Job ID = 7117469 SRX = SRX8639535 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:38:51 prefetch.2.10.7: 1) Downloading 'SRR12116973'... 2020-07-22T06:38:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:43:33 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:43:33 prefetch.2.10.7: 1) 'SRR12116973' was downloaded successfully 2020-07-22T06:43:33 prefetch.2.10.7: 'SRR12116973' has 0 unresolved dependencies Read 21403698 spots for SRR12116973/SRR12116973.sra Written 21403698 spots for SRR12116973/SRR12116973.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: 00:10:41 21403698 reads; of these: 21403698 (100.00%) were paired; of these: 3627517 (16.95%) aligned concordantly 0 times 15642654 (73.08%) aligned concordantly exactly 1 time 2133527 (9.97%) aligned concordantly >1 times ---- 3627517 pairs aligned concordantly 0 times; of these: 532336 (14.67%) aligned discordantly 1 time ---- 3095181 pairs aligned 0 times concordantly or discordantly; of these: 6190362 mates make up the pairs; of these: 5777317 (93.33%) aligned 0 times 203941 (3.29%) aligned exactly 1 time 209104 (3.38%) aligned >1 times 86.50% overall alignment rate Time searching: 00:10:41 Overall time: 00:10:41 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 16 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] 312231 / 18230815 = 0.0171 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 16:04:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.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 16:04:11: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:04:11: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:04:15: 1000000 INFO @ Wed, 22 Jul 2020 16:04:20: 2000000 INFO @ Wed, 22 Jul 2020 16:04:25: 3000000 INFO @ Wed, 22 Jul 2020 16:04:29: 4000000 INFO @ Wed, 22 Jul 2020 16:04:34: 5000000 INFO @ Wed, 22 Jul 2020 16:04:38: 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 16:04:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.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 16:04:40: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:04:40: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:04:43: 7000000 INFO @ Wed, 22 Jul 2020 16:04:46: 1000000 INFO @ Wed, 22 Jul 2020 16:04:49: 8000000 INFO @ Wed, 22 Jul 2020 16:04:52: 2000000 INFO @ Wed, 22 Jul 2020 16:04:54: 9000000 INFO @ Wed, 22 Jul 2020 16:04:58: 3000000 INFO @ Wed, 22 Jul 2020 16:04:59: 10000000 INFO @ Wed, 22 Jul 2020 16:05:04: 4000000 INFO @ Wed, 22 Jul 2020 16:05:04: 11000000 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 16:05:09: 12000000 INFO @ Wed, 22 Jul 2020 16:05:10: 5000000 INFO @ Wed, 22 Jul 2020 16:05:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.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 16:05:10: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:05:10: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:05:15: 13000000 INFO @ Wed, 22 Jul 2020 16:05:16: 6000000 INFO @ Wed, 22 Jul 2020 16:05:16: 1000000 INFO @ Wed, 22 Jul 2020 16:05:20: 14000000 INFO @ Wed, 22 Jul 2020 16:05:22: 7000000 INFO @ Wed, 22 Jul 2020 16:05:22: 2000000 INFO @ Wed, 22 Jul 2020 16:05:25: 15000000 INFO @ Wed, 22 Jul 2020 16:05:28: 8000000 INFO @ Wed, 22 Jul 2020 16:05:28: 3000000 INFO @ Wed, 22 Jul 2020 16:05:30: 16000000 INFO @ Wed, 22 Jul 2020 16:05:34: 9000000 INFO @ Wed, 22 Jul 2020 16:05:34: 4000000 INFO @ Wed, 22 Jul 2020 16:05:36: 17000000 INFO @ Wed, 22 Jul 2020 16:05:40: 10000000 INFO @ Wed, 22 Jul 2020 16:05:40: 5000000 INFO @ Wed, 22 Jul 2020 16:05:41: 18000000 INFO @ Wed, 22 Jul 2020 16:05:46: 11000000 INFO @ Wed, 22 Jul 2020 16:05:46: 6000000 INFO @ Wed, 22 Jul 2020 16:05:46: 19000000 INFO @ Wed, 22 Jul 2020 16:05:51: 20000000 INFO @ Wed, 22 Jul 2020 16:05:51: 12000000 INFO @ Wed, 22 Jul 2020 16:05:52: 7000000 INFO @ Wed, 22 Jul 2020 16:05:57: 21000000 INFO @ Wed, 22 Jul 2020 16:05:57: 8000000 INFO @ Wed, 22 Jul 2020 16:05:57: 13000000 INFO @ Wed, 22 Jul 2020 16:06:02: 22000000 INFO @ Wed, 22 Jul 2020 16:06:03: 9000000 INFO @ Wed, 22 Jul 2020 16:06:04: 14000000 INFO @ Wed, 22 Jul 2020 16:06:07: 23000000 INFO @ Wed, 22 Jul 2020 16:06:09: 10000000 INFO @ Wed, 22 Jul 2020 16:06:10: 15000000 INFO @ Wed, 22 Jul 2020 16:06:13: 24000000 INFO @ Wed, 22 Jul 2020 16:06:14: 11000000 INFO @ Wed, 22 Jul 2020 16:06:16: 16000000 INFO @ Wed, 22 Jul 2020 16:06:18: 25000000 INFO @ Wed, 22 Jul 2020 16:06:20: 12000000 INFO @ Wed, 22 Jul 2020 16:06:21: 17000000 INFO @ Wed, 22 Jul 2020 16:06:23: 26000000 INFO @ Wed, 22 Jul 2020 16:06:26: 13000000 INFO @ Wed, 22 Jul 2020 16:06:27: 18000000 INFO @ Wed, 22 Jul 2020 16:06:29: 27000000 INFO @ Wed, 22 Jul 2020 16:06:32: 14000000 INFO @ Wed, 22 Jul 2020 16:06:33: 19000000 INFO @ Wed, 22 Jul 2020 16:06:34: 28000000 INFO @ Wed, 22 Jul 2020 16:06:37: 15000000 INFO @ Wed, 22 Jul 2020 16:06:39: 29000000 INFO @ Wed, 22 Jul 2020 16:06:39: 20000000 INFO @ Wed, 22 Jul 2020 16:06:43: 16000000 INFO @ Wed, 22 Jul 2020 16:06:44: 30000000 INFO @ Wed, 22 Jul 2020 16:06:45: 21000000 INFO @ Wed, 22 Jul 2020 16:06:49: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:06:50: 31000000 INFO @ Wed, 22 Jul 2020 16:06:51: 22000000 INFO @ Wed, 22 Jul 2020 16:06:55: 18000000 INFO @ Wed, 22 Jul 2020 16:06:55: 32000000 INFO @ Wed, 22 Jul 2020 16:06:57: 23000000 INFO @ Wed, 22 Jul 2020 16:07:00: 33000000 INFO @ Wed, 22 Jul 2020 16:07:00: 19000000 INFO @ Wed, 22 Jul 2020 16:07:03: 24000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:07:05: 34000000 INFO @ Wed, 22 Jul 2020 16:07:06: 20000000 INFO @ Wed, 22 Jul 2020 16:07:09: 25000000 INFO @ Wed, 22 Jul 2020 16:07:11: 35000000 INFO @ Wed, 22 Jul 2020 16:07:12: 21000000 INFO @ Wed, 22 Jul 2020 16:07:15: 26000000 INFO @ Wed, 22 Jul 2020 16:07:16: 36000000 INFO @ Wed, 22 Jul 2020 16:07:18: 22000000 INFO @ Wed, 22 Jul 2020 16:07:18: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:07:18: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:07:18: #1 total tags in treatment: 17466823 INFO @ Wed, 22 Jul 2020 16:07:18: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:07:18: #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 16:07:19: #1 tags after filtering in treatment: 11631994 INFO @ Wed, 22 Jul 2020 16:07:19: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 16:07:19: #1 finished! INFO @ Wed, 22 Jul 2020 16:07:19: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:07:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:07:19: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:07:19: 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 16:07:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.05_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/SRX8639535/SRX8639535.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:07:21: 27000000 INFO @ Wed, 22 Jul 2020 16:07:23: 23000000 INFO @ Wed, 22 Jul 2020 16:07:27: 28000000 INFO @ Wed, 22 Jul 2020 16:07:29: 24000000 INFO @ Wed, 22 Jul 2020 16:07:33: 29000000 INFO @ Wed, 22 Jul 2020 16:07:35: 25000000 INFO @ Wed, 22 Jul 2020 16:07:39: 30000000 INFO @ Wed, 22 Jul 2020 16:07:41: 26000000 INFO @ Wed, 22 Jul 2020 16:07:45: 31000000 INFO @ Wed, 22 Jul 2020 16:07:46: 27000000 INFO @ Wed, 22 Jul 2020 16:07:51: 32000000 INFO @ Wed, 22 Jul 2020 16:07:52: 28000000 INFO @ Wed, 22 Jul 2020 16:07:57: 33000000 INFO @ Wed, 22 Jul 2020 16:07:58: 29000000 INFO @ Wed, 22 Jul 2020 16:08:02: 34000000 INFO @ Wed, 22 Jul 2020 16:08:03: 30000000 INFO @ Wed, 22 Jul 2020 16:08:08: 35000000 INFO @ Wed, 22 Jul 2020 16:08:09: 31000000 INFO @ Wed, 22 Jul 2020 16:08:14: 36000000 INFO @ Wed, 22 Jul 2020 16:08:15: 32000000 INFO @ Wed, 22 Jul 2020 16:08:16: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:08:16: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:08:16: #1 total tags in treatment: 17466823 INFO @ Wed, 22 Jul 2020 16:08:16: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:08:16: #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 16:08:17: #1 tags after filtering in treatment: 11631994 INFO @ Wed, 22 Jul 2020 16:08:17: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 16:08:17: #1 finished! INFO @ Wed, 22 Jul 2020 16:08:17: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:08:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:08:17: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:08:17: 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 16:08:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.10_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/SRX8639535/SRX8639535.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:08:20: 33000000 INFO @ Wed, 22 Jul 2020 16:08:26: 34000000 INFO @ Wed, 22 Jul 2020 16:08:31: 35000000 INFO @ Wed, 22 Jul 2020 16:08:36: 36000000 INFO @ Wed, 22 Jul 2020 16:08:39: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:08:39: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:08:39: #1 total tags in treatment: 17466823 INFO @ Wed, 22 Jul 2020 16:08:39: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:08:39: #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 16:08:39: #1 tags after filtering in treatment: 11631994 INFO @ Wed, 22 Jul 2020 16:08:39: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 16:08:39: #1 finished! INFO @ Wed, 22 Jul 2020 16:08:39: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:08:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:08:40: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:08:40: 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 16:08:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.20_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/SRX8639535/SRX8639535.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639535/SRX8639535.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling