Job ID = 7117429 SRX = SRX8639505 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:38:21 prefetch.2.10.7: 1) Downloading 'SRR12117069'... 2020-07-22T06:38:21 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:43:26 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:43:26 prefetch.2.10.7: 1) 'SRR12117069' was downloaded successfully 2020-07-22T06:43:26 prefetch.2.10.7: 'SRR12117069' has 0 unresolved dependencies Read 26830537 spots for SRR12117069/SRR12117069.sra Written 26830537 spots for SRR12117069/SRR12117069.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 26830537 reads; of these: 26830537 (100.00%) were paired; of these: 3690745 (13.76%) aligned concordantly 0 times 20094116 (74.89%) aligned concordantly exactly 1 time 3045676 (11.35%) aligned concordantly >1 times ---- 3690745 pairs aligned concordantly 0 times; of these: 300282 (8.14%) aligned discordantly 1 time ---- 3390463 pairs aligned 0 times concordantly or discordantly; of these: 6780926 mates make up the pairs; of these: 6313981 (93.11%) aligned 0 times 304282 (4.49%) aligned exactly 1 time 162663 (2.40%) aligned >1 times 88.23% 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] 598054 / 23312537 = 0.0257 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 16:08:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.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 16:08:21: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:08:21: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:08:26: 1000000 INFO @ Wed, 22 Jul 2020 16:08:30: 2000000 INFO @ Wed, 22 Jul 2020 16:08:35: 3000000 INFO @ Wed, 22 Jul 2020 16:08:39: 4000000 INFO @ Wed, 22 Jul 2020 16:08:44: 5000000 INFO @ Wed, 22 Jul 2020 16:08:48: 6000000 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 16:08:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.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 16:08:51: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:08:51: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:08:53: 7000000 INFO @ Wed, 22 Jul 2020 16:08:56: 1000000 INFO @ Wed, 22 Jul 2020 16:08:57: 8000000 INFO @ Wed, 22 Jul 2020 16:09:01: 2000000 INFO @ Wed, 22 Jul 2020 16:09:02: 9000000 INFO @ Wed, 22 Jul 2020 16:09:06: 3000000 INFO @ Wed, 22 Jul 2020 16:09:06: 10000000 INFO @ Wed, 22 Jul 2020 16:09:11: 11000000 INFO @ Wed, 22 Jul 2020 16:09:11: 4000000 INFO @ Wed, 22 Jul 2020 16:09:15: 12000000 INFO @ Wed, 22 Jul 2020 16:09:16: 5000000 BedGraph に変換中... 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 16:09:20: 13000000 INFO @ Wed, 22 Jul 2020 16:09:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.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 16:09:21: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:09:21: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:09:21: 6000000 INFO @ Wed, 22 Jul 2020 16:09:24: 14000000 INFO @ Wed, 22 Jul 2020 16:09:26: 1000000 INFO @ Wed, 22 Jul 2020 16:09:27: 7000000 INFO @ Wed, 22 Jul 2020 16:09:29: 15000000 INFO @ Wed, 22 Jul 2020 16:09:31: 2000000 INFO @ Wed, 22 Jul 2020 16:09:32: 8000000 INFO @ Wed, 22 Jul 2020 16:09:34: 16000000 INFO @ Wed, 22 Jul 2020 16:09:36: 3000000 INFO @ Wed, 22 Jul 2020 16:09:37: 9000000 INFO @ Wed, 22 Jul 2020 16:09:38: 17000000 INFO @ Wed, 22 Jul 2020 16:09:42: 4000000 INFO @ Wed, 22 Jul 2020 16:09:42: 10000000 INFO @ Wed, 22 Jul 2020 16:09:43: 18000000 INFO @ Wed, 22 Jul 2020 16:09:47: 5000000 INFO @ Wed, 22 Jul 2020 16:09:47: 11000000 INFO @ Wed, 22 Jul 2020 16:09:48: 19000000 INFO @ Wed, 22 Jul 2020 16:09:52: 6000000 INFO @ Wed, 22 Jul 2020 16:09:53: 12000000 INFO @ Wed, 22 Jul 2020 16:09:53: 20000000 INFO @ Wed, 22 Jul 2020 16:09:57: 7000000 INFO @ Wed, 22 Jul 2020 16:09:57: 21000000 INFO @ Wed, 22 Jul 2020 16:09:58: 13000000 INFO @ Wed, 22 Jul 2020 16:10:02: 22000000 INFO @ Wed, 22 Jul 2020 16:10:02: 8000000 INFO @ Wed, 22 Jul 2020 16:10:03: 14000000 INFO @ Wed, 22 Jul 2020 16:10:07: 23000000 INFO @ Wed, 22 Jul 2020 16:10:08: 9000000 INFO @ Wed, 22 Jul 2020 16:10:08: 15000000 INFO @ Wed, 22 Jul 2020 16:10:12: 24000000 INFO @ Wed, 22 Jul 2020 16:10:13: 10000000 INFO @ Wed, 22 Jul 2020 16:10:13: 16000000 INFO @ Wed, 22 Jul 2020 16:10:17: 25000000 INFO @ Wed, 22 Jul 2020 16:10:18: 11000000 INFO @ Wed, 22 Jul 2020 16:10:19: 17000000 INFO @ Wed, 22 Jul 2020 16:10:21: 26000000 INFO @ Wed, 22 Jul 2020 16:10:23: 12000000 INFO @ Wed, 22 Jul 2020 16:10:24: 18000000 INFO @ Wed, 22 Jul 2020 16:10:26: 27000000 INFO @ Wed, 22 Jul 2020 16:10:28: 13000000 INFO @ Wed, 22 Jul 2020 16:10:30: 19000000 INFO @ Wed, 22 Jul 2020 16:10:31: 28000000 INFO @ Wed, 22 Jul 2020 16:10:33: 14000000 INFO @ Wed, 22 Jul 2020 16:10:35: 20000000 INFO @ Wed, 22 Jul 2020 16:10:36: 29000000 INFO @ Wed, 22 Jul 2020 16:10:39: 15000000 INFO @ Wed, 22 Jul 2020 16:10:40: 30000000 INFO @ Wed, 22 Jul 2020 16:10:40: 21000000 INFO @ Wed, 22 Jul 2020 16:10:44: 16000000 INFO @ Wed, 22 Jul 2020 16:10:45: 31000000 INFO @ Wed, 22 Jul 2020 16:10:46: 22000000 INFO @ Wed, 22 Jul 2020 16:10:49: 17000000 INFO @ Wed, 22 Jul 2020 16:10:50: 32000000 INFO @ Wed, 22 Jul 2020 16:10:51: 23000000 INFO @ Wed, 22 Jul 2020 16:10:55: 18000000 INFO @ Wed, 22 Jul 2020 16:10:55: 33000000 INFO @ Wed, 22 Jul 2020 16:10:57: 24000000 INFO @ Wed, 22 Jul 2020 16:10:59: 34000000 INFO @ Wed, 22 Jul 2020 16:11:00: 19000000 INFO @ Wed, 22 Jul 2020 16:11:02: 25000000 INFO @ Wed, 22 Jul 2020 16:11:04: 35000000 INFO @ Wed, 22 Jul 2020 16:11:05: 20000000 INFO @ Wed, 22 Jul 2020 16:11:08: 26000000 INFO @ Wed, 22 Jul 2020 16:11:09: 36000000 INFO @ Wed, 22 Jul 2020 16:11:11: 21000000 INFO @ Wed, 22 Jul 2020 16:11:13: 27000000 INFO @ Wed, 22 Jul 2020 16:11:14: 37000000 INFO @ Wed, 22 Jul 2020 16:11:16: 22000000 INFO @ Wed, 22 Jul 2020 16:11:18: 28000000 INFO @ Wed, 22 Jul 2020 16:11:19: 38000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:11:22: 23000000 INFO @ Wed, 22 Jul 2020 16:11:23: 39000000 INFO @ Wed, 22 Jul 2020 16:11:23: 29000000 INFO @ Wed, 22 Jul 2020 16:11:28: 24000000 INFO @ Wed, 22 Jul 2020 16:11:28: 40000000 INFO @ Wed, 22 Jul 2020 16:11:29: 30000000 INFO @ Wed, 22 Jul 2020 16:11:33: 41000000 INFO @ Wed, 22 Jul 2020 16:11:33: 25000000 INFO @ Wed, 22 Jul 2020 16:11:34: 31000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:11:38: 42000000 INFO @ Wed, 22 Jul 2020 16:11:39: 26000000 INFO @ Wed, 22 Jul 2020 16:11:39: 32000000 INFO @ Wed, 22 Jul 2020 16:11:43: 43000000 INFO @ Wed, 22 Jul 2020 16:11:44: 27000000 INFO @ Wed, 22 Jul 2020 16:11:45: 33000000 INFO @ Wed, 22 Jul 2020 16:11:47: 44000000 INFO @ Wed, 22 Jul 2020 16:11:50: 28000000 INFO @ Wed, 22 Jul 2020 16:11:50: 34000000 INFO @ Wed, 22 Jul 2020 16:11:52: 45000000 INFO @ Wed, 22 Jul 2020 16:11:55: 29000000 INFO @ Wed, 22 Jul 2020 16:11:55: 35000000 INFO @ Wed, 22 Jul 2020 16:11:57: 46000000 INFO @ Wed, 22 Jul 2020 16:11:58: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:11:58: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:11:58: #1 total tags in treatment: 22542470 INFO @ Wed, 22 Jul 2020 16:11:58: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:11:58: #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 16:11:58: #1 tags after filtering in treatment: 13781569 INFO @ Wed, 22 Jul 2020 16:11:58: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 22 Jul 2020 16:11:58: #1 finished! INFO @ Wed, 22 Jul 2020 16:11:58: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:11:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:11:59: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:11:59: 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 16:11:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.05_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/SRX8639505/SRX8639505.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:12:01: 36000000 INFO @ Wed, 22 Jul 2020 16:12:01: 30000000 INFO @ Wed, 22 Jul 2020 16:12:06: 37000000 INFO @ Wed, 22 Jul 2020 16:12:06: 31000000 INFO @ Wed, 22 Jul 2020 16:12:12: 38000000 INFO @ Wed, 22 Jul 2020 16:12:12: 32000000 INFO @ Wed, 22 Jul 2020 16:12:17: 39000000 INFO @ Wed, 22 Jul 2020 16:12:17: 33000000 INFO @ Wed, 22 Jul 2020 16:12:22: 40000000 INFO @ Wed, 22 Jul 2020 16:12:23: 34000000 INFO @ Wed, 22 Jul 2020 16:12:28: 41000000 INFO @ Wed, 22 Jul 2020 16:12:28: 35000000 INFO @ Wed, 22 Jul 2020 16:12:33: 42000000 INFO @ Wed, 22 Jul 2020 16:12:34: 36000000 INFO @ Wed, 22 Jul 2020 16:12:39: 43000000 INFO @ Wed, 22 Jul 2020 16:12:40: 37000000 INFO @ Wed, 22 Jul 2020 16:12:44: 44000000 INFO @ Wed, 22 Jul 2020 16:12:45: 38000000 INFO @ Wed, 22 Jul 2020 16:12:49: 45000000 INFO @ Wed, 22 Jul 2020 16:12:51: 39000000 INFO @ Wed, 22 Jul 2020 16:12:55: 46000000 INFO @ Wed, 22 Jul 2020 16:12:56: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:12:56: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:12:56: #1 total tags in treatment: 22542470 INFO @ Wed, 22 Jul 2020 16:12:56: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:12:56: #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 16:12:56: #1 tags after filtering in treatment: 13781569 INFO @ Wed, 22 Jul 2020 16:12:56: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 22 Jul 2020 16:12:56: #1 finished! INFO @ Wed, 22 Jul 2020 16:12:56: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:12:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:12:56: 40000000 INFO @ Wed, 22 Jul 2020 16:12:57: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:12:57: 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 16:12:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.10_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/SRX8639505/SRX8639505.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:13:02: 41000000 INFO @ Wed, 22 Jul 2020 16:13:07: 42000000 INFO @ Wed, 22 Jul 2020 16:13:12: 43000000 INFO @ Wed, 22 Jul 2020 16:13:18: 44000000 INFO @ Wed, 22 Jul 2020 16:13:23: 45000000 INFO @ Wed, 22 Jul 2020 16:13:29: 46000000 INFO @ Wed, 22 Jul 2020 16:13:30: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:13:30: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:13:30: #1 total tags in treatment: 22542470 INFO @ Wed, 22 Jul 2020 16:13:30: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:13:30: #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 16:13:30: #1 tags after filtering in treatment: 13781569 INFO @ Wed, 22 Jul 2020 16:13:30: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 22 Jul 2020 16:13:30: #1 finished! INFO @ Wed, 22 Jul 2020 16:13:30: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:13:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:13:31: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:13:31: 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 16:13:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.20_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/SRX8639505/SRX8639505.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639505/SRX8639505.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling