Job ID = 5791824 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,043,322 reads read : 26,086,644 reads written : 26,086,644 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:08:17 13043322 reads; of these: 13043322 (100.00%) were paired; of these: 2974210 (22.80%) aligned concordantly 0 times 8713270 (66.80%) aligned concordantly exactly 1 time 1355842 (10.39%) aligned concordantly >1 times ---- 2974210 pairs aligned concordantly 0 times; of these: 963944 (32.41%) aligned discordantly 1 time ---- 2010266 pairs aligned 0 times concordantly or discordantly; of these: 4020532 mates make up the pairs; of these: 3473105 (86.38%) aligned 0 times 229443 (5.71%) aligned exactly 1 time 317984 (7.91%) aligned >1 times 86.69% overall alignment rate Time searching: 00:08:17 Overall time: 00:08:17 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] 2824775 / 10961188 = 0.2577 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 Apr 2020 11:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.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 Apr 2020 11:09:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:09:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:09:59: 1000000 INFO @ Wed, 22 Apr 2020 11:10:05: 2000000 INFO @ Wed, 22 Apr 2020 11:10:11: 3000000 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 Apr 2020 11:10:18: 4000000 INFO @ Wed, 22 Apr 2020 11:10:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.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 Apr 2020 11:10:21: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:10:21: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:10:24: 5000000 INFO @ Wed, 22 Apr 2020 11:10:28: 1000000 INFO @ Wed, 22 Apr 2020 11:10:31: 6000000 INFO @ Wed, 22 Apr 2020 11:10:35: 2000000 INFO @ Wed, 22 Apr 2020 11:10:38: 7000000 INFO @ Wed, 22 Apr 2020 11:10:42: 3000000 INFO @ Wed, 22 Apr 2020 11:10:44: 8000000 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 Apr 2020 11:10:49: 4000000 INFO @ Wed, 22 Apr 2020 11:10:51: 9000000 INFO @ Wed, 22 Apr 2020 11:10:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.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 Apr 2020 11:10:51: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:10:51: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:10:56: 5000000 INFO @ Wed, 22 Apr 2020 11:10:59: 10000000 INFO @ Wed, 22 Apr 2020 11:11:00: 1000000 INFO @ Wed, 22 Apr 2020 11:11:04: 6000000 INFO @ Wed, 22 Apr 2020 11:11:06: 11000000 INFO @ Wed, 22 Apr 2020 11:11:08: 2000000 INFO @ Wed, 22 Apr 2020 11:11:11: 7000000 INFO @ Wed, 22 Apr 2020 11:11:14: 12000000 INFO @ Wed, 22 Apr 2020 11:11:17: 3000000 INFO @ Wed, 22 Apr 2020 11:11:19: 8000000 INFO @ Wed, 22 Apr 2020 11:11:22: 13000000 INFO @ Wed, 22 Apr 2020 11:11:26: 4000000 INFO @ Wed, 22 Apr 2020 11:11:27: 9000000 INFO @ Wed, 22 Apr 2020 11:11:30: 14000000 INFO @ Wed, 22 Apr 2020 11:11:34: 5000000 INFO @ Wed, 22 Apr 2020 11:11:34: 10000000 INFO @ Wed, 22 Apr 2020 11:11:37: 15000000 INFO @ Wed, 22 Apr 2020 11:11:42: 11000000 INFO @ Wed, 22 Apr 2020 11:11:43: 6000000 INFO @ Wed, 22 Apr 2020 11:11:45: 16000000 INFO @ Wed, 22 Apr 2020 11:11:50: 12000000 INFO @ Wed, 22 Apr 2020 11:11:52: 7000000 INFO @ Wed, 22 Apr 2020 11:11:52: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:11:52: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:11:52: #1 total tags in treatment: 7463243 INFO @ Wed, 22 Apr 2020 11:11:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:11:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 11:11:52: #1 tags after filtering in treatment: 3588006 INFO @ Wed, 22 Apr 2020 11:11:52: #1 Redundant rate of treatment: 0.52 INFO @ Wed, 22 Apr 2020 11:11:52: #1 finished! INFO @ Wed, 22 Apr 2020 11:11:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:11:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:11:53: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:11:53: 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 Apr 2020 11:11:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.05_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/SRX7756604/SRX7756604.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:11:57: 13000000 INFO @ Wed, 22 Apr 2020 11:12:00: 8000000 INFO @ Wed, 22 Apr 2020 11:12:05: 14000000 INFO @ Wed, 22 Apr 2020 11:12:09: 9000000 INFO @ Wed, 22 Apr 2020 11:12:13: 15000000 INFO @ Wed, 22 Apr 2020 11:12:17: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:12:21: 16000000 INFO @ Wed, 22 Apr 2020 11:12:25: 11000000 INFO @ Wed, 22 Apr 2020 11:12:28: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:12:28: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:12:28: #1 total tags in treatment: 7463243 INFO @ Wed, 22 Apr 2020 11:12:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:12:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 11:12:28: #1 tags after filtering in treatment: 3588006 INFO @ Wed, 22 Apr 2020 11:12:28: #1 Redundant rate of treatment: 0.52 INFO @ Wed, 22 Apr 2020 11:12:28: #1 finished! INFO @ Wed, 22 Apr 2020 11:12:28: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:12:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:12:28: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:12:28: 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 Apr 2020 11:12:28: Process for pairing-model is terminated! BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:12:33: 12000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.10_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/SRX7756604/SRX7756604.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:12:41: 13000000 INFO @ Wed, 22 Apr 2020 11:12:49: 14000000 INFO @ Wed, 22 Apr 2020 11:12:57: 15000000 INFO @ Wed, 22 Apr 2020 11:13:04: 16000000 INFO @ Wed, 22 Apr 2020 11:13:11: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:13:11: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:13:11: #1 total tags in treatment: 7463243 INFO @ Wed, 22 Apr 2020 11:13:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:13:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 11:13:11: #1 tags after filtering in treatment: 3588006 INFO @ Wed, 22 Apr 2020 11:13:11: #1 Redundant rate of treatment: 0.52 INFO @ Wed, 22 Apr 2020 11:13:11: #1 finished! INFO @ Wed, 22 Apr 2020 11:13:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:13:12: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:13:12: 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 Apr 2020 11:13:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.20_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/SRX7756604/SRX7756604.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756604/SRX7756604.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling