Job ID = 5791199 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,304,687 reads read : 14,609,374 reads written : 14,609,374 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: 00:05:28 7304687 reads; of these: 7304687 (100.00%) were paired; of these: 3529120 (48.31%) aligned concordantly 0 times 1930397 (26.43%) aligned concordantly exactly 1 time 1845170 (25.26%) aligned concordantly >1 times ---- 3529120 pairs aligned concordantly 0 times; of these: 308890 (8.75%) aligned discordantly 1 time ---- 3220230 pairs aligned 0 times concordantly or discordantly; of these: 6440460 mates make up the pairs; of these: 5935654 (92.16%) aligned 0 times 76656 (1.19%) aligned exactly 1 time 428150 (6.65%) aligned >1 times 59.37% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 1804196 / 4054852 = 0.4449 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 09:09:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.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 09:09:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:09:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:10:02: 1000000 INFO @ Wed, 22 Apr 2020 09:10:07: 2000000 INFO @ Wed, 22 Apr 2020 09:10:13: 3000000 INFO @ Wed, 22 Apr 2020 09:10:19: 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 09:10:24: 5000000 INFO @ Wed, 22 Apr 2020 09:10:25: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:10:25: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:10:25: #1 total tags in treatment: 2030943 INFO @ Wed, 22 Apr 2020 09:10:25: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:10:25: #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 09:10:25: #1 tags after filtering in treatment: 1365005 INFO @ Wed, 22 Apr 2020 09:10:25: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 09:10:25: #1 finished! INFO @ Wed, 22 Apr 2020 09:10:25: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:10:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:10:25: #2 number of paired peaks: 27 WARNING @ Wed, 22 Apr 2020 09:10:25: Too few paired peaks (27) 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 09:10:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.05_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/SRX6614989/SRX6614989.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:10:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.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 09:10:28: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:10:28: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:10:34: 1000000 INFO @ Wed, 22 Apr 2020 09:10:40: 2000000 INFO @ Wed, 22 Apr 2020 09:10:45: 3000000 INFO @ Wed, 22 Apr 2020 09:10:51: 4000000 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 09:10:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.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 09:10:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:10:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:10:57: 5000000 INFO @ Wed, 22 Apr 2020 09:10:58: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:10:58: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:10:58: #1 total tags in treatment: 2030943 INFO @ Wed, 22 Apr 2020 09:10:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:10:58: #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 09:10:58: #1 tags after filtering in treatment: 1365005 INFO @ Wed, 22 Apr 2020 09:10:58: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 09:10:58: #1 finished! INFO @ Wed, 22 Apr 2020 09:10:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:10:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:10:58: #2 number of paired peaks: 27 WARNING @ Wed, 22 Apr 2020 09:10:58: Too few paired peaks (27) 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 09:10:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.10_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/SRX6614989/SRX6614989.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:11:03: 1000000 INFO @ Wed, 22 Apr 2020 09:11:09: 2000000 INFO @ Wed, 22 Apr 2020 09:11:15: 3000000 INFO @ Wed, 22 Apr 2020 09:11:21: 4000000 INFO @ Wed, 22 Apr 2020 09:11:27: 5000000 INFO @ Wed, 22 Apr 2020 09:11:27: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:11:27: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:11:27: #1 total tags in treatment: 2030943 INFO @ Wed, 22 Apr 2020 09:11:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:11:27: #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 09:11:27: #1 tags after filtering in treatment: 1365005 INFO @ Wed, 22 Apr 2020 09:11:27: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 09:11:27: #1 finished! INFO @ Wed, 22 Apr 2020 09:11:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:11:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:11:27: #2 number of paired peaks: 27 WARNING @ Wed, 22 Apr 2020 09:11:27: Too few paired peaks (27) 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 09:11:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.20_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/SRX6614989/SRX6614989.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614989/SRX6614989.20_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。