742 mates make up the pairs; of these: 4855685 (98.68%) aligned 0 times 10134 (0.21%) aligned exactly 1 time 54923 (1.12%) aligned >1 times 63.37% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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] 1114346 / 4151478 = 0.2684 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 20:21:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.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 20:21:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:21:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:21:26: 1000000 INFO @ Sat, 15 Jan 2022 20:21:30: 2000000 INFO @ Sat, 15 Jan 2022 20:21:35: 3000000 INFO @ Sat, 15 Jan 2022 20:21:39: 4000000 INFO @ Sat, 15 Jan 2022 20:21:44: 5000000 INFO @ Sat, 15 Jan 2022 20:21:48: 6000000 INFO @ Sat, 15 Jan 2022 20:21:49: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 20:21:49: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 20:21:49: #1 total tags in treatment: 3007752 INFO @ Sat, 15 Jan 2022 20:21:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:21:49: #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 20:21:49: #1 tags after filtering in treatment: 2268511 INFO @ Sat, 15 Jan 2022 20:21:49: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 20:21:49: #1 finished! INFO @ Sat, 15 Jan 2022 20:21:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:21:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:21:49: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 20:21:49: Too few paired peaks (30) 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 20:21:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.05_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/SRX9397554/SRX9397554.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 20:21:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.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 20:21:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:21:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:21:56: 1000000 INFO @ Sat, 15 Jan 2022 20:22:02: 2000000 INFO @ Sat, 15 Jan 2022 20:22:07: 3000000 INFO @ Sat, 15 Jan 2022 20:22:12: 4000000 INFO @ Sat, 15 Jan 2022 20:22:18: 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 20:22:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.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 20:22:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:22:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:22:23: 6000000 INFO @ Sat, 15 Jan 2022 20:22:24: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 20:22:24: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 20:22:24: #1 total tags in treatment: 3007752 INFO @ Sat, 15 Jan 2022 20:22:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:22:24: #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 20:22:24: #1 tags after filtering in treatment: 2268511 INFO @ Sat, 15 Jan 2022 20:22:24: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 20:22:24: #1 finished! INFO @ Sat, 15 Jan 2022 20:22:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:22:25: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 20:22:25: Too few paired peaks (30) 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 20:22:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.10_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/SRX9397554/SRX9397554.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:22:27: 1000000 INFO @ Sat, 15 Jan 2022 20:22:31: 2000000 INFO @ Sat, 15 Jan 2022 20:22:36: 3000000 INFO @ Sat, 15 Jan 2022 20:22:40: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:22:44: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:22:49: 6000000 INFO @ Sat, 15 Jan 2022 20:22:49: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 20:22:49: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 20:22:49: #1 total tags in treatment: 3007752 INFO @ Sat, 15 Jan 2022 20:22:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:22:49: #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 20:22:49: #1 tags after filtering in treatment: 2268511 INFO @ Sat, 15 Jan 2022 20:22:49: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 20:22:49: #1 finished! INFO @ Sat, 15 Jan 2022 20:22:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:22:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:22:50: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 20:22:50: Too few paired peaks (30) 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 20:22:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.20_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/SRX9397554/SRX9397554.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9397554/SRX9397554.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling