Job ID = 7117508 SRX = SRX8639537 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:39:36 prefetch.2.10.7: 1) Downloading 'SRR12116975'... 2020-07-22T06:39:36 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:45:05 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:45:05 prefetch.2.10.7: 1) 'SRR12116975' was downloaded successfully 2020-07-22T06:45:05 prefetch.2.10.7: 'SRR12116975' has 0 unresolved dependencies Read 29569659 spots for SRR12116975/SRR12116975.sra Written 29569659 spots for SRR12116975/SRR12116975.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: 00:13:31 29569659 reads; of these: 29569659 (100.00%) were paired; of these: 6386440 (21.60%) aligned concordantly 0 times 20506035 (69.35%) aligned concordantly exactly 1 time 2677184 (9.05%) aligned concordantly >1 times ---- 6386440 pairs aligned concordantly 0 times; of these: 222031 (3.48%) aligned discordantly 1 time ---- 6164409 pairs aligned 0 times concordantly or discordantly; of these: 12328818 mates make up the pairs; of these: 11969699 (97.09%) aligned 0 times 258771 (2.10%) aligned exactly 1 time 100348 (0.81%) aligned >1 times 79.76% overall alignment rate Time searching: 00:13:31 Overall time: 00:13:31 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] 478965 / 23369728 = 0.0205 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 16:10:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.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 @ Wed, 22 Jul 2020 16:10:54: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:10:54: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:10:59: 1000000 INFO @ Wed, 22 Jul 2020 16:11:04: 2000000 INFO @ Wed, 22 Jul 2020 16:11:09: 3000000 INFO @ Wed, 22 Jul 2020 16:11:15: 4000000 INFO @ Wed, 22 Jul 2020 16:11:20: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 16:11:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.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 @ Wed, 22 Jul 2020 16:11:24: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:11:24: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:11:26: 6000000 INFO @ Wed, 22 Jul 2020 16:11:29: 1000000 INFO @ Wed, 22 Jul 2020 16:11:31: 7000000 INFO @ Wed, 22 Jul 2020 16:11:35: 2000000 INFO @ Wed, 22 Jul 2020 16:11:37: 8000000 INFO @ Wed, 22 Jul 2020 16:11:40: 3000000 INFO @ Wed, 22 Jul 2020 16:11:42: 9000000 INFO @ Wed, 22 Jul 2020 16:11:46: 4000000 INFO @ Wed, 22 Jul 2020 16:11:48: 10000000 BedGraph に変換中... INFO @ Wed, 22 Jul 2020 16:11:52: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 16:11:53: 11000000 INFO @ Wed, 22 Jul 2020 16:11:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.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 @ Wed, 22 Jul 2020 16:11:54: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:11:54: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:11:58: 6000000 INFO @ Wed, 22 Jul 2020 16:11:59: 12000000 INFO @ Wed, 22 Jul 2020 16:12:00: 1000000 INFO @ Wed, 22 Jul 2020 16:12:04: 7000000 INFO @ Wed, 22 Jul 2020 16:12:05: 13000000 INFO @ Wed, 22 Jul 2020 16:12:06: 2000000 INFO @ Wed, 22 Jul 2020 16:12:09: 8000000 INFO @ Wed, 22 Jul 2020 16:12:10: 14000000 INFO @ Wed, 22 Jul 2020 16:12:12: 3000000 INFO @ Wed, 22 Jul 2020 16:12:15: 9000000 INFO @ Wed, 22 Jul 2020 16:12:16: 15000000 INFO @ Wed, 22 Jul 2020 16:12:18: 4000000 INFO @ Wed, 22 Jul 2020 16:12:21: 10000000 INFO @ Wed, 22 Jul 2020 16:12:22: 16000000 INFO @ Wed, 22 Jul 2020 16:12:23: 5000000 INFO @ Wed, 22 Jul 2020 16:12:27: 11000000 INFO @ Wed, 22 Jul 2020 16:12:28: 17000000 INFO @ Wed, 22 Jul 2020 16:12:30: 6000000 INFO @ Wed, 22 Jul 2020 16:12:33: 12000000 INFO @ Wed, 22 Jul 2020 16:12:34: 18000000 INFO @ Wed, 22 Jul 2020 16:12:36: 7000000 INFO @ Wed, 22 Jul 2020 16:12:38: 13000000 INFO @ Wed, 22 Jul 2020 16:12:40: 19000000 INFO @ Wed, 22 Jul 2020 16:12:42: 8000000 INFO @ Wed, 22 Jul 2020 16:12:44: 14000000 INFO @ Wed, 22 Jul 2020 16:12:46: 20000000 INFO @ Wed, 22 Jul 2020 16:12:48: 9000000 INFO @ Wed, 22 Jul 2020 16:12:50: 15000000 INFO @ Wed, 22 Jul 2020 16:12:52: 21000000 INFO @ Wed, 22 Jul 2020 16:12:54: 10000000 INFO @ Wed, 22 Jul 2020 16:12:56: 16000000 INFO @ Wed, 22 Jul 2020 16:12:58: 22000000 INFO @ Wed, 22 Jul 2020 16:13:00: 11000000 INFO @ Wed, 22 Jul 2020 16:13:01: 17000000 INFO @ Wed, 22 Jul 2020 16:13:04: 23000000 INFO @ Wed, 22 Jul 2020 16:13:06: 12000000 INFO @ Wed, 22 Jul 2020 16:13:07: 18000000 INFO @ Wed, 22 Jul 2020 16:13:10: 24000000 INFO @ Wed, 22 Jul 2020 16:13:13: 13000000 INFO @ Wed, 22 Jul 2020 16:13:13: 19000000 INFO @ Wed, 22 Jul 2020 16:13:16: 25000000 INFO @ Wed, 22 Jul 2020 16:13:19: 14000000 INFO @ Wed, 22 Jul 2020 16:13:19: 20000000 INFO @ Wed, 22 Jul 2020 16:13:23: 26000000 INFO @ Wed, 22 Jul 2020 16:13:25: 15000000 INFO @ Wed, 22 Jul 2020 16:13:25: 21000000 INFO @ Wed, 22 Jul 2020 16:13:29: 27000000 INFO @ Wed, 22 Jul 2020 16:13:31: 22000000 INFO @ Wed, 22 Jul 2020 16:13:31: 16000000 INFO @ Wed, 22 Jul 2020 16:13:35: 28000000 INFO @ Wed, 22 Jul 2020 16:13:37: 23000000 INFO @ Wed, 22 Jul 2020 16:13:37: 17000000 INFO @ Wed, 22 Jul 2020 16:13:41: 29000000 INFO @ Wed, 22 Jul 2020 16:13:43: 24000000 INFO @ Wed, 22 Jul 2020 16:13:43: 18000000 INFO @ Wed, 22 Jul 2020 16:13:48: 30000000 INFO @ Wed, 22 Jul 2020 16:13:49: 25000000 INFO @ Wed, 22 Jul 2020 16:13:50: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:13:54: 31000000 INFO @ Wed, 22 Jul 2020 16:13:55: 26000000 INFO @ Wed, 22 Jul 2020 16:13:56: 20000000 INFO @ Wed, 22 Jul 2020 16:14:00: 32000000 INFO @ Wed, 22 Jul 2020 16:14:01: 27000000 INFO @ Wed, 22 Jul 2020 16:14:02: 21000000 INFO @ Wed, 22 Jul 2020 16:14:06: 33000000 INFO @ Wed, 22 Jul 2020 16:14:07: 28000000 INFO @ Wed, 22 Jul 2020 16:14:08: 22000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:14:12: 34000000 INFO @ Wed, 22 Jul 2020 16:14:13: 29000000 INFO @ Wed, 22 Jul 2020 16:14:13: 23000000 INFO @ Wed, 22 Jul 2020 16:14:18: 35000000 INFO @ Wed, 22 Jul 2020 16:14:19: 30000000 INFO @ Wed, 22 Jul 2020 16:14:19: 24000000 INFO @ Wed, 22 Jul 2020 16:14:25: 36000000 INFO @ Wed, 22 Jul 2020 16:14:25: 31000000 INFO @ Wed, 22 Jul 2020 16:14:26: 25000000 INFO @ Wed, 22 Jul 2020 16:14:31: 37000000 INFO @ Wed, 22 Jul 2020 16:14:31: 32000000 INFO @ Wed, 22 Jul 2020 16:14:32: 26000000 INFO @ Wed, 22 Jul 2020 16:14:37: 38000000 INFO @ Wed, 22 Jul 2020 16:14:38: 33000000 INFO @ Wed, 22 Jul 2020 16:14:38: 27000000 INFO @ Wed, 22 Jul 2020 16:14:43: 39000000 INFO @ Wed, 22 Jul 2020 16:14:44: 28000000 INFO @ Wed, 22 Jul 2020 16:14:44: 34000000 INFO @ Wed, 22 Jul 2020 16:14:49: 40000000 INFO @ Wed, 22 Jul 2020 16:14:50: 35000000 INFO @ Wed, 22 Jul 2020 16:14:50: 29000000 INFO @ Wed, 22 Jul 2020 16:14:55: 41000000 INFO @ Wed, 22 Jul 2020 16:14:56: 36000000 INFO @ Wed, 22 Jul 2020 16:14:56: 30000000 INFO @ Wed, 22 Jul 2020 16:15:01: 42000000 INFO @ Wed, 22 Jul 2020 16:15:02: 37000000 INFO @ Wed, 22 Jul 2020 16:15:02: 31000000 INFO @ Wed, 22 Jul 2020 16:15:07: 43000000 INFO @ Wed, 22 Jul 2020 16:15:08: 38000000 INFO @ Wed, 22 Jul 2020 16:15:08: 32000000 INFO @ Wed, 22 Jul 2020 16:15:14: 44000000 INFO @ Wed, 22 Jul 2020 16:15:14: 39000000 INFO @ Wed, 22 Jul 2020 16:15:15: 33000000 INFO @ Wed, 22 Jul 2020 16:15:20: 45000000 INFO @ Wed, 22 Jul 2020 16:15:20: 40000000 INFO @ Wed, 22 Jul 2020 16:15:21: 34000000 INFO @ Wed, 22 Jul 2020 16:15:26: 46000000 INFO @ Wed, 22 Jul 2020 16:15:26: 41000000 