Job ID = 7114190 SRX = SRX8462192 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:55:00 prefetch.2.10.7: 1) Downloading 'SRR11915651'... 2020-07-22T05:55:00 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:55:42 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:55:43 prefetch.2.10.7: 'SRR11915651' is valid 2020-07-22T05:55:43 prefetch.2.10.7: 1) 'SRR11915651' was downloaded successfully 2020-07-22T05:55:43 prefetch.2.10.7: 'SRR11915651' has 0 unresolved dependencies Read 5759968 spots for SRR11915651/SRR11915651.sra Written 5759968 spots for SRR11915651/SRR11915651.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: 00:02:12 5759968 reads; of these: 5759968 (100.00%) were paired; of these: 4005419 (69.54%) aligned concordantly 0 times 1478394 (25.67%) aligned concordantly exactly 1 time 276155 (4.79%) aligned concordantly >1 times ---- 4005419 pairs aligned concordantly 0 times; of these: 17106 (0.43%) aligned discordantly 1 time ---- 3988313 pairs aligned 0 times concordantly or discordantly; of these: 7976626 mates make up the pairs; of these: 7930083 (99.42%) aligned 0 times 33030 (0.41%) aligned exactly 1 time 13513 (0.17%) aligned >1 times 31.16% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 449486 / 1770877 = 0.2538 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 15:00:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.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 15:00:11: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:00:11: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:00:17: 1000000 INFO @ Wed, 22 Jul 2020 15:00:22: 2000000 INFO @ Wed, 22 Jul 2020 15:00:26: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:00:26: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:00:26: #1 total tags in treatment: 1306482 INFO @ Wed, 22 Jul 2020 15:00:26: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:00:26: #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 15:00:26: #1 tags after filtering in treatment: 1129024 INFO @ Wed, 22 Jul 2020 15:00:26: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Jul 2020 15:00:26: #1 finished! INFO @ Wed, 22 Jul 2020 15:00:26: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:00:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:00:26: #2 number of paired peaks: 60 WARNING @ Wed, 22 Jul 2020 15:00:26: Too few paired peaks (60) 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 15:00:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.05_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/SRX8462192/SRX8462192.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 15:00:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.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 15:00:41: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:00:41: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:00:46: 1000000 INFO @ Wed, 22 Jul 2020 15:00:52: 2000000 INFO @ Wed, 22 Jul 2020 15:00:55: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:00:55: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:00:55: #1 total tags in treatment: 1306482 INFO @ Wed, 22 Jul 2020 15:00:55: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:00:55: #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 15:00:56: #1 tags after filtering in treatment: 1129024 INFO @ Wed, 22 Jul 2020 15:00:56: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Jul 2020 15:00:56: #1 finished! INFO @ Wed, 22 Jul 2020 15:00:56: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:00:56: #2 number of paired peaks: 60 WARNING @ Wed, 22 Jul 2020 15:00:56: Too few paired peaks (60) 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 15:00:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.10_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/SRX8462192/SRX8462192.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 15:01:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.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 15:01:11: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:01:11: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:01:16: 1000000 INFO @ Wed, 22 Jul 2020 15:01:22: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:01:25: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:01:25: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:01:25: #1 total tags in treatment: 1306482 INFO @ Wed, 22 Jul 2020 15:01:25: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:01:25: #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 15:01:25: #1 tags after filtering in treatment: 1129024 INFO @ Wed, 22 Jul 2020 15:01:25: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Jul 2020 15:01:25: #1 finished! INFO @ Wed, 22 Jul 2020 15:01:25: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:01:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:01:26: #2 number of paired peaks: 60 WARNING @ Wed, 22 Jul 2020 15:01:26: Too few paired peaks (60) 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 15:01:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.20_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/SRX8462192/SRX8462192.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462192/SRX8462192.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。