Job ID = 7111630 SRX = SRX8357662 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:08:28 prefetch.2.10.7: 1) Downloading 'SRR11806250'... 2020-07-22T05:08:28 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:09:02 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:09:03 prefetch.2.10.7: 'SRR11806250' is valid 2020-07-22T05:09:03 prefetch.2.10.7: 1) 'SRR11806250' was downloaded successfully 2020-07-22T05:09:03 prefetch.2.10.7: 'SRR11806250' has 0 unresolved dependencies Read 9174030 spots for SRR11806250/SRR11806250.sra Written 9174030 spots for SRR11806250/SRR11806250.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: 00:04:22 9174030 reads; of these: 9174030 (100.00%) were paired; of these: 2789468 (30.41%) aligned concordantly 0 times 5120833 (55.82%) aligned concordantly exactly 1 time 1263729 (13.78%) aligned concordantly >1 times ---- 2789468 pairs aligned concordantly 0 times; of these: 70741 (2.54%) aligned discordantly 1 time ---- 2718727 pairs aligned 0 times concordantly or discordantly; of these: 5437454 mates make up the pairs; of these: 5040212 (92.69%) aligned 0 times 160565 (2.95%) aligned exactly 1 time 236677 (4.35%) aligned >1 times 72.53% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 2309308 / 6432950 = 0.3590 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 14:16:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.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 14:16:48: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:16:48: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:16:52: 1000000 INFO @ Wed, 22 Jul 2020 14:16:56: 2000000 INFO @ Wed, 22 Jul 2020 14:17:00: 3000000 INFO @ Wed, 22 Jul 2020 14:17:04: 4000000 INFO @ Wed, 22 Jul 2020 14:17:08: 5000000 INFO @ Wed, 22 Jul 2020 14:17:12: 6000000 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 14:17:16: 7000000 INFO @ Wed, 22 Jul 2020 14:17:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.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 14:17:17: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:17:17: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:17:20: 8000000 INFO @ Wed, 22 Jul 2020 14:17:21: 1000000 INFO @ Wed, 22 Jul 2020 14:17:23: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:17:23: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:17:23: #1 total tags in treatment: 4101672 INFO @ Wed, 22 Jul 2020 14:17:23: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:17:23: #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 14:17:23: #1 tags after filtering in treatment: 2712690 INFO @ Wed, 22 Jul 2020 14:17:23: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Jul 2020 14:17:23: #1 finished! INFO @ Wed, 22 Jul 2020 14:17:23: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:17:24: #2 number of paired peaks: 31 WARNING @ Wed, 22 Jul 2020 14:17:24: Too few paired peaks (31) 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 14:17:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.05_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/SRX8357662/SRX8357662.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:17:25: 2000000 INFO @ Wed, 22 Jul 2020 14:17:29: 3000000 INFO @ Wed, 22 Jul 2020 14:17:33: 4000000 INFO @ Wed, 22 Jul 2020 14:17:37: 5000000 INFO @ Wed, 22 Jul 2020 14:17:41: 6000000 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 14:17:45: 7000000 INFO @ Wed, 22 Jul 2020 14:17:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.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 14:17:47: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:17:47: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:17:49: 8000000 INFO @ Wed, 22 Jul 2020 14:17:51: 1000000 INFO @ Wed, 22 Jul 2020 14:17:52: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:17:52: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:17:52: #1 total tags in treatment: 4101672 INFO @ Wed, 22 Jul 2020 14:17:52: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:17:52: #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 14:17:52: #1 tags after filtering in treatment: 2712690 INFO @ Wed, 22 Jul 2020 14:17:52: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Jul 2020 14:17:52: #1 finished! INFO @ Wed, 22 Jul 2020 14:17:52: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:17:53: #2 number of paired peaks: 31 WARNING @ Wed, 22 Jul 2020 14:17:53: Too few paired peaks (31) 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 14:17:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.10_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/SRX8357662/SRX8357662.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:17:55: 2000000 INFO @ Wed, 22 Jul 2020 14:17:59: 3000000 INFO @ Wed, 22 Jul 2020 14:18:03: 4000000 INFO @ Wed, 22 Jul 2020 14:18:07: 5000000 INFO @ Wed, 22 Jul 2020 14:18:11: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 14:18:15: 7000000 INFO @ Wed, 22 Jul 2020 14:18:19: 8000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:18:22: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:18:22: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:18:22: #1 total tags in treatment: 4101672 INFO @ Wed, 22 Jul 2020 14:18:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:18:22: #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 14:18:22: #1 tags after filtering in treatment: 2712690 INFO @ Wed, 22 Jul 2020 14:18:22: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Jul 2020 14:18:22: #1 finished! INFO @ Wed, 22 Jul 2020 14:18:22: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:18:22: #2 number of paired peaks: 31 WARNING @ Wed, 22 Jul 2020 14:18:22: Too few paired peaks (31) 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 14:18:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357662/SRX8357662.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling