Job ID = 14521758 SRX = SRX9399058 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5397184 spots for SRR12935339/SRR12935339.sra Written 5397184 spots for SRR12935339/SRR12935339.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: 00:02:19 5397184 reads; of these: 5397184 (100.00%) were paired; of these: 748792 (13.87%) aligned concordantly 0 times 4096678 (75.90%) aligned concordantly exactly 1 time 551714 (10.22%) aligned concordantly >1 times ---- 748792 pairs aligned concordantly 0 times; of these: 178141 (23.79%) aligned discordantly 1 time ---- 570651 pairs aligned 0 times concordantly or discordantly; of these: 1141302 mates make up the pairs; of these: 842707 (73.84%) aligned 0 times 226064 (19.81%) aligned exactly 1 time 72531 (6.36%) aligned >1 times 92.19% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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] 353502 / 4763511 = 0.0742 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 21:37:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.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 21:37:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:37:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:37:25: 1000000 INFO @ Sat, 15 Jan 2022 21:37:29: 2000000 INFO @ Sat, 15 Jan 2022 21:37:33: 3000000 INFO @ Sat, 15 Jan 2022 21:37:37: 4000000 INFO @ Sat, 15 Jan 2022 21:37:41: 5000000 INFO @ Sat, 15 Jan 2022 21:37:45: 6000000 INFO @ Sat, 15 Jan 2022 21:37:49: 7000000 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 21:37:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.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 21:37:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:37:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:37:53: 8000000 INFO @ Sat, 15 Jan 2022 21:37:56: 1000000 INFO @ Sat, 15 Jan 2022 21:37:57: 9000000 INFO @ Sat, 15 Jan 2022 21:37:58: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:37:58: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:37:58: #1 total tags in treatment: 4298284 INFO @ Sat, 15 Jan 2022 21:37:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:37:58: #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 21:37:58: #1 tags after filtering in treatment: 3047447 INFO @ Sat, 15 Jan 2022 21:37:58: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 21:37:58: #1 finished! INFO @ Sat, 15 Jan 2022 21:37:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:37:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:37:58: #2 number of paired peaks: 2 WARNING @ Sat, 15 Jan 2022 21:37:58: Too few paired peaks (2) 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 21:37:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.05_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/SRX9399058/SRX9399058.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:38:00: 2000000 INFO @ Sat, 15 Jan 2022 21:38:05: 3000000 INFO @ Sat, 15 Jan 2022 21:38:09: 4000000 INFO @ Sat, 15 Jan 2022 21:38:14: 5000000 INFO @ Sat, 15 Jan 2022 21:38:18: 6000000 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 21:38:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.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 21:38:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:38:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:38:23: 7000000 INFO @ Sat, 15 Jan 2022 21:38:26: 1000000 INFO @ Sat, 15 Jan 2022 21:38:28: 8000000 INFO @ Sat, 15 Jan 2022 21:38:31: 2000000 INFO @ Sat, 15 Jan 2022 21:38:32: 9000000 INFO @ Sat, 15 Jan 2022 21:38:34: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:38:34: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:38:34: #1 total tags in treatment: 4298284 INFO @ Sat, 15 Jan 2022 21:38:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:38:34: #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 21:38:34: #1 tags after filtering in treatment: 3047447 INFO @ Sat, 15 Jan 2022 21:38:34: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 21:38:34: #1 finished! INFO @ Sat, 15 Jan 2022 21:38:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:38:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:38:34: #2 number of paired peaks: 2 WARNING @ Sat, 15 Jan 2022 21:38:34: Too few paired peaks (2) 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 21:38:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.10_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/SRX9399058/SRX9399058.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:38:35: 3000000 INFO @ Sat, 15 Jan 2022 21:38:40: 4000000 INFO @ Sat, 15 Jan 2022 21:38:45: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:38:49: 6000000 INFO @ Sat, 15 Jan 2022 21:38:54: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:38:59: 8000000 INFO @ Sat, 15 Jan 2022 21:39:03: 9000000 INFO @ Sat, 15 Jan 2022 21:39:05: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:39:05: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:39:05: #1 total tags in treatment: 4298284 INFO @ Sat, 15 Jan 2022 21:39:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:39:05: #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 21:39:05: #1 tags after filtering in treatment: 3047447 INFO @ Sat, 15 Jan 2022 21:39:05: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 21:39:05: #1 finished! INFO @ Sat, 15 Jan 2022 21:39:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:39:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:39:05: #2 number of paired peaks: 2 WARNING @ Sat, 15 Jan 2022 21:39:05: Too few paired peaks (2) 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 21:39:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.20_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/SRX9399058/SRX9399058.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399058/SRX9399058.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling