Job ID = 14521597 SRX = SRX9399109 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6591045 spots for SRR12935390/SRR12935390.sra Written 6591045 spots for SRR12935390/SRR12935390.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: 00:06:09 6591045 reads; of these: 6591045 (100.00%) were paired; of these: 500377 (7.59%) aligned concordantly 0 times 4076355 (61.85%) aligned concordantly exactly 1 time 2014313 (30.56%) aligned concordantly >1 times ---- 500377 pairs aligned concordantly 0 times; of these: 35238 (7.04%) aligned discordantly 1 time ---- 465139 pairs aligned 0 times concordantly or discordantly; of these: 930278 mates make up the pairs; of these: 781423 (84.00%) aligned 0 times 88315 (9.49%) aligned exactly 1 time 60540 (6.51%) aligned >1 times 94.07% overall alignment rate Time searching: 00:06:09 Overall time: 00:06:09 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] 2369701 / 6120402 = 0.3872 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 21:22:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.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 21:22:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:22:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:22:09: 1000000 INFO @ Sat, 15 Jan 2022 21:22:16: 2000000 INFO @ Sat, 15 Jan 2022 21:22:23: 3000000 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 21:22:30: 4000000 INFO @ Sat, 15 Jan 2022 21:22:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.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 21:22:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:22:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:22:38: 5000000 INFO @ Sat, 15 Jan 2022 21:22:39: 1000000 INFO @ Sat, 15 Jan 2022 21:22:45: 6000000 INFO @ Sat, 15 Jan 2022 21:22:46: 2000000 INFO @ Sat, 15 Jan 2022 21:22:53: 7000000 INFO @ Sat, 15 Jan 2022 21:22:53: 3000000 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 21:22:59: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:22:59: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:22:59: #1 total tags in treatment: 3725221 INFO @ Sat, 15 Jan 2022 21:22:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:22:59: #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 21:22:59: #1 tags after filtering in treatment: 2484499 INFO @ Sat, 15 Jan 2022 21:22:59: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 21:22:59: #1 finished! INFO @ Sat, 15 Jan 2022 21:22:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:22:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:22:59: #2 number of paired peaks: 26 WARNING @ Sat, 15 Jan 2022 21:22:59: Too few paired peaks (26) 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 21:22:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.05_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/SRX9399109/SRX9399109.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:23:01: 4000000 INFO @ Sat, 15 Jan 2022 21:23:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.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 21:23:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:23:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:23:08: 5000000 INFO @ Sat, 15 Jan 2022 21:23:09: 1000000 INFO @ Sat, 15 Jan 2022 21:23:15: 6000000 INFO @ Sat, 15 Jan 2022 21:23:18: 2000000 INFO @ Sat, 15 Jan 2022 21:23:23: 7000000 INFO @ Sat, 15 Jan 2022 21:23:27: 3000000 INFO @ Sat, 15 Jan 2022 21:23:28: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:23:28: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:23:28: #1 total tags in treatment: 3725221 INFO @ Sat, 15 Jan 2022 21:23:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:23:28: #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 21:23:28: #1 tags after filtering in treatment: 2484499 INFO @ Sat, 15 Jan 2022 21:23:28: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 21:23:28: #1 finished! INFO @ Sat, 15 Jan 2022 21:23:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:23:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:23:28: #2 number of paired peaks: 26 WARNING @ Sat, 15 Jan 2022 21:23:28: Too few paired peaks (26) 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 21:23:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.10_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/SRX9399109/SRX9399109.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:23:35: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:23:44: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:23:53: 6000000 INFO @ Sat, 15 Jan 2022 21:24:01: 7000000 INFO @ Sat, 15 Jan 2022 21:24:07: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:24:07: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:24:07: #1 total tags in treatment: 3725221 INFO @ Sat, 15 Jan 2022 21:24:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:24:07: #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 21:24:07: #1 tags after filtering in treatment: 2484499 INFO @ Sat, 15 Jan 2022 21:24:07: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 21:24:07: #1 finished! INFO @ Sat, 15 Jan 2022 21:24:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:24:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:24:07: #2 number of paired peaks: 26 WARNING @ Sat, 15 Jan 2022 21:24:07: Too few paired peaks (26) 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 21:24:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399109/SRX9399109.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling