Job ID = 14521362 SRX = SRX8952648 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13956796 spots for SRR12458238/SRR12458238.sra Written 13956796 spots for SRR12458238/SRR12458238.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: 00:03:55 13956796 reads; of these: 13956796 (100.00%) were paired; of these: 8673156 (62.14%) aligned concordantly 0 times 4573902 (32.77%) aligned concordantly exactly 1 time 709738 (5.09%) aligned concordantly >1 times ---- 8673156 pairs aligned concordantly 0 times; of these: 402389 (4.64%) aligned discordantly 1 time ---- 8270767 pairs aligned 0 times concordantly or discordantly; of these: 16541534 mates make up the pairs; of these: 15590291 (94.25%) aligned 0 times 643336 (3.89%) aligned exactly 1 time 307907 (1.86%) aligned >1 times 44.15% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 1388729 / 5650881 = 0.2458 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 21:02:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.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 21:02:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:02:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:02:53: 1000000 INFO @ Sat, 15 Jan 2022 21:02:59: 2000000 INFO @ Sat, 15 Jan 2022 21:03:04: 3000000 INFO @ Sat, 15 Jan 2022 21:03:09: 4000000 INFO @ Sat, 15 Jan 2022 21:03:14: 5000000 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 21:03:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.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 21:03:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:03:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:03:20: 6000000 INFO @ Sat, 15 Jan 2022 21:03:23: 1000000 INFO @ Sat, 15 Jan 2022 21:03:25: 7000000 INFO @ Sat, 15 Jan 2022 21:03:29: 2000000 INFO @ Sat, 15 Jan 2022 21:03:31: 8000000 INFO @ Sat, 15 Jan 2022 21:03:34: 3000000 INFO @ Sat, 15 Jan 2022 21:03:37: 9000000 INFO @ Sat, 15 Jan 2022 21:03:39: 4000000 INFO @ Sat, 15 Jan 2022 21:03:40: #1 tag size is determined as 43 bps INFO @ Sat, 15 Jan 2022 21:03:40: #1 tag size = 43 INFO @ Sat, 15 Jan 2022 21:03:40: #1 total tags in treatment: 3967828 INFO @ Sat, 15 Jan 2022 21:03:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:03:40: #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 21:03:40: #1 tags after filtering in treatment: 3146087 INFO @ Sat, 15 Jan 2022 21:03:40: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 21:03:40: #1 finished! INFO @ Sat, 15 Jan 2022 21:03:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:03:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:03:40: #2 number of paired peaks: 52 WARNING @ Sat, 15 Jan 2022 21:03:40: Too few paired peaks (52) 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 21:03:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.05_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/SRX8952648/SRX8952648.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:03:44: 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 21:03:48: 6000000 INFO @ Sat, 15 Jan 2022 21:03:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.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 21:03:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:03:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:03:53: 7000000 INFO @ Sat, 15 Jan 2022 21:03:53: 1000000 INFO @ Sat, 15 Jan 2022 21:03:58: 8000000 INFO @ Sat, 15 Jan 2022 21:03:58: 2000000 INFO @ Sat, 15 Jan 2022 21:04:03: 3000000 INFO @ Sat, 15 Jan 2022 21:04:03: 9000000 INFO @ Sat, 15 Jan 2022 21:04:05: #1 tag size is determined as 43 bps INFO @ Sat, 15 Jan 2022 21:04:05: #1 tag size = 43 INFO @ Sat, 15 Jan 2022 21:04:05: #1 total tags in treatment: 3967828 INFO @ Sat, 15 Jan 2022 21:04:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:04:05: #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 21:04:06: #1 tags after filtering in treatment: 3146087 INFO @ Sat, 15 Jan 2022 21:04:06: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 21:04:06: #1 finished! INFO @ Sat, 15 Jan 2022 21:04:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:04:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:04:06: #2 number of paired peaks: 52 WARNING @ Sat, 15 Jan 2022 21:04:06: Too few paired peaks (52) 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 21:04:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.10_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/SRX8952648/SRX8952648.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:04:07: 4000000 INFO @ Sat, 15 Jan 2022 21:04:12: 5000000 INFO @ Sat, 15 Jan 2022 21:04:16: 6000000 INFO @ Sat, 15 Jan 2022 21:04:21: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:04:25: 8000000 INFO @ Sat, 15 Jan 2022 21:04:30: 9000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:04:32: #1 tag size is determined as 43 bps INFO @ Sat, 15 Jan 2022 21:04:32: #1 tag size = 43 INFO @ Sat, 15 Jan 2022 21:04:32: #1 total tags in treatment: 3967828 INFO @ Sat, 15 Jan 2022 21:04:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:04:32: #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 21:04:32: #1 tags after filtering in treatment: 3146087 INFO @ Sat, 15 Jan 2022 21:04:32: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 21:04:32: #1 finished! INFO @ Sat, 15 Jan 2022 21:04:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:04:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:04:32: #2 number of paired peaks: 52 WARNING @ Sat, 15 Jan 2022 21:04:32: Too few paired peaks (52) 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 21:04:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.20_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/SRX8952648/SRX8952648.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952648/SRX8952648.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling