Job ID = 5791160 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,852,142 reads read : 27,704,284 reads written : 27,704,284 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: 00:16:41 13852142 reads; of these: 13852142 (100.00%) were paired; of these: 8282774 (59.79%) aligned concordantly 0 times 4461006 (32.20%) aligned concordantly exactly 1 time 1108362 (8.00%) aligned concordantly >1 times ---- 8282774 pairs aligned concordantly 0 times; of these: 3586381 (43.30%) aligned discordantly 1 time ---- 4696393 pairs aligned 0 times concordantly or discordantly; of these: 9392786 mates make up the pairs; of these: 7744762 (82.45%) aligned 0 times 317744 (3.38%) aligned exactly 1 time 1330280 (14.16%) aligned >1 times 72.04% overall alignment rate Time searching: 00:16:41 Overall time: 00:16:41 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] 1644092 / 8973606 = 0.1832 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 09:28:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.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 09:28:40: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:28:40: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:28:46: 1000000 INFO @ Wed, 22 Apr 2020 09:28:52: 2000000 INFO @ Wed, 22 Apr 2020 09:28:57: 3000000 INFO @ Wed, 22 Apr 2020 09:29:03: 4000000 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 09:29:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.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 09:29:09: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:29:09: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:29:09: 5000000 INFO @ Wed, 22 Apr 2020 09:29:15: 6000000 INFO @ Wed, 22 Apr 2020 09:29:17: 1000000 INFO @ Wed, 22 Apr 2020 09:29:21: 7000000 INFO @ Wed, 22 Apr 2020 09:29:24: 2000000 INFO @ Wed, 22 Apr 2020 09:29:27: 8000000 INFO @ Wed, 22 Apr 2020 09:29:30: 3000000 INFO @ Wed, 22 Apr 2020 09:29:33: 9000000 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 09:29:36: 4000000 INFO @ Wed, 22 Apr 2020 09:29:39: 10000000 INFO @ Wed, 22 Apr 2020 09:29:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.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 09:29:40: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:29:40: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:29:43: 5000000 INFO @ Wed, 22 Apr 2020 09:29:45: 11000000 INFO @ Wed, 22 Apr 2020 09:29:47: 1000000 INFO @ Wed, 22 Apr 2020 09:29:49: 6000000 INFO @ Wed, 22 Apr 2020 09:29:51: 12000000 INFO @ Wed, 22 Apr 2020 09:29:55: 7000000 INFO @ Wed, 22 Apr 2020 09:29:55: 2000000 INFO @ Wed, 22 Apr 2020 09:29:57: 13000000 INFO @ Wed, 22 Apr 2020 09:30:01: 8000000 INFO @ Wed, 22 Apr 2020 09:30:03: 3000000 INFO @ Wed, 22 Apr 2020 09:30:04: 14000000 INFO @ Wed, 22 Apr 2020 09:30:07: 9000000 INFO @ Wed, 22 Apr 2020 09:30:10: 15000000 INFO @ Wed, 22 Apr 2020 09:30:10: 4000000 INFO @ Wed, 22 Apr 2020 09:30:13: 10000000 INFO @ Wed, 22 Apr 2020 09:30:16: 16000000 INFO @ Wed, 22 Apr 2020 09:30:18: 5000000 INFO @ Wed, 22 Apr 2020 09:30:19: 11000000 INFO @ Wed, 22 Apr 2020 09:30:20: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:30:20: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:30:20: #1 total tags in treatment: 4522001 INFO @ Wed, 22 Apr 2020 09:30:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:30:20: #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 09:30:20: #1 tags after filtering in treatment: 2931965 INFO @ Wed, 22 Apr 2020 09:30:20: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Apr 2020 09:30:20: #1 finished! INFO @ Wed, 22 Apr 2020 09:30:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:30:20: #2 number of paired peaks: 5 WARNING @ Wed, 22 Apr 2020 09:30:20: Too few paired peaks (5) 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 09:30:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.05_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/SRX6614954/SRX6614954.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:30:25: 12000000 INFO @ Wed, 22 Apr 2020 09:30:25: 6000000 INFO @ Wed, 22 Apr 2020 09:30:31: 13000000 INFO @ Wed, 22 Apr 2020 09:30:33: 7000000 INFO @ Wed, 22 Apr 2020 09:30:38: 14000000 INFO @ Wed, 22 Apr 2020 09:30:41: 8000000 INFO @ Wed, 22 Apr 2020 09:30:44: 15000000 INFO @ Wed, 22 Apr 2020 09:30:48: 9000000 INFO @ Wed, 22 Apr 2020 09:30:50: 16000000 INFO @ Wed, 22 Apr 2020 09:30:54: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:30:54: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:30:54: #1 total tags in treatment: 4522001 INFO @ Wed, 22 Apr 2020 09:30:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:30:54: #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 09:30:54: #1 tags after filtering in treatment: 2931965 INFO @ Wed, 22 Apr 2020 09:30:54: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Apr 2020 09:30:54: #1 finished! INFO @ Wed, 22 Apr 2020 09:30:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:30:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:30:54: #2 number of paired peaks: 5 WARNING @ Wed, 22 Apr 2020 09:30:54: Too few paired peaks (5) 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 09:30:54: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 09:30:56: 10000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.10_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/SRX6614954/SRX6614954.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:31:03: 11000000 INFO @ Wed, 22 Apr 2020 09:31:11: 12000000 INFO @ Wed, 22 Apr 2020 09:31:18: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:31:26: 14000000 INFO @ Wed, 22 Apr 2020 09:31:33: 15000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:31:41: 16000000 INFO @ Wed, 22 Apr 2020 09:31:46: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:31:46: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:31:46: #1 total tags in treatment: 4522001 INFO @ Wed, 22 Apr 2020 09:31:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:31:46: #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 09:31:46: #1 tags after filtering in treatment: 2931965 INFO @ Wed, 22 Apr 2020 09:31:46: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Apr 2020 09:31:46: #1 finished! INFO @ Wed, 22 Apr 2020 09:31:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:31:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:31:46: #2 number of paired peaks: 5 WARNING @ Wed, 22 Apr 2020 09:31:46: Too few paired peaks (5) 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 09:31:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.20_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/SRX6614954/SRX6614954.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614954/SRX6614954.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling