Job ID = 14519830 SRX = SRX9369653 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2680124 spots for SRR12904754/SRR12904754.sra Written 2680124 spots for SRR12904754/SRR12904754.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: 00:02:10 2680124 reads; of these: 2680124 (100.00%) were paired; of these: 422629 (15.77%) aligned concordantly 0 times 1962725 (73.23%) aligned concordantly exactly 1 time 294770 (11.00%) aligned concordantly >1 times ---- 422629 pairs aligned concordantly 0 times; of these: 75262 (17.81%) aligned discordantly 1 time ---- 347367 pairs aligned 0 times concordantly or discordantly; of these: 694734 mates make up the pairs; of these: 652287 (93.89%) aligned 0 times 18833 (2.71%) aligned exactly 1 time 23614 (3.40%) aligned >1 times 87.83% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 172480 / 2326233 = 0.0741 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 17:53:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.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 17:53:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:53:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:53:42: 1000000 INFO @ Sat, 15 Jan 2022 17:53:50: 2000000 INFO @ Sat, 15 Jan 2022 17:53:58: 3000000 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 17:54:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.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 17:54:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:54:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:54:05: 4000000 INFO @ Sat, 15 Jan 2022 17:54:08: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 17:54:08: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 17:54:08: #1 total tags in treatment: 2088618 INFO @ Sat, 15 Jan 2022 17:54:08: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:54:08: #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 17:54:08: #1 tags after filtering in treatment: 1719911 INFO @ Sat, 15 Jan 2022 17:54:08: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Jan 2022 17:54:08: #1 finished! INFO @ Sat, 15 Jan 2022 17:54:08: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:54:08: #2 number of paired peaks: 29 WARNING @ Sat, 15 Jan 2022 17:54:08: 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 @ Sat, 15 Jan 2022 17:54:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:54:14: 1000000 INFO @ Sat, 15 Jan 2022 17:54:23: 2000000 INFO @ Sat, 15 Jan 2022 17:54:31: 3000000 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 17:54:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.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 17:54:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:54:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:54:40: 4000000 INFO @ Sat, 15 Jan 2022 17:54:43: 1000000 INFO @ Sat, 15 Jan 2022 17:54:43: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 17:54:43: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 17:54:43: #1 total tags in treatment: 2088618 INFO @ Sat, 15 Jan 2022 17:54:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:54:43: #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 17:54:43: #1 tags after filtering in treatment: 1719911 INFO @ Sat, 15 Jan 2022 17:54:43: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Jan 2022 17:54:43: #1 finished! INFO @ Sat, 15 Jan 2022 17:54:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:54:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:54:43: #2 number of paired peaks: 29 WARNING @ Sat, 15 Jan 2022 17:54:43: 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 @ Sat, 15 Jan 2022 17:54:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:54:51: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:54:59: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:55:07: 4000000 INFO @ Sat, 15 Jan 2022 17:55:10: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 17:55:10: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 17:55:10: #1 total tags in treatment: 2088618 INFO @ Sat, 15 Jan 2022 17:55:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:55:10: #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 17:55:10: #1 tags after filtering in treatment: 1719911 INFO @ Sat, 15 Jan 2022 17:55:10: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Jan 2022 17:55:10: #1 finished! INFO @ Sat, 15 Jan 2022 17:55:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:55:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:55:10: #2 number of paired peaks: 29 WARNING @ Sat, 15 Jan 2022 17:55:10: 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 @ Sat, 15 Jan 2022 17:55:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369653/SRX9369653.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling