Job ID = 7108095 SRX = SRX7438933 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7535621 spots for SRR10764999/SRR10764999.sra Written 7535621 spots for SRR10764999/SRR10764999.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: 00:03:22 7535621 reads; of these: 7535621 (100.00%) were paired; of these: 2012802 (26.71%) aligned concordantly 0 times 4753289 (63.08%) aligned concordantly exactly 1 time 769530 (10.21%) aligned concordantly >1 times ---- 2012802 pairs aligned concordantly 0 times; of these: 259586 (12.90%) aligned discordantly 1 time ---- 1753216 pairs aligned 0 times concordantly or discordantly; of these: 3506432 mates make up the pairs; of these: 3366699 (96.01%) aligned 0 times 38328 (1.09%) aligned exactly 1 time 101405 (2.89%) aligned >1 times 77.66% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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] 173733 / 5763315 = 0.0301 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 13:30:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.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 13:30:55: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:30:55: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:30:59: 1000000 INFO @ Wed, 22 Jul 2020 13:31:04: 2000000 INFO @ Wed, 22 Jul 2020 13:31:09: 3000000 INFO @ Wed, 22 Jul 2020 13:31:13: 4000000 INFO @ Wed, 22 Jul 2020 13:31:18: 5000000 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 13:31:23: 6000000 INFO @ Wed, 22 Jul 2020 13:31:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.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 13:31:24: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:31:24: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:31:28: 7000000 INFO @ Wed, 22 Jul 2020 13:31:31: 1000000 INFO @ Wed, 22 Jul 2020 13:31:34: 8000000 INFO @ Wed, 22 Jul 2020 13:31:37: 2000000 INFO @ Wed, 22 Jul 2020 13:31:40: 9000000 INFO @ Wed, 22 Jul 2020 13:31:43: 3000000 INFO @ Wed, 22 Jul 2020 13:31:45: 10000000 INFO @ Wed, 22 Jul 2020 13:31:49: 4000000 INFO @ Wed, 22 Jul 2020 13:31:51: 11000000 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 13:31:53: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 13:31:53: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 13:31:53: #1 total tags in treatment: 5353099 INFO @ Wed, 22 Jul 2020 13:31:53: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:31:53: #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 13:31:53: #1 tags after filtering in treatment: 4460383 INFO @ Wed, 22 Jul 2020 13:31:53: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Jul 2020 13:31:53: #1 finished! INFO @ Wed, 22 Jul 2020 13:31:53: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:31:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:31:53: #2 number of paired peaks: 26 WARNING @ Wed, 22 Jul 2020 13:31:53: 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 @ Wed, 22 Jul 2020 13:31:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.05_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/SRX7438933/SRX7438933.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:31:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.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 13:31:54: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:31:54: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:31:55: 5000000 INFO @ Wed, 22 Jul 2020 13:32:00: 1000000 INFO @ Wed, 22 Jul 2020 13:32:02: 6000000 INFO @ Wed, 22 Jul 2020 13:32:06: 2000000 INFO @ Wed, 22 Jul 2020 13:32:08: 7000000 INFO @ Wed, 22 Jul 2020 13:32:12: 3000000 INFO @ Wed, 22 Jul 2020 13:32:15: 8000000 INFO @ Wed, 22 Jul 2020 13:32:17: 4000000 INFO @ Wed, 22 Jul 2020 13:32:21: 9000000 INFO @ Wed, 22 Jul 2020 13:32:23: 5000000 INFO @ Wed, 22 Jul 2020 13:32:28: 10000000 INFO @ Wed, 22 Jul 2020 13:32:29: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:32:34: 11000000 INFO @ Wed, 22 Jul 2020 13:32:35: 7000000 INFO @ Wed, 22 Jul 2020 13:32:36: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 13:32:36: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 13:32:36: #1 total tags in treatment: 5353099 INFO @ Wed, 22 Jul 2020 13:32:36: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:32:36: #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 13:32:36: #1 tags after filtering in treatment: 4460383 INFO @ Wed, 22 Jul 2020 13:32:36: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Jul 2020 13:32:36: #1 finished! INFO @ Wed, 22 Jul 2020 13:32:36: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:32:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:32:36: #2 number of paired peaks: 26 WARNING @ Wed, 22 Jul 2020 13:32:36: 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 @ Wed, 22 Jul 2020 13:32:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.10_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/SRX7438933/SRX7438933.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:32:40: 8000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:32:45: 9000000 INFO @ Wed, 22 Jul 2020 13:32:51: 10000000 INFO @ Wed, 22 Jul 2020 13:32:56: 11000000 INFO @ Wed, 22 Jul 2020 13:32:57: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 13:32:57: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 13:32:57: #1 total tags in treatment: 5353099 INFO @ Wed, 22 Jul 2020 13:32:57: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:32:57: #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 13:32:57: #1 tags after filtering in treatment: 4460383 INFO @ Wed, 22 Jul 2020 13:32:57: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Jul 2020 13:32:57: #1 finished! INFO @ Wed, 22 Jul 2020 13:32:57: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:32:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:32:58: #2 number of paired peaks: 26 WARNING @ Wed, 22 Jul 2020 13:32:58: 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 @ Wed, 22 Jul 2020 13:32:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.20_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/SRX7438933/SRX7438933.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7438933/SRX7438933.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling