Job ID = 12531637 SRX = SRX4555017 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15074202 spots for SRR7696707/SRR7696707.sra Written 15074202 spots for SRR7696707/SRR7696707.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:15 15074202 reads; of these: 15074202 (100.00%) were paired; of these: 950030 (6.30%) aligned concordantly 0 times 8125953 (53.91%) aligned concordantly exactly 1 time 5998219 (39.79%) aligned concordantly >1 times ---- 950030 pairs aligned concordantly 0 times; of these: 58701 (6.18%) aligned discordantly 1 time ---- 891329 pairs aligned 0 times concordantly or discordantly; of these: 1782658 mates make up the pairs; of these: 1448131 (81.23%) aligned 0 times 185372 (10.40%) aligned exactly 1 time 149155 (8.37%) aligned >1 times 95.20% overall alignment rate Time searching: 00:23:16 Overall time: 00:23:16 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 20 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] 2312290 / 6638096 = 0.3483 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:22:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.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, 17 Apr 2021 09:22:07: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:22:07: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:22:14: 1000000 INFO @ Sat, 17 Apr 2021 09:22:21: 2000000 INFO @ Sat, 17 Apr 2021 09:22:28: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:22:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.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, 17 Apr 2021 09:22:36: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:22:36: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:22:37: 4000000 INFO @ Sat, 17 Apr 2021 09:22:45: 5000000 INFO @ Sat, 17 Apr 2021 09:22:45: 1000000 INFO @ Sat, 17 Apr 2021 09:22:53: 6000000 INFO @ Sat, 17 Apr 2021 09:22:54: 2000000 INFO @ Sat, 17 Apr 2021 09:23:00: 7000000 INFO @ Sat, 17 Apr 2021 09:23:04: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:23:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.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, 17 Apr 2021 09:23:06: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:23:06: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:23:08: 8000000 INFO @ Sat, 17 Apr 2021 09:23:13: 4000000 INFO @ Sat, 17 Apr 2021 09:23:15: 9000000 INFO @ Sat, 17 Apr 2021 09:23:16: 1000000 INFO @ Sat, 17 Apr 2021 09:23:22: 10000000 INFO @ Sat, 17 Apr 2021 09:23:23: 5000000 INFO @ Sat, 17 Apr 2021 09:23:25: 2000000 INFO @ Sat, 17 Apr 2021 09:23:28: 11000000 INFO @ Sat, 17 Apr 2021 09:23:32: 6000000 INFO @ Sat, 17 Apr 2021 09:23:35: 12000000 INFO @ Sat, 17 Apr 2021 09:23:35: 3000000 INFO @ Sat, 17 Apr 2021 09:23:41: 13000000 INFO @ Sat, 17 Apr 2021 09:23:41: 7000000 INFO @ Sat, 17 Apr 2021 09:23:44: 4000000 INFO @ Sat, 17 Apr 2021 09:23:49: 14000000 INFO @ Sat, 17 Apr 2021 09:23:51: 8000000 INFO @ Sat, 17 Apr 2021 09:23:54: 5000000 INFO @ Sat, 17 Apr 2021 09:23:55: 15000000 INFO @ Sat, 17 Apr 2021 09:24:01: 9000000 INFO @ Sat, 17 Apr 2021 09:24:03: 6000000 INFO @ Sat, 17 Apr 2021 09:24:04: 16000000 INFO @ Sat, 17 Apr 2021 09:24:10: 10000000 INFO @ Sat, 17 Apr 2021 09:24:13: 7000000 INFO @ Sat, 17 Apr 2021 09:24:14: 17000000 INFO @ Sat, 17 Apr 2021 09:24:19: 11000000 INFO @ Sat, 17 Apr 2021 09:24:23: 8000000 INFO @ Sat, 17 Apr 2021 09:24:23: 18000000 INFO @ Sat, 17 Apr 2021 09:24:27: 12000000 INFO @ Sat, 17 Apr 2021 09:24:32: 9000000 INFO @ Sat, 17 Apr 2021 09:24:34: 19000000 INFO @ Sat, 17 Apr 2021 09:24:35: 13000000 INFO @ Sat, 17 Apr 2021 09:24:41: 10000000 INFO @ Sat, 17 Apr 2021 09:24:44: 14000000 INFO @ Sat, 17 Apr 2021 09:24:44: 20000000 INFO @ Sat, 17 Apr 2021 09:24:50: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:24:52: 15000000 INFO @ Sat, 17 Apr 2021 09:24:55: 21000000 INFO @ Sat, 17 Apr 2021 09:24:58: 12000000 INFO @ Sat, 17 Apr 2021 09:25:01: 16000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:25:05: 22000000 INFO @ Sat, 17 Apr 2021 09:25:07: 13000000 INFO @ Sat, 17 Apr 2021 09:25:09: 17000000 INFO @ Sat, 17 Apr 2021 09:25:15: 14000000 INFO @ Sat, 17 Apr 2021 09:25:16: 23000000 INFO @ Sat, 17 Apr 2021 09:25:18: 18000000 INFO @ Sat, 17 Apr 2021 09:25:24: 15000000 INFO @ Sat, 17 Apr 2021 09:25:27: 24000000 INFO @ Sat, 17 Apr 2021 09:25:28: 19000000 INFO @ Sat, 17 Apr 2021 09:25:28: #1 tag size is determined as 70 bps INFO @ Sat, 17 Apr 2021 09:25:28: #1 tag size = 70 INFO @ Sat, 17 Apr 2021 09:25:28: #1 total tags in treatment: 11814915 INFO @ Sat, 17 Apr 2021 09:25:28: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:25:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:25:28: #1 tags after filtering in treatment: 3416572 INFO @ Sat, 17 Apr 2021 09:25:28: #1 Redundant rate of treatment: 0.71 INFO @ Sat, 17 Apr 2021 09:25:28: #1 finished! INFO @ Sat, 17 Apr 2021 09:25:28: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:25:28: #2 number of paired peaks: 35 WARNING @ Sat, 17 Apr 2021 09:25:28: Too few paired peaks (35) 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, 17 Apr 2021 09:25:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.05_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/SRX4555017/SRX4555017.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:25:33: 16000000 INFO @ Sat, 17 Apr 2021 09:25:37: 20000000 INFO @ Sat, 17 Apr 2021 09:25:41: 17000000 INFO @ Sat, 17 Apr 2021 09:25:46: 21000000 INFO @ Sat, 17 Apr 2021 09:25:49: 18000000 INFO @ Sat, 17 Apr 2021 09:25:56: 22000000 INFO @ Sat, 17 Apr 2021 09:25:59: 19000000 INFO @ Sat, 17 Apr 2021 09:26:05: 23000000 INFO @ Sat, 17 Apr 2021 09:26:08: 20000000 INFO @ Sat, 17 Apr 2021 09:26:14: 24000000 INFO @ Sat, 17 Apr 2021 09:26:15: #1 tag size is determined as 70 bps INFO @ Sat, 17 Apr 2021 09:26:15: #1 tag size = 70 INFO @ Sat, 17 Apr 2021 09:26:15: #1 total tags in treatment: 11814915 INFO @ Sat, 17 Apr 2021 09:26:15: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:26:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:26:16: #1 tags after filtering in treatment: 3416572 INFO @ Sat, 17 Apr 2021 09:26:16: #1 Redundant rate of treatment: 0.71 INFO @ Sat, 17 Apr 2021 09:26:16: #1 finished! INFO @ Sat, 17 Apr 2021 09:26:16: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:26:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:26:16: #2 number of paired peaks: 35 WARNING @ Sat, 17 Apr 2021 09:26:16: Too few paired peaks (35) 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, 17 Apr 2021 09:26:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.10_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/SRX4555017/SRX4555017.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:26:17: 21000000 INFO @ Sat, 17 Apr 2021 09:26:26: 22000000 INFO @ Sat, 17 Apr 2021 09:26:35: 23000000 INFO @ Sat, 17 Apr 2021 09:26:44: 24000000 INFO @ Sat, 17 Apr 2021 09:26:44: #1 tag size is determined as 70 bps INFO @ Sat, 17 Apr 2021 09:26:44: #1 tag size = 70 INFO @ Sat, 17 Apr 2021 09:26:44: #1 total tags in treatment: 11814915 INFO @ Sat, 17 Apr 2021 09:26:44: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:26:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:26:45: #1 tags after filtering in treatment: 3416572 INFO @ Sat, 17 Apr 2021 09:26:45: #1 Redundant rate of treatment: 0.71 INFO @ Sat, 17 Apr 2021 09:26:45: #1 finished! INFO @ Sat, 17 Apr 2021 09:26:45: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:26:45: #2 number of paired peaks: 35 WARNING @ Sat, 17 Apr 2021 09:26:45: Too few paired peaks (35) 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, 17 Apr 2021 09:26:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.20_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/SRX4555017/SRX4555017.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4555017/SRX4555017.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling