Job ID = 7110493 SRX = SRX8053695 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8829075 spots for SRR11477536/SRR11477536.sra Written 8829075 spots for SRR11477536/SRR11477536.sra 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: 00:04:56 8829075 reads; of these: 8829075 (100.00%) were paired; of these: 1718047 (19.46%) aligned concordantly 0 times 5714494 (64.72%) aligned concordantly exactly 1 time 1396534 (15.82%) aligned concordantly >1 times ---- 1718047 pairs aligned concordantly 0 times; of these: 699327 (40.70%) aligned discordantly 1 time ---- 1018720 pairs aligned 0 times concordantly or discordantly; of these: 2037440 mates make up the pairs; of these: 975304 (47.87%) aligned 0 times 566560 (27.81%) aligned exactly 1 time 495576 (24.32%) aligned >1 times 94.48% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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_sort_core] merging from 8 files... [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] 5291669 / 7471417 = 0.7083 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 Jul 2020 14:09:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.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 Jul 2020 14:09:21: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:09:21: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:09:26: 1000000 INFO @ Wed, 22 Jul 2020 14:09:31: 2000000 INFO @ Wed, 22 Jul 2020 14:09:36: 3000000 INFO @ Wed, 22 Jul 2020 14:09:41: 4000000 INFO @ Wed, 22 Jul 2020 14:09:46: 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 Jul 2020 14:09:50: 6000000 INFO @ Wed, 22 Jul 2020 14:09:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.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 Jul 2020 14:09:51: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:09:51: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:09:51: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 14:09:51: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 14:09:51: #1 total tags in treatment: 2021590 INFO @ Wed, 22 Jul 2020 14:09:51: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:09:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:09:51: #1 tags after filtering in treatment: 1552614 INFO @ Wed, 22 Jul 2020 14:09:51: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Jul 2020 14:09:51: #1 finished! INFO @ Wed, 22 Jul 2020 14:09:51: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:09:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:09:51: #2 number of paired peaks: 35 WARNING @ Wed, 22 Jul 2020 14:09:51: Too few paired peaks (35) 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 Jul 2020 14:09:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.05_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/SRX8053695/SRX8053695.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:09:56: 1000000 INFO @ Wed, 22 Jul 2020 14:10:01: 2000000 INFO @ Wed, 22 Jul 2020 14:10:06: 3000000 INFO @ Wed, 22 Jul 2020 14:10:11: 4000000 INFO @ Wed, 22 Jul 2020 14:10:16: 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 Jul 2020 14:10:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.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 Jul 2020 14:10:21: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:10:21: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:10:21: 6000000 INFO @ Wed, 22 Jul 2020 14:10:21: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 14:10:21: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 14:10:21: #1 total tags in treatment: 2021590 INFO @ Wed, 22 Jul 2020 14:10:21: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:10:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:10:21: #1 tags after filtering in treatment: 1552614 INFO @ Wed, 22 Jul 2020 14:10:21: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Jul 2020 14:10:21: #1 finished! INFO @ Wed, 22 Jul 2020 14:10:21: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:10:21: #2 number of paired peaks: 35 WARNING @ Wed, 22 Jul 2020 14:10:21: Too few paired peaks (35) 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 Jul 2020 14:10:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.10_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/SRX8053695/SRX8053695.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:10:27: 1000000 INFO @ Wed, 22 Jul 2020 14:10:33: 2000000 INFO @ Wed, 22 Jul 2020 14:10:39: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 14:10:44: 4000000 INFO @ Wed, 22 Jul 2020 14:10:49: 5000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:10:54: 6000000 INFO @ Wed, 22 Jul 2020 14:10:54: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 14:10:54: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 14:10:54: #1 total tags in treatment: 2021590 INFO @ Wed, 22 Jul 2020 14:10:54: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:10:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:10:54: #1 tags after filtering in treatment: 1552614 INFO @ Wed, 22 Jul 2020 14:10:54: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Jul 2020 14:10:54: #1 finished! INFO @ Wed, 22 Jul 2020 14:10:54: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:10:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:10:54: #2 number of paired peaks: 35 WARNING @ Wed, 22 Jul 2020 14:10:54: Too few paired peaks (35) 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 Jul 2020 14:10:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.20_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/SRX8053695/SRX8053695.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8053695/SRX8053695.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling