Job ID = 5791781 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,369,700 reads read : 12,739,400 reads written : 12,739,400 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: 00:03:23 6369700 reads; of these: 6369700 (100.00%) were paired; of these: 500422 (7.86%) aligned concordantly 0 times 5018956 (78.79%) aligned concordantly exactly 1 time 850322 (13.35%) aligned concordantly >1 times ---- 500422 pairs aligned concordantly 0 times; of these: 216041 (43.17%) aligned discordantly 1 time ---- 284381 pairs aligned 0 times concordantly or discordantly; of these: 568762 mates make up the pairs; of these: 420770 (73.98%) aligned 0 times 53531 (9.41%) aligned exactly 1 time 94461 (16.61%) aligned >1 times 96.70% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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] 249068 / 6083635 = 0.0409 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 10:49:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.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 10:49:12: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:49:12: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:49:18: 1000000 INFO @ Wed, 22 Apr 2020 10:49:24: 2000000 INFO @ Wed, 22 Apr 2020 10:49:31: 3000000 INFO @ Wed, 22 Apr 2020 10:49:37: 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 10:49:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.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 10:49:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:49:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:49:44: 5000000 INFO @ Wed, 22 Apr 2020 10:49:46: 1000000 INFO @ Wed, 22 Apr 2020 10:49:50: 6000000 INFO @ Wed, 22 Apr 2020 10:49:52: 2000000 INFO @ Wed, 22 Apr 2020 10:49:56: 3000000 INFO @ Wed, 22 Apr 2020 10:49:57: 7000000 INFO @ Wed, 22 Apr 2020 10:50:01: 4000000 INFO @ Wed, 22 Apr 2020 10:50:03: 8000000 INFO @ Wed, 22 Apr 2020 10:50:05: 5000000 INFO @ Wed, 22 Apr 2020 10:50:09: 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 10:50:10: 6000000 INFO @ Wed, 22 Apr 2020 10:50:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.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 10:50:12: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:50:12: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:50:14: 7000000 INFO @ Wed, 22 Apr 2020 10:50:16: 10000000 INFO @ Wed, 22 Apr 2020 10:50:17: 1000000 INFO @ Wed, 22 Apr 2020 10:50:18: 8000000 INFO @ Wed, 22 Apr 2020 10:50:21: 2000000 INFO @ Wed, 22 Apr 2020 10:50:22: 11000000 INFO @ Wed, 22 Apr 2020 10:50:23: 9000000 INFO @ Wed, 22 Apr 2020 10:50:26: 3000000 INFO @ Wed, 22 Apr 2020 10:50:27: 10000000 INFO @ Wed, 22 Apr 2020 10:50:28: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 10:50:28: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 10:50:28: #1 total tags in treatment: 5624818 INFO @ Wed, 22 Apr 2020 10:50:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:50:28: #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 10:50:28: #1 tags after filtering in treatment: 4461878 INFO @ Wed, 22 Apr 2020 10:50:28: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 10:50:28: #1 finished! INFO @ Wed, 22 Apr 2020 10:50:28: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:50:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:50:28: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 10:50:28: Too few paired peaks (29) 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 10:50:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:50:30: 4000000 INFO @ Wed, 22 Apr 2020 10:50:33: 11000000 INFO @ Wed, 22 Apr 2020 10:50:35: 5000000 INFO @ Wed, 22 Apr 2020 10:50:39: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 10:50:39: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 10:50:39: #1 total tags in treatment: 5624818 INFO @ Wed, 22 Apr 2020 10:50:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:50:39: #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 10:50:39: 6000000 INFO @ Wed, 22 Apr 2020 10:50:39: #1 tags after filtering in treatment: 4461878 INFO @ Wed, 22 Apr 2020 10:50:39: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 10:50:39: #1 finished! INFO @ Wed, 22 Apr 2020 10:50:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:50:39: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 10:50:39: Too few paired peaks (29) 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 10:50:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.10_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/SRX7741032/SRX7741032.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:50:44: 7000000 INFO @ Wed, 22 Apr 2020 10:50:48: 8000000 INFO @ Wed, 22 Apr 2020 10:50:54: 9000000 INFO @ Wed, 22 Apr 2020 10:50:59: 10000000 INFO @ Wed, 22 Apr 2020 10:51:03: 11000000 INFO @ Wed, 22 Apr 2020 10:51:07: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 10:51:07: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 10:51:07: #1 total tags in treatment: 5624818 INFO @ Wed, 22 Apr 2020 10:51:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:51:07: #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 10:51:07: #1 tags after filtering in treatment: 4461878 INFO @ Wed, 22 Apr 2020 10:51:07: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 10:51:07: #1 finished! INFO @ Wed, 22 Apr 2020 10:51:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:51:07: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 10:51:07: Too few paired peaks (29) 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 10:51:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.20_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/SRX7741032/SRX7741032.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741032/SRX7741032.20_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。