Job ID = 12531586 SRX = SRX3789219 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28517373 spots for SRR6833139/SRR6833139.sra Written 28517373 spots for SRR6833139/SRR6833139.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: 00:18:23 28517373 reads; of these: 28517373 (100.00%) were paired; of these: 4554138 (15.97%) aligned concordantly 0 times 14475904 (50.76%) aligned concordantly exactly 1 time 9487331 (33.27%) aligned concordantly >1 times ---- 4554138 pairs aligned concordantly 0 times; of these: 1687473 (37.05%) aligned discordantly 1 time ---- 2866665 pairs aligned 0 times concordantly or discordantly; of these: 5733330 mates make up the pairs; of these: 2518164 (43.92%) aligned 0 times 485932 (8.48%) aligned exactly 1 time 2729234 (47.60%) aligned >1 times 95.58% overall alignment rate Time searching: 00:18:23 Overall time: 00:18:23 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 24 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] 13356950 / 25370752 = 0.5265 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 08:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.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 08:52:00: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:52:00: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:52:07: 1000000 INFO @ Sat, 17 Apr 2021 08:52:13: 2000000 INFO @ Sat, 17 Apr 2021 08:52:20: 3000000 INFO @ Sat, 17 Apr 2021 08:52:26: 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 08:52:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.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 08:52:30: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:52:30: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:52:33: 5000000 INFO @ Sat, 17 Apr 2021 08:52:37: 1000000 INFO @ Sat, 17 Apr 2021 08:52:40: 6000000 INFO @ Sat, 17 Apr 2021 08:52:44: 2000000 INFO @ Sat, 17 Apr 2021 08:52:47: 7000000 INFO @ Sat, 17 Apr 2021 08:52:50: 3000000 INFO @ Sat, 17 Apr 2021 08:52:54: 8000000 INFO @ Sat, 17 Apr 2021 08:52:57: 4000000 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 08:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.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 08:53:00: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:53:00: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:53:02: 9000000 INFO @ Sat, 17 Apr 2021 08:53:04: 5000000 INFO @ Sat, 17 Apr 2021 08:53:07: 1000000 INFO @ Sat, 17 Apr 2021 08:53:09: 10000000 INFO @ Sat, 17 Apr 2021 08:53:11: 6000000 INFO @ Sat, 17 Apr 2021 08:53:14: 2000000 INFO @ Sat, 17 Apr 2021 08:53:16: 11000000 INFO @ Sat, 17 Apr 2021 08:53:18: 7000000 INFO @ Sat, 17 Apr 2021 08:53:21: 3000000 INFO @ Sat, 17 Apr 2021 08:53:24: 12000000 INFO @ Sat, 17 Apr 2021 08:53:25: 8000000 INFO @ Sat, 17 Apr 2021 08:53:28: 4000000 INFO @ Sat, 17 Apr 2021 08:53:31: 13000000 INFO @ Sat, 17 Apr 2021 08:53:31: 9000000 INFO @ Sat, 17 Apr 2021 08:53:35: 5000000 INFO @ Sat, 17 Apr 2021 08:53:38: 14000000 INFO @ Sat, 17 Apr 2021 08:53:38: 10000000 INFO @ Sat, 17 Apr 2021 08:53:41: 6000000 INFO @ Sat, 17 Apr 2021 08:53:45: 11000000 INFO @ Sat, 17 Apr 2021 08:53:45: 15000000 INFO @ Sat, 17 Apr 2021 08:53:48: 7000000 INFO @ Sat, 17 Apr 2021 08:53:52: 12000000 INFO @ Sat, 17 Apr 2021 08:53:53: 16000000 INFO @ Sat, 17 Apr 2021 08:53:55: 8000000 INFO @ Sat, 17 Apr 2021 08:53:59: 13000000 INFO @ Sat, 17 Apr 2021 08:54:00: 17000000 INFO @ Sat, 17 Apr 2021 08:54:01: 9000000 INFO @ Sat, 17 Apr 2021 08:54:06: 14000000 INFO @ Sat, 17 Apr 2021 08:54:07: 18000000 INFO @ Sat, 17 Apr 2021 08:54:08: 10000000 INFO @ Sat, 17 Apr 2021 08:54:13: 15000000 INFO @ Sat, 17 Apr 2021 08:54:14: 19000000 INFO @ Sat, 17 Apr 2021 08:54:16: 11000000 INFO @ Sat, 17 Apr 2021 08:54:20: 16000000 INFO @ Sat, 17 Apr 2021 08:54:22: 20000000 INFO @ Sat, 17 Apr 2021 08:54:22: 12000000 INFO @ Sat, 17 Apr 2021 08:54:27: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:54:29: 21000000 INFO @ Sat, 17 Apr 2021 08:54:29: 13000000 INFO @ Sat, 17 Apr 2021 08:54:33: 18000000 INFO @ Sat, 17 Apr 2021 08:54:36: 14000000 INFO @ Sat, 17 Apr 2021 08:54:36: 22000000 INFO @ Sat, 17 Apr 2021 08:54:40: 19000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:54:43: 15000000 INFO @ Sat, 17 Apr 2021 08:54:44: 23000000 INFO @ Sat, 17 Apr 2021 08:54:47: 20000000 INFO @ Sat, 17 Apr 2021 08:54:50: 16000000 INFO @ Sat, 17 Apr 2021 08:54:51: 24000000 INFO @ Sat, 17 Apr 2021 08:54:54: 21000000 INFO @ Sat, 17 Apr 2021 08:54:57: 17000000 INFO @ Sat, 17 Apr 2021 08:54:58: 25000000 INFO @ Sat, 17 Apr 2021 08:55:01: 22000000 INFO @ Sat, 17 Apr 2021 08:55:03: 18000000 INFO @ Sat, 17 Apr 2021 08:55:06: 26000000 INFO @ Sat, 17 Apr 2021 08:55:07: 23000000 INFO @ Sat, 17 Apr 2021 08:55:10: 19000000 INFO @ Sat, 17 Apr 2021 08:55:13: 27000000 INFO @ Sat, 17 Apr 2021 08:55:14: 24000000 INFO @ Sat, 17 Apr 2021 08:55:17: 20000000 INFO @ Sat, 17 Apr 2021 08:55:19: #1 tag size is determined as 50 bps INFO @ Sat, 17 Apr 2021 08:55:19: #1 tag size = 50 INFO @ Sat, 17 Apr 2021 08:55:19: #1 total tags in treatment: 11066590 INFO @ Sat, 17 Apr 2021 08:55:19: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:55:19: #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 08:55:19: #1 tags after filtering in treatment: 4283251 INFO @ Sat, 17 Apr 2021 08:55:19: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 17 Apr 2021 08:55:19: #1 finished! INFO @ Sat, 17 Apr 2021 08:55:19: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:55:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:55:19: #2 number of paired peaks: 35 WARNING @ Sat, 17 Apr 2021 08:55:19: 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 08:55:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.05_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/SRX3789219/SRX3789219.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:55:21: 25000000 INFO @ Sat, 17 Apr 2021 08:55:23: 21000000 INFO @ Sat, 17 Apr 2021 08:55:27: 26000000 INFO @ Sat, 17 Apr 2021 08:55:30: 22000000 INFO @ Sat, 17 Apr 2021 08:55:34: 27000000 INFO @ Sat, 17 Apr 2021 08:55:36: 23000000 INFO @ Sat, 17 Apr 2021 08:55:39: #1 tag size is determined as 50 bps INFO @ Sat, 17 Apr 2021 08:55:39: #1 tag size = 50 INFO @ Sat, 17 Apr 2021 08:55:39: #1 total tags in treatment: 11066590 INFO @ Sat, 17 Apr 2021 08:55:39: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:55:39: #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 08:55:39: #1 tags after filtering in treatment: 4283251 INFO @ Sat, 17 Apr 2021 08:55:39: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 17 Apr 2021 08:55:39: #1 finished! INFO @ Sat, 17 Apr 2021 08:55:39: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:55:40: #2 number of paired peaks: 35 WARNING @ Sat, 17 Apr 2021 08:55:40: 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 08:55:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.10_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/SRX3789219/SRX3789219.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:55:43: 24000000 INFO @ Sat, 17 Apr 2021 08:55:49: 25000000 INFO @ Sat, 17 Apr 2021 08:55:55: 26000000 INFO @ Sat, 17 Apr 2021 08:56:01: 27000000 INFO @ Sat, 17 Apr 2021 08:56:05: #1 tag size is determined as 50 bps INFO @ Sat, 17 Apr 2021 08:56:05: #1 tag size = 50 INFO @ Sat, 17 Apr 2021 08:56:05: #1 total tags in treatment: 11066590 INFO @ Sat, 17 Apr 2021 08:56:05: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:56:05: #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 08:56:06: #1 tags after filtering in treatment: 4283251 INFO @ Sat, 17 Apr 2021 08:56:06: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 17 Apr 2021 08:56:06: #1 finished! INFO @ Sat, 17 Apr 2021 08:56:06: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:56:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:56:06: #2 number of paired peaks: 35 WARNING @ Sat, 17 Apr 2021 08:56:06: 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 08:56:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.20_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/SRX3789219/SRX3789219.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3789219/SRX3789219.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling