Job ID = 5790988 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,260,784 reads read : 6,521,568 reads written : 6,521,568 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: 00:02:06 3260784 reads; of these: 3260784 (100.00%) were paired; of these: 213382 (6.54%) aligned concordantly 0 times 2744413 (84.16%) aligned concordantly exactly 1 time 302989 (9.29%) aligned concordantly >1 times ---- 213382 pairs aligned concordantly 0 times; of these: 1253 (0.59%) aligned discordantly 1 time ---- 212129 pairs aligned 0 times concordantly or discordantly; of these: 424258 mates make up the pairs; of these: 405948 (95.68%) aligned 0 times 15028 (3.54%) aligned exactly 1 time 3282 (0.77%) aligned >1 times 93.78% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 20307 / 3013334 = 0.0067 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 08:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.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 08:15:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:39: 1000000 INFO @ Wed, 22 Apr 2020 08:15:44: 2000000 INFO @ Wed, 22 Apr 2020 08:15:49: 3000000 INFO @ Wed, 22 Apr 2020 08:15:55: 4000000 INFO @ Wed, 22 Apr 2020 08:16:00: 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 Apr 2020 08:16:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.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 08:16:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:05: 6000000 INFO @ Wed, 22 Apr 2020 08:16:06: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:06: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:06: #1 total tags in treatment: 3027095 INFO @ Wed, 22 Apr 2020 08:16:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:06: #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 08:16:06: #1 tags after filtering in treatment: 2797173 INFO @ Wed, 22 Apr 2020 08:16:06: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 22 Apr 2020 08:16:06: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:06: #2 number of paired peaks: 24 WARNING @ Wed, 22 Apr 2020 08:16:06: Too few paired peaks (24) 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 08:16:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.05_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/SRX5874487/SRX5874487.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:11: 1000000 INFO @ Wed, 22 Apr 2020 08:16:17: 2000000 INFO @ Wed, 22 Apr 2020 08:16:24: 3000000 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 08:16:31: 4000000 INFO @ Wed, 22 Apr 2020 08:16:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.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 08:16:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:37: 5000000 INFO @ Wed, 22 Apr 2020 08:16:41: 1000000 INFO @ Wed, 22 Apr 2020 08:16:45: 6000000 INFO @ Wed, 22 Apr 2020 08:16:45: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:45: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:45: #1 total tags in treatment: 3027095 INFO @ Wed, 22 Apr 2020 08:16:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:45: #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 08:16:45: #1 tags after filtering in treatment: 2797173 INFO @ Wed, 22 Apr 2020 08:16:45: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 22 Apr 2020 08:16:45: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:45: #2 number of paired peaks: 24 WARNING @ Wed, 22 Apr 2020 08:16:45: Too few paired peaks (24) 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 08:16:45: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 08:16:47: 2000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.10_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/SRX5874487/SRX5874487.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:53: 3000000 INFO @ Wed, 22 Apr 2020 08:16:59: 4000000 INFO @ Wed, 22 Apr 2020 08:17:04: 5000000 INFO @ Wed, 22 Apr 2020 08:17:10: 6000000 INFO @ Wed, 22 Apr 2020 08:17:10: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:17:10: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:17:10: #1 total tags in treatment: 3027095 INFO @ Wed, 22 Apr 2020 08:17:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:17:10: #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 08:17:11: #1 tags after filtering in treatment: 2797173 INFO @ Wed, 22 Apr 2020 08:17:11: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 22 Apr 2020 08:17:11: #1 finished! INFO @ Wed, 22 Apr 2020 08:17:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:17:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:17:11: #2 number of paired peaks: 24 WARNING @ Wed, 22 Apr 2020 08:17:11: Too few paired peaks (24) 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 08:17:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.20_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/SRX5874487/SRX5874487.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874487/SRX5874487.20_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。