Job ID = 7117974 SRX = SRX8639563 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T07:00:45 prefetch.2.10.7: 1) Downloading 'SRR12117001'... 2020-07-22T07:00:45 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T07:03:12 prefetch.2.10.7: HTTPS download succeed 2020-07-22T07:03:12 prefetch.2.10.7: 1) 'SRR12117001' was downloaded successfully 2020-07-22T07:03:12 prefetch.2.10.7: 'SRR12117001' has 0 unresolved dependencies Read 22841680 spots for SRR12117001/SRR12117001.sra Written 22841680 spots for SRR12117001/SRR12117001.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: 00:07:57 22841680 reads; of these: 22841680 (100.00%) were paired; of these: 12060824 (52.80%) aligned concordantly 0 times 9781950 (42.83%) aligned concordantly exactly 1 time 998906 (4.37%) aligned concordantly >1 times ---- 12060824 pairs aligned concordantly 0 times; of these: 415768 (3.45%) aligned discordantly 1 time ---- 11645056 pairs aligned 0 times concordantly or discordantly; of these: 23290112 mates make up the pairs; of these: 23025774 (98.87%) aligned 0 times 166634 (0.72%) aligned exactly 1 time 97704 (0.42%) aligned >1 times 49.60% overall alignment rate Time searching: 00:07:57 Overall time: 00:07:57 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 12 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] 116732 / 11174742 = 0.0104 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 16:17:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.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 16:17:54: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:17:54: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:17:59: 1000000 INFO @ Wed, 22 Jul 2020 16:18:05: 2000000 INFO @ Wed, 22 Jul 2020 16:18:10: 3000000 INFO @ Wed, 22 Jul 2020 16:18:16: 4000000 INFO @ Wed, 22 Jul 2020 16:18:21: 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 16:18:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.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 16:18:24: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:18:24: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:18:26: 6000000 INFO @ Wed, 22 Jul 2020 16:18:30: 1000000 INFO @ Wed, 22 Jul 2020 16:18:31: 7000000 INFO @ Wed, 22 Jul 2020 16:18:36: 2000000 INFO @ Wed, 22 Jul 2020 16:18:37: 8000000 INFO @ Wed, 22 Jul 2020 16:18:42: 9000000 INFO @ Wed, 22 Jul 2020 16:18:42: 3000000 INFO @ Wed, 22 Jul 2020 16:18:48: 10000000 INFO @ Wed, 22 Jul 2020 16:18:48: 4000000 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 16:18:53: 11000000 INFO @ Wed, 22 Jul 2020 16:18:54: 5000000 INFO @ Wed, 22 Jul 2020 16:18:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.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 16:18:54: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:18:54: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:18:59: 12000000 INFO @ Wed, 22 Jul 2020 16:19:00: 6000000 INFO @ Wed, 22 Jul 2020 16:19:00: 1000000 INFO @ Wed, 22 Jul 2020 16:19:05: 13000000 INFO @ Wed, 22 Jul 2020 16:19:05: 2000000 INFO @ Wed, 22 Jul 2020 16:19:06: 7000000 INFO @ Wed, 22 Jul 2020 16:19:11: 14000000 INFO @ Wed, 22 Jul 2020 16:19:11: 3000000 INFO @ Wed, 22 Jul 2020 16:19:12: 8000000 INFO @ Wed, 22 Jul 2020 16:19:16: 15000000 INFO @ Wed, 22 Jul 2020 16:19:17: 4000000 INFO @ Wed, 22 Jul 2020 16:19:17: 9000000 INFO @ Wed, 22 Jul 2020 16:19:22: 16000000 INFO @ Wed, 22 Jul 2020 16:19:23: 5000000 INFO @ Wed, 22 Jul 2020 16:19:23: 10000000 INFO @ Wed, 22 Jul 2020 16:19:28: 17000000 INFO @ Wed, 22 Jul 2020 16:19:29: 6000000 INFO @ Wed, 22 Jul 2020 16:19:29: 11000000 INFO @ Wed, 22 Jul 2020 16:19:34: 18000000 INFO @ Wed, 22 Jul 2020 16:19:35: 12000000 INFO @ Wed, 22 Jul 2020 16:19:35: 7000000 INFO @ Wed, 22 Jul 2020 16:19:40: 19000000 INFO @ Wed, 22 Jul 2020 16:19:41: 13000000 INFO @ Wed, 22 Jul 2020 16:19:41: 8000000 INFO @ Wed, 22 Jul 2020 16:19:45: 20000000 INFO @ Wed, 22 Jul 2020 16:19:46: 14000000 INFO @ Wed, 22 Jul 2020 16:19:48: 9000000 INFO @ Wed, 22 Jul 2020 16:19:51: 21000000 INFO @ Wed, 22 Jul 2020 16:19:52: 15000000 INFO @ Wed, 22 Jul 2020 16:19:54: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:19:57: 22000000 INFO @ Wed, 22 Jul 2020 16:19:58: 16000000 INFO @ Wed, 22 Jul 2020 16:19:59: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:19:59: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:19:59: #1 total tags in treatment: 10665883 INFO @ Wed, 22 Jul 2020 16:19:59: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:19:59: #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 16:20:00: #1 tags after filtering in treatment: 7133752 INFO @ Wed, 22 Jul 2020 16:20:00: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 16:20:00: #1 finished! INFO @ Wed, 22 Jul 2020 16:20:00: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:20:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:20:00: 11000000 INFO @ Wed, 22 Jul 2020 16:20:00: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:20:00: 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 16:20:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.05_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/SRX8639563/SRX8639563.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:20:03: 17000000 INFO @ Wed, 22 Jul 2020 16:20:06: 12000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:20:09: 18000000 INFO @ Wed, 22 Jul 2020 16:20:12: 13000000 INFO @ Wed, 22 Jul 2020 16:20:15: 19000000 INFO @ Wed, 22 Jul 2020 16:20:18: 14000000 INFO @ Wed, 22 Jul 2020 16:20:20: 20000000 INFO @ Wed, 22 Jul 2020 16:20:24: 15000000 INFO @ Wed, 22 Jul 2020 16:20:26: 21000000 INFO @ Wed, 22 Jul 2020 16:20:31: 16000000 INFO @ Wed, 22 Jul 2020 16:20:32: 22000000 INFO @ Wed, 22 Jul 2020 16:20:34: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:20:34: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:20:34: #1 total tags in treatment: 10665883 INFO @ Wed, 22 Jul 2020 16:20:34: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:20:34: #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 16:20:34: #1 tags after filtering in treatment: 7133752 INFO @ Wed, 22 Jul 2020 16:20:34: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 16:20:34: #1 finished! INFO @ Wed, 22 Jul 2020 16:20:34: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:20:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:20:35: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:20:35: 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 16:20:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.10_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/SRX8639563/SRX8639563.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:20:36: 17000000 INFO @ Wed, 22 Jul 2020 16:20:42: 18000000 INFO @ Wed, 22 Jul 2020 16:20:48: 19000000 INFO @ Wed, 22 Jul 2020 16:20:53: 20000000 INFO @ Wed, 22 Jul 2020 16:20:59: 21000000 INFO @ Wed, 22 Jul 2020 16:21:05: 22000000 INFO @ Wed, 22 Jul 2020 16:21:07: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:21:07: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:21:07: #1 total tags in treatment: 10665883 INFO @ Wed, 22 Jul 2020 16:21:07: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:21:07: #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 16:21:07: #1 tags after filtering in treatment: 7133752 INFO @ Wed, 22 Jul 2020 16:21:07: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 16:21:07: #1 finished! INFO @ Wed, 22 Jul 2020 16:21:07: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:21:08: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:21:08: 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 16:21:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.20_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/SRX8639563/SRX8639563.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639563/SRX8639563.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling