Job ID = 12531641 SRX = SRX4555021 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14714687 spots for SRR7696714/SRR7696714.sra Written 14714687 spots for SRR7696714/SRR7696714.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: 00:17:08 14714687 reads; of these: 14714687 (100.00%) were paired; of these: 854369 (5.81%) aligned concordantly 0 times 8400205 (57.09%) aligned concordantly exactly 1 time 5460113 (37.11%) aligned concordantly >1 times ---- 854369 pairs aligned concordantly 0 times; of these: 53409 (6.25%) aligned discordantly 1 time ---- 800960 pairs aligned 0 times concordantly or discordantly; of these: 1601920 mates make up the pairs; of these: 1315796 (82.14%) aligned 0 times 167543 (10.46%) aligned exactly 1 time 118581 (7.40%) aligned >1 times 95.53% overall alignment rate Time searching: 00:17:08 Overall time: 00:17:08 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] 2180547 / 6620656 = 0.3294 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 09:14:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.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 09:14:32: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:14:32: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:14:39: 1000000 INFO @ Sat, 17 Apr 2021 09:14:46: 2000000 INFO @ Sat, 17 Apr 2021 09:14:53: 3000000 INFO @ Sat, 17 Apr 2021 09:14:59: 4000000 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 09:15:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.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 09:15:02: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:15:02: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:15:07: 5000000 INFO @ Sat, 17 Apr 2021 09:15:10: 1000000 INFO @ Sat, 17 Apr 2021 09:15:14: 6000000 INFO @ Sat, 17 Apr 2021 09:15:18: 2000000 INFO @ Sat, 17 Apr 2021 09:15:22: 7000000 INFO @ Sat, 17 Apr 2021 09:15:26: 3000000 BedGraph に変換中... INFO @ Sat, 17 Apr 2021 09:15:30: 8000000 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 09:15:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.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 09:15:32: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:15:32: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:15:34: 4000000 INFO @ Sat, 17 Apr 2021 09:15:39: 9000000 INFO @ Sat, 17 Apr 2021 09:15:42: 1000000 INFO @ Sat, 17 Apr 2021 09:15:42: 5000000 INFO @ Sat, 17 Apr 2021 09:15:47: 10000000 INFO @ Sat, 17 Apr 2021 09:15:51: 6000000 INFO @ Sat, 17 Apr 2021 09:15:51: 2000000 INFO @ Sat, 17 Apr 2021 09:15:56: 11000000 INFO @ Sat, 17 Apr 2021 09:15:59: 7000000 INFO @ Sat, 17 Apr 2021 09:16:01: 3000000 INFO @ Sat, 17 Apr 2021 09:16:03: 12000000 INFO @ Sat, 17 Apr 2021 09:16:08: 8000000 INFO @ Sat, 17 Apr 2021 09:16:11: 4000000 INFO @ Sat, 17 Apr 2021 09:16:11: 13000000 INFO @ Sat, 17 Apr 2021 09:16:16: 9000000 INFO @ Sat, 17 Apr 2021 09:16:19: 14000000 INFO @ Sat, 17 Apr 2021 09:16:20: 5000000 INFO @ Sat, 17 Apr 2021 09:16:25: 10000000 INFO @ Sat, 17 Apr 2021 09:16:27: 15000000 INFO @ Sat, 17 Apr 2021 09:16:30: 6000000 INFO @ Sat, 17 Apr 2021 09:16:33: 11000000 INFO @ Sat, 17 Apr 2021 09:16:35: 16000000 INFO @ Sat, 17 Apr 2021 09:16:39: 7000000 INFO @ Sat, 17 Apr 2021 09:16:41: 12000000 INFO @ Sat, 17 Apr 2021 09:16:43: 17000000 INFO @ Sat, 17 Apr 2021 09:16:49: 8000000 INFO @ Sat, 17 Apr 2021 09:16:49: 13000000 INFO @ Sat, 17 Apr 2021 09:16:51: 18000000 INFO @ Sat, 17 Apr 2021 09:16:57: 14000000 INFO @ Sat, 17 Apr 2021 09:16:58: 9000000 INFO @ Sat, 17 Apr 2021 09:16:59: 19000000 INFO @ Sat, 17 Apr 2021 09:17:05: 15000000 INFO @ Sat, 17 Apr 2021 09:17:08: 10000000 INFO @ Sat, 17 Apr 2021 09:17:08: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:17:13: 16000000 INFO @ Sat, 17 Apr 2021 09:17:16: 21000000 INFO @ Sat, 17 Apr 2021 09:17:17: 11000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:17:21: 17000000 INFO @ Sat, 17 Apr 2021 09:17:25: 22000000 INFO @ Sat, 17 Apr 2021 09:17:26: 12000000 INFO @ Sat, 17 Apr 2021 09:17:29: 18000000 INFO @ Sat, 17 Apr 2021 09:17:33: 23000000 INFO @ Sat, 17 Apr 2021 09:17:35: 13000000 INFO @ Sat, 17 Apr 2021 09:17:37: 19000000 INFO @ Sat, 17 Apr 2021 09:17:40: #1 tag size is determined as 77 bps INFO @ Sat, 17 Apr 2021 09:17:40: #1 tag size = 77 INFO @ Sat, 17 Apr 2021 09:17:40: #1 total tags in treatment: 11682823 INFO @ Sat, 17 Apr 2021 09:17:40: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:17:40: #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 09:17:40: #1 tags after filtering in treatment: 3145214 INFO @ Sat, 17 Apr 2021 09:17:40: #1 Redundant rate of treatment: 0.73 INFO @ Sat, 17 Apr 2021 09:17:40: #1 finished! INFO @ Sat, 17 Apr 2021 09:17:40: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:17:40: #2 number of paired peaks: 33 WARNING @ Sat, 17 Apr 2021 09:17:40: Too few paired peaks (33) 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 09:17:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.05_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/SRX4555021/SRX4555021.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:17:44: 14000000 INFO @ Sat, 17 Apr 2021 09:17:46: 20000000 INFO @ Sat, 17 Apr 2021 09:17:54: 15000000 INFO @ Sat, 17 Apr 2021 09:17:54: 21000000 INFO @ Sat, 17 Apr 2021 09:18:02: 22000000 INFO @ Sat, 17 Apr 2021 09:18:03: 16000000 INFO @ Sat, 17 Apr 2021 09:18:11: 23000000 INFO @ Sat, 17 Apr 2021 09:18:11: 17000000 INFO @ Sat, 17 Apr 2021 09:18:17: #1 tag size is determined as 77 bps INFO @ Sat, 17 Apr 2021 09:18:17: #1 tag size = 77 INFO @ Sat, 17 Apr 2021 09:18:17: #1 total tags in treatment: 11682823 INFO @ Sat, 17 Apr 2021 09:18:17: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:18:17: #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 09:18:18: #1 tags after filtering in treatment: 3145214 INFO @ Sat, 17 Apr 2021 09:18:18: #1 Redundant rate of treatment: 0.73 INFO @ Sat, 17 Apr 2021 09:18:18: #1 finished! INFO @ Sat, 17 Apr 2021 09:18:18: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:18:18: #2 number of paired peaks: 33 WARNING @ Sat, 17 Apr 2021 09:18:18: Too few paired peaks (33) 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 09:18:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.10_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/SRX4555021/SRX4555021.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:18:20: 18000000 INFO @ Sat, 17 Apr 2021 09:18:29: 19000000 INFO @ Sat, 17 Apr 2021 09:18:37: 20000000 INFO @ Sat, 17 Apr 2021 09:18:46: 21000000 INFO @ Sat, 17 Apr 2021 09:18:54: 22000000 INFO @ Sat, 17 Apr 2021 09:19:02: 23000000 INFO @ Sat, 17 Apr 2021 09:19:09: #1 tag size is determined as 77 bps INFO @ Sat, 17 Apr 2021 09:19:09: #1 tag size = 77 INFO @ Sat, 17 Apr 2021 09:19:09: #1 total tags in treatment: 11682823 INFO @ Sat, 17 Apr 2021 09:19:09: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:19:09: #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 09:19:09: #1 tags after filtering in treatment: 3145214 INFO @ Sat, 17 Apr 2021 09:19:09: #1 Redundant rate of treatment: 0.73 INFO @ Sat, 17 Apr 2021 09:19:09: #1 finished! INFO @ Sat, 17 Apr 2021 09:19:09: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:19:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:19:09: #2 number of paired peaks: 33 WARNING @ Sat, 17 Apr 2021 09:19:09: Too few paired peaks (33) 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 09:19:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.20_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/SRX4555021/SRX4555021.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4555021/SRX4555021.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling