Job ID = 5791727 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,355,007 reads read : 10,710,014 reads written : 10,710,014 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: 00:02:15 5355007 reads; of these: 5355007 (100.00%) were paired; of these: 200096 (3.74%) aligned concordantly 0 times 4529989 (84.59%) aligned concordantly exactly 1 time 624922 (11.67%) aligned concordantly >1 times ---- 200096 pairs aligned concordantly 0 times; of these: 35668 (17.83%) aligned discordantly 1 time ---- 164428 pairs aligned 0 times concordantly or discordantly; of these: 328856 mates make up the pairs; of these: 288947 (87.86%) aligned 0 times 26429 (8.04%) aligned exactly 1 time 13480 (4.10%) aligned >1 times 97.30% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 184640 / 5188812 = 0.0356 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 10:43:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.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 10:43:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:43:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:43:39: 1000000 INFO @ Wed, 22 Apr 2020 10:43:44: 2000000 INFO @ Wed, 22 Apr 2020 10:43:48: 3000000 INFO @ Wed, 22 Apr 2020 10:43:53: 4000000 INFO @ Wed, 22 Apr 2020 10:43:57: 5000000 INFO @ Wed, 22 Apr 2020 10:44:02: 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 10:44:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.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 10:44:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:44:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:44:06: 7000000 INFO @ Wed, 22 Apr 2020 10:44:10: 1000000 INFO @ Wed, 22 Apr 2020 10:44:12: 8000000 INFO @ Wed, 22 Apr 2020 10:44:16: 2000000 INFO @ Wed, 22 Apr 2020 10:44:17: 9000000 INFO @ Wed, 22 Apr 2020 10:44:22: 3000000 INFO @ Wed, 22 Apr 2020 10:44:22: 10000000 INFO @ Wed, 22 Apr 2020 10:44:22: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 10:44:22: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 10:44:22: #1 total tags in treatment: 4970711 INFO @ Wed, 22 Apr 2020 10:44:22: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:44:22: #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 10:44:22: #1 tags after filtering in treatment: 3930419 INFO @ Wed, 22 Apr 2020 10:44:22: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 10:44:22: #1 finished! INFO @ Wed, 22 Apr 2020 10:44:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:44:22: #2 number of paired peaks: 54 WARNING @ Wed, 22 Apr 2020 10:44:22: Too few paired peaks (54) 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 10:44:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.05_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/SRX7741019/SRX7741019.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:44:27: 4000000 INFO @ Wed, 22 Apr 2020 10:44:33: 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 10:44:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.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 10:44:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:44:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:44:38: 6000000 INFO @ Wed, 22 Apr 2020 10:44:41: 1000000 INFO @ Wed, 22 Apr 2020 10:44:44: 7000000 INFO @ Wed, 22 Apr 2020 10:44:46: 2000000 INFO @ Wed, 22 Apr 2020 10:44:50: 8000000 INFO @ Wed, 22 Apr 2020 10:44:52: 3000000 INFO @ Wed, 22 Apr 2020 10:44:55: 9000000 INFO @ Wed, 22 Apr 2020 10:44:58: 4000000 INFO @ Wed, 22 Apr 2020 10:45:01: 10000000 INFO @ Wed, 22 Apr 2020 10:45:01: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 10:45:01: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 10:45:01: #1 total tags in treatment: 4970711 INFO @ Wed, 22 Apr 2020 10:45:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:45:01: #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 10:45:01: #1 tags after filtering in treatment: 3930419 INFO @ Wed, 22 Apr 2020 10:45:01: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 10:45:01: #1 finished! INFO @ Wed, 22 Apr 2020 10:45:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:45:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:45:01: #2 number of paired peaks: 54 WARNING @ Wed, 22 Apr 2020 10:45:01: Too few paired peaks (54) 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 10:45:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.10_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/SRX7741019/SRX7741019.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:45:03: 5000000 INFO @ Wed, 22 Apr 2020 10:45:09: 6000000 INFO @ Wed, 22 Apr 2020 10:45:14: 7000000 INFO @ Wed, 22 Apr 2020 10:45:19: 8000000 INFO @ Wed, 22 Apr 2020 10:45:25: 9000000 INFO @ Wed, 22 Apr 2020 10:45:30: 10000000 INFO @ Wed, 22 Apr 2020 10:45:30: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 10:45:30: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 10:45:30: #1 total tags in treatment: 4970711 INFO @ Wed, 22 Apr 2020 10:45:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:45:30: #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 10:45:30: #1 tags after filtering in treatment: 3930419 INFO @ Wed, 22 Apr 2020 10:45:30: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 10:45:30: #1 finished! INFO @ Wed, 22 Apr 2020 10:45:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:45:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:45:30: #2 number of paired peaks: 54 WARNING @ Wed, 22 Apr 2020 10:45:30: Too few paired peaks (54) 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 10:45:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.20_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/SRX7741019/SRX7741019.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741019/SRX7741019.20_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。