INFO @ Wed, 22 Jul 2020 16:15:27: 35000000 INFO @ Wed, 22 Jul 2020 16:15:27: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:15:27: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:15:27: #1 total tags in treatment: 22704514 INFO @ Wed, 22 Jul 2020 16:15:27: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:15:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:15:28: #1 tags after filtering in treatment: 13757389 INFO @ Wed, 22 Jul 2020 16:15:28: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 22 Jul 2020 16:15:28: #1 finished! INFO @ Wed, 22 Jul 2020 16:15:28: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:15:29: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:15:29: Too few paired peaks (0) 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 @ Wed, 22 Jul 2020 16:15:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.05_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/SRX8639537/SRX8639537.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:15:32: 42000000 INFO @ Wed, 22 Jul 2020 16:15:33: 36000000 INFO @ Wed, 22 Jul 2020 16:15:38: 43000000 INFO @ Wed, 22 Jul 2020 16:15:39: 37000000 INFO @ Wed, 22 Jul 2020 16:15:44: 44000000 INFO @ Wed, 22 Jul 2020 16:15:45: 38000000 INFO @ Wed, 22 Jul 2020 16:15:50: 45000000 INFO @ Wed, 22 Jul 2020 16:15:51: 39000000 INFO @ Wed, 22 Jul 2020 16:15:56: 46000000 INFO @ Wed, 22 Jul 2020 16:15:57: 40000000 INFO @ Wed, 22 Jul 2020 16:15:58: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:15:58: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:15:58: #1 total tags in treatment: 22704514 INFO @ Wed, 22 Jul 2020 16:15:58: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:15:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:15:58: #1 tags after filtering in treatment: 13757389 INFO @ Wed, 22 Jul 2020 16:15:58: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 22 Jul 2020 16:15:58: #1 finished! INFO @ Wed, 22 Jul 2020 16:15:58: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:15:59: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:15:59: Too few paired peaks (0) 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 @ Wed, 22 Jul 2020 16:15:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.10_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/SRX8639537/SRX8639537.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:16:03: 41000000 INFO @ Wed, 22 Jul 2020 16:16:09: 42000000 INFO @ Wed, 22 Jul 2020 16:16:14: 43000000 INFO @ Wed, 22 Jul 2020 16:16:20: 44000000 INFO @ Wed, 22 Jul 2020 16:16:26: 45000000 INFO @ Wed, 22 Jul 2020 16:16:31: 46000000 INFO @ Wed, 22 Jul 2020 16:16:33: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:16:33: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:16:33: #1 total tags in treatment: 22704514 INFO @ Wed, 22 Jul 2020 16:16:33: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:16:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:16:33: #1 tags after filtering in treatment: 13757389 INFO @ Wed, 22 Jul 2020 16:16:33: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 22 Jul 2020 16:16:33: #1 finished! INFO @ Wed, 22 Jul 2020 16:16:33: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:16:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:16:34: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:16:34: Too few paired peaks (0) 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 @ Wed, 22 Jul 2020 16:16:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.20_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/SRX8639537/SRX8639537.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639537/SRX8639537.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling