Job ID = 14522061 SRX = SRX9067214 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5670611 spots for SRR12580367/SRR12580367.sra Written 5670611 spots for SRR12580367/SRR12580367.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: 00:02:13 5670611 reads; of these: 5670611 (100.00%) were paired; of these: 840725 (14.83%) aligned concordantly 0 times 4040968 (71.26%) aligned concordantly exactly 1 time 788918 (13.91%) aligned concordantly >1 times ---- 840725 pairs aligned concordantly 0 times; of these: 54620 (6.50%) aligned discordantly 1 time ---- 786105 pairs aligned 0 times concordantly or discordantly; of these: 1572210 mates make up the pairs; of these: 1404808 (89.35%) aligned 0 times 121629 (7.74%) aligned exactly 1 time 45773 (2.91%) aligned >1 times 87.61% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 2812749 / 4877520 = 0.5767 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 22:10:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.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 @ Sat, 15 Jan 2022 22:10:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:10:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:10:06: 1000000 INFO @ Sat, 15 Jan 2022 22:10:11: 2000000 INFO @ Sat, 15 Jan 2022 22:10:16: 3000000 INFO @ Sat, 15 Jan 2022 22:10:20: 4000000 INFO @ Sat, 15 Jan 2022 22:10:22: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 22:10:22: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 22:10:22: #1 total tags in treatment: 2029472 INFO @ Sat, 15 Jan 2022 22:10:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:10:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 22:10:22: #1 tags after filtering in treatment: 1590361 INFO @ Sat, 15 Jan 2022 22:10:22: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 22:10:22: #1 finished! INFO @ Sat, 15 Jan 2022 22:10:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:10:22: #2 number of paired peaks: 28 WARNING @ Sat, 15 Jan 2022 22:10:22: Too few paired peaks (28) 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 @ Sat, 15 Jan 2022 22:10:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.05_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/SRX9067214/SRX9067214.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 22:10:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.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 @ Sat, 15 Jan 2022 22:10:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:10:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:10:36: 1000000 INFO @ Sat, 15 Jan 2022 22:10:41: 2000000 INFO @ Sat, 15 Jan 2022 22:10:46: 3000000 INFO @ Sat, 15 Jan 2022 22:10:50: 4000000 INFO @ Sat, 15 Jan 2022 22:10:51: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 22:10:51: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 22:10:51: #1 total tags in treatment: 2029472 INFO @ Sat, 15 Jan 2022 22:10:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:10:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 22:10:51: #1 tags after filtering in treatment: 1590361 INFO @ Sat, 15 Jan 2022 22:10:51: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 22:10:51: #1 finished! INFO @ Sat, 15 Jan 2022 22:10:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:10:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:10:52: #2 number of paired peaks: 28 WARNING @ Sat, 15 Jan 2022 22:10:52: Too few paired peaks (28) 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 @ Sat, 15 Jan 2022 22:10:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.10_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/SRX9067214/SRX9067214.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 22:11:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.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 @ Sat, 15 Jan 2022 22:11:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:11:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:11:06: 1000000 INFO @ Sat, 15 Jan 2022 22:11:11: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:11:15: 3000000 INFO @ Sat, 15 Jan 2022 22:11:20: 4000000 INFO @ Sat, 15 Jan 2022 22:11:21: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 22:11:21: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 22:11:21: #1 total tags in treatment: 2029472 INFO @ Sat, 15 Jan 2022 22:11:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:11:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 22:11:21: #1 tags after filtering in treatment: 1590361 INFO @ Sat, 15 Jan 2022 22:11:21: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 22:11:21: #1 finished! INFO @ Sat, 15 Jan 2022 22:11:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:11:22: #2 number of paired peaks: 28 WARNING @ Sat, 15 Jan 2022 22:11:22: Too few paired peaks (28) 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 @ Sat, 15 Jan 2022 22:11:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.20_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/SRX9067214/SRX9067214.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067214/SRX9067214.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。