Job ID = 5791124 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,854,655 reads read : 13,709,310 reads written : 13,709,310 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: 00:02:31 6854655 reads; of these: 6854655 (100.00%) were paired; of these: 1329355 (19.39%) aligned concordantly 0 times 4775725 (69.67%) aligned concordantly exactly 1 time 749575 (10.94%) aligned concordantly >1 times ---- 1329355 pairs aligned concordantly 0 times; of these: 2420 (0.18%) aligned discordantly 1 time ---- 1326935 pairs aligned 0 times concordantly or discordantly; of these: 2653870 mates make up the pairs; of these: 2581620 (97.28%) aligned 0 times 57962 (2.18%) aligned exactly 1 time 14288 (0.54%) aligned >1 times 81.17% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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_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] 494757 / 5526960 = 0.0895 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 08:40:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.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 08:40:33: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:40:33: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:40:37: 1000000 INFO @ Wed, 22 Apr 2020 08:40:41: 2000000 INFO @ Wed, 22 Apr 2020 08:40:45: 3000000 INFO @ Wed, 22 Apr 2020 08:40:49: 4000000 INFO @ Wed, 22 Apr 2020 08:40:52: 5000000 INFO @ Wed, 22 Apr 2020 08:40:56: 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 Apr 2020 08:41:00: 7000000 INFO @ Wed, 22 Apr 2020 08:41:04: 8000000 INFO @ Wed, 22 Apr 2020 08:41:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.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 08:41:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:41:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:41:07: 9000000 INFO @ Wed, 22 Apr 2020 08:41:08: 1000000 INFO @ Wed, 22 Apr 2020 08:41:11: 10000000 INFO @ Wed, 22 Apr 2020 08:41:12: 2000000 INFO @ Wed, 22 Apr 2020 08:41:12: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 08:41:12: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 08:41:12: #1 total tags in treatment: 5030570 INFO @ Wed, 22 Apr 2020 08:41:12: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:41:12: #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 08:41:12: #1 tags after filtering in treatment: 3357564 INFO @ Wed, 22 Apr 2020 08:41:12: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 08:41:12: #1 finished! INFO @ Wed, 22 Apr 2020 08:41:12: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:41:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:41:12: #2 number of paired peaks: 5 WARNING @ Wed, 22 Apr 2020 08:41:12: 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 08:41:12: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 08:41:15: 3000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.05_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/SRX6614920/SRX6614920.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:41:20: 4000000 INFO @ Wed, 22 Apr 2020 08:41:24: 5000000 INFO @ Wed, 22 Apr 2020 08:41:28: 6000000 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 08:41:32: 7000000 INFO @ Wed, 22 Apr 2020 08:41:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.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 08:41:33: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:41:33: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:41:36: 8000000 INFO @ Wed, 22 Apr 2020 08:41:38: 1000000 INFO @ Wed, 22 Apr 2020 08:41:40: 9000000 INFO @ Wed, 22 Apr 2020 08:41:43: 2000000 INFO @ Wed, 22 Apr 2020 08:41:44: 10000000 INFO @ Wed, 22 Apr 2020 08:41:45: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 08:41:45: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 08:41:45: #1 total tags in treatment: 5030570 INFO @ Wed, 22 Apr 2020 08:41:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:41:45: #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 08:41:45: #1 tags after filtering in treatment: 3357564 INFO @ Wed, 22 Apr 2020 08:41:45: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 08:41:45: #1 finished! INFO @ Wed, 22 Apr 2020 08:41:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:41:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:41:45: #2 number of paired peaks: 5 WARNING @ Wed, 22 Apr 2020 08:41:45: 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 08:41:45: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 08:41:47: 3000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.10_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/SRX6614920/SRX6614920.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:41:52: 4000000 INFO @ Wed, 22 Apr 2020 08:41:57: 5000000 INFO @ Wed, 22 Apr 2020 08:42:01: 6000000 INFO @ Wed, 22 Apr 2020 08:42:06: 7000000 INFO @ Wed, 22 Apr 2020 08:42:10: 8000000 INFO @ Wed, 22 Apr 2020 08:42:15: 9000000 INFO @ Wed, 22 Apr 2020 08:42:20: 10000000 INFO @ Wed, 22 Apr 2020 08:42:20: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 08:42:20: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 08:42:20: #1 total tags in treatment: 5030570 INFO @ Wed, 22 Apr 2020 08:42:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:42:20: #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 08:42:20: #1 tags after filtering in treatment: 3357564 INFO @ Wed, 22 Apr 2020 08:42:20: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 08:42:20: #1 finished! INFO @ Wed, 22 Apr 2020 08:42:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:42:20: #2 number of paired peaks: 5 WARNING @ Wed, 22 Apr 2020 08:42:20: 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 08:42:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.20_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/SRX6614920/SRX6614920.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614920/SRX6614920.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。