Job ID = 14521634 SRX = SRX9399016 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3570565 spots for SRR12935298/SRR12935298.sra Written 3570565 spots for SRR12935298/SRR12935298.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: 00:01:35 3570565 reads; of these: 3570565 (100.00%) were paired; of these: 599723 (16.80%) aligned concordantly 0 times 2541033 (71.17%) aligned concordantly exactly 1 time 429809 (12.04%) aligned concordantly >1 times ---- 599723 pairs aligned concordantly 0 times; of these: 232189 (38.72%) aligned discordantly 1 time ---- 367534 pairs aligned 0 times concordantly or discordantly; of these: 735068 mates make up the pairs; of these: 434083 (59.05%) aligned 0 times 194327 (26.44%) aligned exactly 1 time 106658 (14.51%) aligned >1 times 93.92% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 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] 271137 / 3016445 = 0.0899 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 21:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.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 21:19:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:19:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:19:47: 1000000 INFO @ Sat, 15 Jan 2022 21:19:51: 2000000 INFO @ Sat, 15 Jan 2022 21:19:55: 3000000 INFO @ Sat, 15 Jan 2022 21:19:59: 4000000 INFO @ Sat, 15 Jan 2022 21:20:03: 5000000 INFO @ Sat, 15 Jan 2022 21:20:07: 6000000 INFO @ Sat, 15 Jan 2022 21:20:08: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:20:08: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:20:08: #1 total tags in treatment: 2700934 INFO @ Sat, 15 Jan 2022 21:20:08: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:20:08: #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 21:20:08: #1 tags after filtering in treatment: 2035145 INFO @ Sat, 15 Jan 2022 21:20:08: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:20:08: #1 finished! INFO @ Sat, 15 Jan 2022 21:20:08: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:20:08: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 21:20:08: 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 21:20:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.05_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/SRX9399016/SRX9399016.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.05_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 21:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.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 21:20:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:20:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:20:18: 1000000 INFO @ Sat, 15 Jan 2022 21:20:23: 2000000 INFO @ Sat, 15 Jan 2022 21:20:29: 3000000 INFO @ Sat, 15 Jan 2022 21:20:34: 4000000 INFO @ Sat, 15 Jan 2022 21:20:39: 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 21:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.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 21:20:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:20:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:20:44: 6000000 INFO @ Sat, 15 Jan 2022 21:20:45: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:20:45: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:20:45: #1 total tags in treatment: 2700934 INFO @ Sat, 15 Jan 2022 21:20:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:20:45: #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 21:20:45: #1 tags after filtering in treatment: 2035145 INFO @ Sat, 15 Jan 2022 21:20:45: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:20:45: #1 finished! INFO @ Sat, 15 Jan 2022 21:20:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:20:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:20:45: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 21:20:45: 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 21:20:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.10_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/SRX9399016/SRX9399016.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:20:48: 1000000 INFO @ Sat, 15 Jan 2022 21:20:53: 2000000 INFO @ Sat, 15 Jan 2022 21:20:58: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:21:03: 4000000 INFO @ Sat, 15 Jan 2022 21:21:08: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:21:13: 6000000 INFO @ Sat, 15 Jan 2022 21:21:14: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:21:14: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:21:14: #1 total tags in treatment: 2700934 INFO @ Sat, 15 Jan 2022 21:21:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:21:14: #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 21:21:14: #1 tags after filtering in treatment: 2035145 INFO @ Sat, 15 Jan 2022 21:21:14: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:21:14: #1 finished! INFO @ Sat, 15 Jan 2022 21:21:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:21:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:21:14: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 21:21:14: 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 21:21:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.20_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/SRX9399016/SRX9399016.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399016/SRX9399016.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling