Job ID = 14519756 SRX = SRX8754217 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4843643 spots for SRR12246288/SRR12246288.sra Written 4843643 spots for SRR12246288/SRR12246288.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: 00:02:07 4843643 reads; of these: 4843643 (100.00%) were paired; of these: 238707 (4.93%) aligned concordantly 0 times 3821503 (78.90%) aligned concordantly exactly 1 time 783433 (16.17%) aligned concordantly >1 times ---- 238707 pairs aligned concordantly 0 times; of these: 87978 (36.86%) aligned discordantly 1 time ---- 150729 pairs aligned 0 times concordantly or discordantly; of these: 301458 mates make up the pairs; of these: 218426 (72.46%) aligned 0 times 33942 (11.26%) aligned exactly 1 time 49090 (16.28%) aligned >1 times 97.75% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 78265 / 4690598 = 0.0167 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 17:43:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.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 17:43:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:43:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:43:49: 1000000 INFO @ Sat, 15 Jan 2022 17:43:53: 2000000 INFO @ Sat, 15 Jan 2022 17:43:57: 3000000 INFO @ Sat, 15 Jan 2022 17:44:01: 4000000 INFO @ Sat, 15 Jan 2022 17:44:05: 5000000 INFO @ Sat, 15 Jan 2022 17:44:09: 6000000 INFO @ Sat, 15 Jan 2022 17:44:13: 7000000 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 17:44:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.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 17:44:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:44:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:44:17: 8000000 INFO @ Sat, 15 Jan 2022 17:44:20: 1000000 INFO @ Sat, 15 Jan 2022 17:44:21: 9000000 INFO @ Sat, 15 Jan 2022 17:44:23: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 17:44:23: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 17:44:23: #1 total tags in treatment: 4527110 INFO @ Sat, 15 Jan 2022 17:44:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:44:23: #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 17:44:23: #1 tags after filtering in treatment: 3690059 INFO @ Sat, 15 Jan 2022 17:44:23: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Jan 2022 17:44:23: #1 finished! INFO @ Sat, 15 Jan 2022 17:44:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:44:23: #2 number of paired peaks: 28 WARNING @ Sat, 15 Jan 2022 17:44:23: Too few paired peaks (28) 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 17:44:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 198 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:44:24: 2000000 INFO @ Sat, 15 Jan 2022 17:44:28: 3000000 INFO @ Sat, 15 Jan 2022 17:44:32: 4000000 INFO @ Sat, 15 Jan 2022 17:44:36: 5000000 INFO @ Sat, 15 Jan 2022 17:44:40: 6000000 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 17:44:44: 7000000 INFO @ Sat, 15 Jan 2022 17:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.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 17:44:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:44:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:44:48: 8000000 INFO @ Sat, 15 Jan 2022 17:44:50: 1000000 INFO @ Sat, 15 Jan 2022 17:44:52: 9000000 INFO @ Sat, 15 Jan 2022 17:44:54: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 17:44:54: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 17:44:54: #1 total tags in treatment: 4527110 INFO @ Sat, 15 Jan 2022 17:44:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:44:54: #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 17:44:54: #1 tags after filtering in treatment: 3690059 INFO @ Sat, 15 Jan 2022 17:44:54: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Jan 2022 17:44:54: #1 finished! INFO @ Sat, 15 Jan 2022 17:44:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:44:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:44:54: #2 number of paired peaks: 28 WARNING @ Sat, 15 Jan 2022 17:44:54: Too few paired peaks (28) 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 17:44:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.10_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/SRX8754217/SRX8754217.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:44:55: 2000000 INFO @ Sat, 15 Jan 2022 17:45:00: 3000000 INFO @ Sat, 15 Jan 2022 17:45:05: 4000000 INFO @ Sat, 15 Jan 2022 17:45:10: 5000000 INFO @ Sat, 15 Jan 2022 17:45:14: 6000000 INFO @ Sat, 15 Jan 2022 17:45:19: 7000000 INFO @ Sat, 15 Jan 2022 17:45:24: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:45:29: 9000000 INFO @ Sat, 15 Jan 2022 17:45:30: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 17:45:30: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 17:45:30: #1 total tags in treatment: 4527110 INFO @ Sat, 15 Jan 2022 17:45:30: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:45:30: #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 17:45:30: #1 tags after filtering in treatment: 3690059 INFO @ Sat, 15 Jan 2022 17:45:30: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Jan 2022 17:45:30: #1 finished! INFO @ Sat, 15 Jan 2022 17:45:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:45:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:45:30: #2 number of paired peaks: 28 WARNING @ Sat, 15 Jan 2022 17:45:30: Too few paired peaks (28) 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 17:45:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.20_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/SRX8754217/SRX8754217.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8754217/SRX8754217.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。