Job ID = 5791066 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,048,818 reads read : 12,097,636 reads written : 12,097,636 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: 00:02:05 6048818 reads; of these: 6048818 (100.00%) were paired; of these: 2013823 (33.29%) aligned concordantly 0 times 3678125 (60.81%) aligned concordantly exactly 1 time 356870 (5.90%) aligned concordantly >1 times ---- 2013823 pairs aligned concordantly 0 times; of these: 67285 (3.34%) aligned discordantly 1 time ---- 1946538 pairs aligned 0 times concordantly or discordantly; of these: 3893076 mates make up the pairs; of these: 2681591 (68.88%) aligned 0 times 1091732 (28.04%) aligned exactly 1 time 119753 (3.08%) aligned >1 times 77.83% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 804454 / 4088933 = 0.1967 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 08:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.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 08:32:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:32:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:32:41: 1000000 INFO @ Wed, 22 Apr 2020 08:32:45: 2000000 INFO @ Wed, 22 Apr 2020 08:32:50: 3000000 INFO @ Wed, 22 Apr 2020 08:32:55: 4000000 INFO @ Wed, 22 Apr 2020 08:32:59: 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 08:33:04: 6000000 INFO @ Wed, 22 Apr 2020 08:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.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 08:33:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:33:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:33:09: 7000000 INFO @ Wed, 22 Apr 2020 08:33:11: 1000000 INFO @ Wed, 22 Apr 2020 08:33:14: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:33:14: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:33:14: #1 total tags in treatment: 3239061 INFO @ Wed, 22 Apr 2020 08:33:14: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:33:14: #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 08:33:14: #1 tags after filtering in treatment: 2772371 INFO @ Wed, 22 Apr 2020 08:33:14: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Apr 2020 08:33:14: #1 finished! INFO @ Wed, 22 Apr 2020 08:33:14: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:33:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:33:14: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 08:33:14: Too few paired peaks (28) 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 08:33:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.05_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/SRX5883290/SRX5883290.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:33:16: 2000000 INFO @ Wed, 22 Apr 2020 08:33:22: 3000000 INFO @ Wed, 22 Apr 2020 08:33:27: 4000000 INFO @ Wed, 22 Apr 2020 08:33:32: 5000000 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 08:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.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 08:33:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:33:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:33:37: 6000000 INFO @ Wed, 22 Apr 2020 08:33:42: 1000000 INFO @ Wed, 22 Apr 2020 08:33:43: 7000000 INFO @ Wed, 22 Apr 2020 08:33:47: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:33:47: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:33:47: #1 total tags in treatment: 3239061 INFO @ Wed, 22 Apr 2020 08:33:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:33:47: #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 08:33:47: #1 tags after filtering in treatment: 2772371 INFO @ Wed, 22 Apr 2020 08:33:47: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Apr 2020 08:33:47: #1 finished! INFO @ Wed, 22 Apr 2020 08:33:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:33:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:33:48: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 08:33:48: Too few paired peaks (28) 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 08:33:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.10_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/SRX5883290/SRX5883290.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:33:48: 2000000 INFO @ Wed, 22 Apr 2020 08:33:53: 3000000 INFO @ Wed, 22 Apr 2020 08:33:59: 4000000 INFO @ Wed, 22 Apr 2020 08:34:04: 5000000 INFO @ Wed, 22 Apr 2020 08:34:09: 6000000 INFO @ Wed, 22 Apr 2020 08:34:15: 7000000 INFO @ Wed, 22 Apr 2020 08:34:19: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:34:19: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:34:19: #1 total tags in treatment: 3239061 INFO @ Wed, 22 Apr 2020 08:34:19: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:34:19: #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 08:34:19: #1 tags after filtering in treatment: 2772371 INFO @ Wed, 22 Apr 2020 08:34:19: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Apr 2020 08:34:19: #1 finished! INFO @ Wed, 22 Apr 2020 08:34:19: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:34:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:34:19: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 08:34:19: Too few paired peaks (28) 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 08:34:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.20_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/SRX5883290/SRX5883290.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883290/SRX5883290.20_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。