Job ID = 14521600 SRX = SRX9399112 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8512757 spots for SRR12935393/SRR12935393.sra Written 8512757 spots for SRR12935393/SRR12935393.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: 00:03:41 8512757 reads; of these: 8512757 (100.00%) were paired; of these: 619146 (7.27%) aligned concordantly 0 times 5535472 (65.03%) aligned concordantly exactly 1 time 2358139 (27.70%) aligned concordantly >1 times ---- 619146 pairs aligned concordantly 0 times; of these: 55194 (8.91%) aligned discordantly 1 time ---- 563952 pairs aligned 0 times concordantly or discordantly; of these: 1127904 mates make up the pairs; of these: 904473 (80.19%) aligned 0 times 138254 (12.26%) aligned exactly 1 time 85177 (7.55%) aligned >1 times 94.69% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 2763519 / 7940461 = 0.3480 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 21:19:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.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 21:19:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:19:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:19:28: 1000000 INFO @ Sat, 15 Jan 2022 21:19:33: 2000000 INFO @ Sat, 15 Jan 2022 21:19:37: 3000000 INFO @ Sat, 15 Jan 2022 21:19:42: 4000000 INFO @ Sat, 15 Jan 2022 21:19:47: 5000000 INFO @ Sat, 15 Jan 2022 21:19:51: 6000000 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 21:19:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.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 21:19:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:19:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:19:56: 7000000 INFO @ Sat, 15 Jan 2022 21:19:58: 1000000 INFO @ Sat, 15 Jan 2022 21:20:01: 8000000 INFO @ Sat, 15 Jan 2022 21:20:03: 2000000 INFO @ Sat, 15 Jan 2022 21:20:05: 9000000 INFO @ Sat, 15 Jan 2022 21:20:08: 3000000 INFO @ Sat, 15 Jan 2022 21:20:10: 10000000 INFO @ Sat, 15 Jan 2022 21:20:12: 4000000 INFO @ Sat, 15 Jan 2022 21:20:13: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 21:20:13: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 21:20:13: #1 total tags in treatment: 5136068 INFO @ Sat, 15 Jan 2022 21:20:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:20:13: #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 21:20:13: #1 tags after filtering in treatment: 3209967 INFO @ Sat, 15 Jan 2022 21:20:13: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 21:20:13: #1 finished! INFO @ Sat, 15 Jan 2022 21:20:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:20:13: #2 number of paired peaks: 26 WARNING @ Sat, 15 Jan 2022 21:20:13: Too few paired peaks (26) 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 21:20:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.05_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/SRX9399112/SRX9399112.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:20:17: 5000000 INFO @ Sat, 15 Jan 2022 21:20:22: 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 21:20:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.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 21:20:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:20:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:20:26: 7000000 INFO @ Sat, 15 Jan 2022 21:20:28: 1000000 INFO @ Sat, 15 Jan 2022 21:20:31: 8000000 INFO @ Sat, 15 Jan 2022 21:20:32: 2000000 INFO @ Sat, 15 Jan 2022 21:20:36: 9000000 INFO @ Sat, 15 Jan 2022 21:20:37: 3000000 INFO @ Sat, 15 Jan 2022 21:20:41: 10000000 INFO @ Sat, 15 Jan 2022 21:20:41: 4000000 INFO @ Sat, 15 Jan 2022 21:20:43: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 21:20:43: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 21:20:43: #1 total tags in treatment: 5136068 INFO @ Sat, 15 Jan 2022 21:20:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:20:43: #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 21:20:44: #1 tags after filtering in treatment: 3209967 INFO @ Sat, 15 Jan 2022 21:20:44: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 21:20:44: #1 finished! INFO @ Sat, 15 Jan 2022 21:20:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:20:44: #2 number of paired peaks: 26 WARNING @ Sat, 15 Jan 2022 21:20:44: Too few paired peaks (26) 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 21:20:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.10_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/SRX9399112/SRX9399112.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:20:45: 5000000 INFO @ Sat, 15 Jan 2022 21:20:49: 6000000 INFO @ Sat, 15 Jan 2022 21:20:53: 7000000 INFO @ Sat, 15 Jan 2022 21:20:57: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:21:01: 9000000 INFO @ Sat, 15 Jan 2022 21:21:05: 10000000 INFO @ Sat, 15 Jan 2022 21:21:08: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 21:21:08: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 21:21:08: #1 total tags in treatment: 5136068 INFO @ Sat, 15 Jan 2022 21:21:08: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:21:08: #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 21:21:08: #1 tags after filtering in treatment: 3209967 INFO @ Sat, 15 Jan 2022 21:21:08: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 21:21:08: #1 finished! INFO @ Sat, 15 Jan 2022 21:21:08: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:21:08: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:21:08: #2 number of paired peaks: 26 WARNING @ Sat, 15 Jan 2022 21:21:08: Too few paired peaks (26) 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 21:21:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.20_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/SRX9399112/SRX9399112.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399112/SRX9399112.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling