Job ID = 7111114 SRX = SRX8053696 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 38386777 spots for SRR11477537/SRR11477537.sra Written 38386777 spots for SRR11477537/SRR11477537.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: 00:20:28 38386777 reads; of these: 38386777 (100.00%) were paired; of these: 8458841 (22.04%) aligned concordantly 0 times 24889779 (64.84%) aligned concordantly exactly 1 time 5038157 (13.12%) aligned concordantly >1 times ---- 8458841 pairs aligned concordantly 0 times; of these: 3939751 (46.58%) aligned discordantly 1 time ---- 4519090 pairs aligned 0 times concordantly or discordantly; of these: 9038180 mates make up the pairs; of these: 4525191 (50.07%) aligned 0 times 2539102 (28.09%) aligned exactly 1 time 1973887 (21.84%) aligned >1 times 94.11% overall alignment rate Time searching: 00:20:28 Overall time: 00:20:28 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 32 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] 27834822 / 32352779 = 0.8604 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 14:36:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.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 14:36:47: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:36:47: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:36:52: 1000000 INFO @ Wed, 22 Jul 2020 14:36:57: 2000000 INFO @ Wed, 22 Jul 2020 14:37:02: 3000000 INFO @ Wed, 22 Jul 2020 14:37:07: 4000000 INFO @ Wed, 22 Jul 2020 14:37:13: 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 14:37:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.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 14:37:16: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:37:16: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:37:18: 6000000 INFO @ Wed, 22 Jul 2020 14:37:22: 1000000 INFO @ Wed, 22 Jul 2020 14:37:25: 7000000 INFO @ Wed, 22 Jul 2020 14:37:28: 2000000 INFO @ Wed, 22 Jul 2020 14:37:31: 8000000 INFO @ Wed, 22 Jul 2020 14:37:33: 3000000 INFO @ Wed, 22 Jul 2020 14:37:37: 9000000 INFO @ Wed, 22 Jul 2020 14:37:39: 4000000 INFO @ Wed, 22 Jul 2020 14:37:44: 10000000 INFO @ Wed, 22 Jul 2020 14:37:45: 5000000 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 14:37:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.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 14:37:46: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:37:46: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:37:50: 11000000 INFO @ Wed, 22 Jul 2020 14:37:50: 6000000 INFO @ Wed, 22 Jul 2020 14:37:53: 1000000 INFO @ Wed, 22 Jul 2020 14:37:56: 7000000 INFO @ Wed, 22 Jul 2020 14:37:57: 12000000 INFO @ Wed, 22 Jul 2020 14:37:59: 2000000 INFO @ Wed, 22 Jul 2020 14:38:02: 8000000 INFO @ Wed, 22 Jul 2020 14:38:03: 13000000 INFO @ Wed, 22 Jul 2020 14:38:06: 3000000 INFO @ Wed, 22 Jul 2020 14:38:07: 9000000 INFO @ Wed, 22 Jul 2020 14:38:10: 14000000 INFO @ Wed, 22 Jul 2020 14:38:12: 4000000 INFO @ Wed, 22 Jul 2020 14:38:13: 10000000 INFO @ Wed, 22 Jul 2020 14:38:16: 15000000 INFO @ Wed, 22 Jul 2020 14:38:19: 5000000 INFO @ Wed, 22 Jul 2020 14:38:19: 11000000 INFO @ Wed, 22 Jul 2020 14:38:22: 16000000 INFO @ Wed, 22 Jul 2020 14:38:25: 12000000 INFO @ Wed, 22 Jul 2020 14:38:25: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 14:38:25: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 14:38:25: #1 total tags in treatment: 4111296 INFO @ Wed, 22 Jul 2020 14:38:25: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:38:25: #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 14:38:25: #1 tags after filtering in treatment: 3033262 INFO @ Wed, 22 Jul 2020 14:38:25: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 22 Jul 2020 14:38:25: #1 finished! INFO @ Wed, 22 Jul 2020 14:38:25: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:38:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:38:25: #2 number of paired peaks: 30 WARNING @ Wed, 22 Jul 2020 14:38:25: Too few paired peaks (30) 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 14:38:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.05_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/SRX8053696/SRX8053696.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:38:25: 6000000 INFO @ Wed, 22 Jul 2020 14:38:30: 13000000 INFO @ Wed, 22 Jul 2020 14:38:32: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 14:38:36: 14000000 INFO @ Wed, 22 Jul 2020 14:38:38: 8000000 INFO @ Wed, 22 Jul 2020 14:38:41: 15000000 INFO @ Wed, 22 Jul 2020 14:38:45: 9000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:38:47: 16000000 INFO @ Wed, 22 Jul 2020 14:38:51: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 14:38:51: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 14:38:51: #1 total tags in treatment: 4111296 INFO @ Wed, 22 Jul 2020 14:38:51: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:38:51: #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 14:38:51: #1 tags after filtering in treatment: 3033262 INFO @ Wed, 22 Jul 2020 14:38:51: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 22 Jul 2020 14:38:51: #1 finished! INFO @ Wed, 22 Jul 2020 14:38:51: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:38:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:38:51: #2 number of paired peaks: 30 WARNING @ Wed, 22 Jul 2020 14:38:51: Too few paired peaks (30) 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 14:38:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.10_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/SRX8053696/SRX8053696.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:38:51: 10000000 INFO @ Wed, 22 Jul 2020 14:38:57: 11000000 INFO @ Wed, 22 Jul 2020 14:39:02: 12000000 INFO @ Wed, 22 Jul 2020 14:39:08: 13000000 INFO @ Wed, 22 Jul 2020 14:39:13: 14000000 INFO @ Wed, 22 Jul 2020 14:39:18: 15000000 INFO @ Wed, 22 Jul 2020 14:39:23: 16000000 INFO @ Wed, 22 Jul 2020 14:39:26: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 14:39:26: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 14:39:26: #1 total tags in treatment: 4111296 INFO @ Wed, 22 Jul 2020 14:39:26: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:39:26: #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 14:39:26: #1 tags after filtering in treatment: 3033262 INFO @ Wed, 22 Jul 2020 14:39:26: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 22 Jul 2020 14:39:26: #1 finished! INFO @ Wed, 22 Jul 2020 14:39:26: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:39:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:39:26: #2 number of paired peaks: 30 WARNING @ Wed, 22 Jul 2020 14:39:26: Too few paired peaks (30) 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 14:39:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.20_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/SRX8053696/SRX8053696.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8053696/SRX8053696.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling