Job ID = 5790952 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,065,389 reads read : 6,130,778 reads written : 6,130,778 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: 00:02:00 3065389 reads; of these: 3065389 (100.00%) were paired; of these: 139004 (4.53%) aligned concordantly 0 times 2534361 (82.68%) aligned concordantly exactly 1 time 392024 (12.79%) aligned concordantly >1 times ---- 139004 pairs aligned concordantly 0 times; of these: 1492 (1.07%) aligned discordantly 1 time ---- 137512 pairs aligned 0 times concordantly or discordantly; of these: 275024 mates make up the pairs; of these: 260446 (94.70%) aligned 0 times 11124 (4.04%) aligned exactly 1 time 3454 (1.26%) aligned >1 times 95.75% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 41898 / 2920752 = 0.0143 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 08:13:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.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 08:13:15: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:15: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:22: 1000000 INFO @ Wed, 22 Apr 2020 08:13:29: 2000000 INFO @ Wed, 22 Apr 2020 08:13:36: 3000000 INFO @ Wed, 22 Apr 2020 08:13:43: 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 08:13:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.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 08:13:45: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:45: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:50: 5000000 INFO @ Wed, 22 Apr 2020 08:13:52: 1000000 INFO @ Wed, 22 Apr 2020 08:13:55: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:13:55: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:13:55: #1 total tags in treatment: 2884490 INFO @ Wed, 22 Apr 2020 08:13:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:55: #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 08:13:55: #1 tags after filtering in treatment: 2579486 INFO @ Wed, 22 Apr 2020 08:13:55: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Apr 2020 08:13:55: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:56: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 08:13:56: 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 08:13:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.05_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/SRX5874467/SRX5874467.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:13:59: 2000000 INFO @ Wed, 22 Apr 2020 08:14:06: 3000000 INFO @ Wed, 22 Apr 2020 08:14:13: 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 08:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.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 08:14:15: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:14:15: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:14:20: 5000000 INFO @ Wed, 22 Apr 2020 08:14:22: 1000000 INFO @ Wed, 22 Apr 2020 08:14:25: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:14:25: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:14:25: #1 total tags in treatment: 2884490 INFO @ Wed, 22 Apr 2020 08:14:25: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:14:25: #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 08:14:25: #1 tags after filtering in treatment: 2579486 INFO @ Wed, 22 Apr 2020 08:14:25: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Apr 2020 08:14:25: #1 finished! INFO @ Wed, 22 Apr 2020 08:14:25: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:14:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:14:26: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 08:14:26: 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 08:14:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.10_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/SRX5874467/SRX5874467.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:14:29: 2000000 INFO @ Wed, 22 Apr 2020 08:14:36: 3000000 INFO @ Wed, 22 Apr 2020 08:14:43: 4000000 INFO @ Wed, 22 Apr 2020 08:14:50: 5000000 INFO @ Wed, 22 Apr 2020 08:14:55: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:14:55: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:14:55: #1 total tags in treatment: 2884490 INFO @ Wed, 22 Apr 2020 08:14:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:14:55: #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 08:14:55: #1 tags after filtering in treatment: 2579486 INFO @ Wed, 22 Apr 2020 08:14:55: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Apr 2020 08:14:55: #1 finished! INFO @ Wed, 22 Apr 2020 08:14:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:14:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:14:55: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 08:14:55: 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 08:14:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.20_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/SRX5874467/SRX5874467.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874467/SRX5874467.20_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。