Job ID = 6527987 SRX = SRX3632911 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:36:21 prefetch.2.10.7: 1) Downloading 'SRR6655557'... 2020-06-29T14:36:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:39:54 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:39:55 prefetch.2.10.7: 'SRR6655557' is valid 2020-06-29T14:39:55 prefetch.2.10.7: 1) 'SRR6655557' was downloaded successfully 2020-06-29T14:39:55 prefetch.2.10.7: 'SRR6655557' has 0 unresolved dependencies Read 7930858 spots for SRR6655557/SRR6655557.sra Written 7930858 spots for SRR6655557/SRR6655557.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: 00:15:29 7930858 reads; of these: 7930858 (100.00%) were paired; of these: 722384 (9.11%) aligned concordantly 0 times 6265230 (79.00%) aligned concordantly exactly 1 time 943244 (11.89%) aligned concordantly >1 times ---- 722384 pairs aligned concordantly 0 times; of these: 267608 (37.05%) aligned discordantly 1 time ---- 454776 pairs aligned 0 times concordantly or discordantly; of these: 909552 mates make up the pairs; of these: 507737 (55.82%) aligned 0 times 291046 (32.00%) aligned exactly 1 time 110769 (12.18%) aligned >1 times 96.80% overall alignment rate Time searching: 00:15:29 Overall time: 00:15:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 234941 / 7355901 = 0.0319 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 @ Tue, 30 Jun 2020 00:07:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 30 Jun 2020 00:07:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:07:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:08:03: 1000000 INFO @ Tue, 30 Jun 2020 00:08:10: 2000000 INFO @ Tue, 30 Jun 2020 00:08:17: 3000000 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 @ Tue, 30 Jun 2020 00:08:25: 4000000 INFO @ Tue, 30 Jun 2020 00:08:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 30 Jun 2020 00:08:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:08:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:08:32: 5000000 INFO @ Tue, 30 Jun 2020 00:08:32: 1000000 INFO @ Tue, 30 Jun 2020 00:08:39: 2000000 INFO @ Tue, 30 Jun 2020 00:08:39: 6000000 INFO @ Tue, 30 Jun 2020 00:08:46: 3000000 INFO @ Tue, 30 Jun 2020 00:08:46: 7000000 INFO @ Tue, 30 Jun 2020 00:08:53: 4000000 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 @ Tue, 30 Jun 2020 00:08:54: 8000000 INFO @ Tue, 30 Jun 2020 00:08:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 30 Jun 2020 00:08:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:08:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:09:01: 9000000 INFO @ Tue, 30 Jun 2020 00:09:01: 5000000 INFO @ Tue, 30 Jun 2020 00:09:05: 1000000 INFO @ Tue, 30 Jun 2020 00:09:08: 10000000 INFO @ Tue, 30 Jun 2020 00:09:09: 6000000 INFO @ Tue, 30 Jun 2020 00:09:13: 2000000 INFO @ Tue, 30 Jun 2020 00:09:17: 11000000 INFO @ Tue, 30 Jun 2020 00:09:17: 7000000 INFO @ Tue, 30 Jun 2020 00:09:21: 3000000 INFO @ Tue, 30 Jun 2020 00:09:25: 8000000 INFO @ Tue, 30 Jun 2020 00:09:25: 12000000 INFO @ Tue, 30 Jun 2020 00:09:29: 4000000 INFO @ Tue, 30 Jun 2020 00:09:33: 9000000 INFO @ Tue, 30 Jun 2020 00:09:34: 13000000 INFO @ Tue, 30 Jun 2020 00:09:37: 5000000 INFO @ Tue, 30 Jun 2020 00:09:41: 10000000 INFO @ Tue, 30 Jun 2020 00:09:42: 14000000 INFO @ Tue, 30 Jun 2020 00:09:45: 6000000 INFO @ Tue, 30 Jun 2020 00:09:50: 11000000 INFO @ Tue, 30 Jun 2020 00:09:50: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 00:09:50: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 00:09:50: #1 total tags in treatment: 6984799 INFO @ Tue, 30 Jun 2020 00:09:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:09:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:09:50: #1 tags after filtering in treatment: 6464924 INFO @ Tue, 30 Jun 2020 00:09:50: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 30 Jun 2020 00:09:50: #1 finished! INFO @ Tue, 30 Jun 2020 00:09:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:09:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:09:50: #2 number of paired peaks: 34 WARNING @ Tue, 30 Jun 2020 00:09:50: Too few paired peaks (34) 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 @ Tue, 30 Jun 2020 00:09:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.05_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/dm3/SRX3632911/SRX3632911.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:09:53: 7000000 INFO @ Tue, 30 Jun 2020 00:09:58: 12000000 INFO @ Tue, 30 Jun 2020 00:10:01: 8000000 INFO @ Tue, 30 Jun 2020 00:10:06: 13000000 INFO @ Tue, 30 Jun 2020 00:10:10: 9000000 INFO @ Tue, 30 Jun 2020 00:10:15: 14000000 INFO @ Tue, 30 Jun 2020 00:10:18: 10000000 INFO @ Tue, 30 Jun 2020 00:10:22: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 00:10:22: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 00:10:22: #1 total tags in treatment: 6984799 INFO @ Tue, 30 Jun 2020 00:10:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:10:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:10:22: #1 tags after filtering in treatment: 6464924 INFO @ Tue, 30 Jun 2020 00:10:22: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 30 Jun 2020 00:10:22: #1 finished! INFO @ Tue, 30 Jun 2020 00:10:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:10:22: #2 number of paired peaks: 34 WARNING @ Tue, 30 Jun 2020 00:10:22: Too few paired peaks (34) 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 @ Tue, 30 Jun 2020 00:10:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.10_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/dm3/SRX3632911/SRX3632911.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:10:26: 11000000 INFO @ Tue, 30 Jun 2020 00:10:33: 12000000 INFO @ Tue, 30 Jun 2020 00:10:41: 13000000 INFO @ Tue, 30 Jun 2020 00:10:48: 14000000 INFO @ Tue, 30 Jun 2020 00:10:54: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 00:10:54: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 00:10:54: #1 total tags in treatment: 6984799 INFO @ Tue, 30 Jun 2020 00:10:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:10:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:10:54: #1 tags after filtering in treatment: 6464924 INFO @ Tue, 30 Jun 2020 00:10:54: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 30 Jun 2020 00:10:54: #1 finished! INFO @ Tue, 30 Jun 2020 00:10:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:10:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:10:55: #2 number of paired peaks: 34 WARNING @ Tue, 30 Jun 2020 00:10:55: Too few paired peaks (34) 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 @ Tue, 30 Jun 2020 00:10:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.20_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/dm3/SRX3632911/SRX3632911.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632911/SRX3632911.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。