Job ID = 5791019 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,684,067 reads read : 9,368,134 reads written : 9,368,134 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: 00:02:02 4684067 reads; of these: 4684067 (100.00%) were paired; of these: 230185 (4.91%) aligned concordantly 0 times 3905757 (83.38%) aligned concordantly exactly 1 time 548125 (11.70%) aligned concordantly >1 times ---- 230185 pairs aligned concordantly 0 times; of these: 1809 (0.79%) aligned discordantly 1 time ---- 228376 pairs aligned 0 times concordantly or discordantly; of these: 456752 mates make up the pairs; of these: 418754 (91.68%) aligned 0 times 30039 (6.58%) aligned exactly 1 time 7959 (1.74%) aligned >1 times 95.53% overall alignment rate Time searching: 00:02:02 Overall time: 00:02:02 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] 544370 / 4455340 = 0.1222 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 08:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.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 08:22:02: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:22:02: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:22:07: 1000000 INFO @ Wed, 22 Apr 2020 08:22:12: 2000000 INFO @ Wed, 22 Apr 2020 08:22:16: 3000000 INFO @ Wed, 22 Apr 2020 08:22:21: 4000000 INFO @ Wed, 22 Apr 2020 08:22:25: 5000000 INFO @ Wed, 22 Apr 2020 08:22:30: 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 08:22:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.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 08:22:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:22:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:22:35: 7000000 INFO @ Wed, 22 Apr 2020 08:22:38: 1000000 INFO @ Wed, 22 Apr 2020 08:22:40: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:22:40: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:22:40: #1 total tags in treatment: 3909686 INFO @ Wed, 22 Apr 2020 08:22:40: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:22:40: #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 08:22:40: #1 tags after filtering in treatment: 3375786 INFO @ Wed, 22 Apr 2020 08:22:40: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Apr 2020 08:22:40: #1 finished! INFO @ Wed, 22 Apr 2020 08:22:40: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:22:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:22:40: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 08:22:40: 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 08:22:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.05_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/SRX5874515/SRX5874515.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:22:44: 2000000 INFO @ Wed, 22 Apr 2020 08:22:50: 3000000 INFO @ Wed, 22 Apr 2020 08:22:55: 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 08:23:01: 5000000 INFO @ Wed, 22 Apr 2020 08:23:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.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 08:23:02: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:23:02: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:23:07: 6000000 INFO @ Wed, 22 Apr 2020 08:23:08: 1000000 INFO @ Wed, 22 Apr 2020 08:23:13: 7000000 INFO @ Wed, 22 Apr 2020 08:23:14: 2000000 INFO @ Wed, 22 Apr 2020 08:23:18: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:23:18: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:23:18: #1 total tags in treatment: 3909686 INFO @ Wed, 22 Apr 2020 08:23:18: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:23:18: #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 08:23:18: #1 tags after filtering in treatment: 3375786 INFO @ Wed, 22 Apr 2020 08:23:18: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Apr 2020 08:23:18: #1 finished! INFO @ Wed, 22 Apr 2020 08:23:18: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:23:18: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 08:23:18: 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 08:23:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.10_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/SRX5874515/SRX5874515.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:23:20: 3000000 INFO @ Wed, 22 Apr 2020 08:23:26: 4000000 INFO @ Wed, 22 Apr 2020 08:23:31: 5000000 INFO @ Wed, 22 Apr 2020 08:23:37: 6000000 INFO @ Wed, 22 Apr 2020 08:23:43: 7000000 INFO @ Wed, 22 Apr 2020 08:23:47: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:23:47: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:23:47: #1 total tags in treatment: 3909686 INFO @ Wed, 22 Apr 2020 08:23:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:23:47: #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 08:23:47: #1 tags after filtering in treatment: 3375786 INFO @ Wed, 22 Apr 2020 08:23:47: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Apr 2020 08:23:47: #1 finished! INFO @ Wed, 22 Apr 2020 08:23:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:23:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:23:47: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 08:23:47: 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 08:23:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.20_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/SRX5874515/SRX5874515.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874515/SRX5874515.20_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。