Job ID = 6527990 SRX = SRX3632917 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T13:54:00 prefetch.2.10.7: 1) Downloading 'SRR6655569'... 2020-06-29T13:54:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:57:30 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:57:30 prefetch.2.10.7: 1) 'SRR6655569' was downloaded successfully 2020-06-29T13:57:30 prefetch.2.10.7: 'SRR6655569' has 0 unresolved dependencies Read 12943893 spots for SRR6655569/SRR6655569.sra Written 12943893 spots for SRR6655569/SRR6655569.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: 00:26:14 12943893 reads; of these: 12943893 (100.00%) were paired; of these: 1008875 (7.79%) aligned concordantly 0 times 9161695 (70.78%) aligned concordantly exactly 1 time 2773323 (21.43%) aligned concordantly >1 times ---- 1008875 pairs aligned concordantly 0 times; of these: 271772 (26.94%) aligned discordantly 1 time ---- 737103 pairs aligned 0 times concordantly or discordantly; of these: 1474206 mates make up the pairs; of these: 920873 (62.47%) aligned 0 times 314730 (21.35%) aligned exactly 1 time 238603 (16.19%) aligned >1 times 96.44% overall alignment rate Time searching: 00:26:14 Overall time: 00:26:14 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 12 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] 818518 / 12170001 = 0.0673 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 @ Mon, 29 Jun 2020 23:37:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.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 @ Mon, 29 Jun 2020 23:37:20: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:37:20: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:37:26: 1000000 INFO @ Mon, 29 Jun 2020 23:37:31: 2000000 INFO @ Mon, 29 Jun 2020 23:37:37: 3000000 INFO @ Mon, 29 Jun 2020 23:37:43: 4000000 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 @ Mon, 29 Jun 2020 23:37:49: 5000000 INFO @ Mon, 29 Jun 2020 23:37:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.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 @ Mon, 29 Jun 2020 23:37:50: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:37:50: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:37:56: 6000000 INFO @ Mon, 29 Jun 2020 23:37:57: 1000000 INFO @ Mon, 29 Jun 2020 23:38:03: 7000000 INFO @ Mon, 29 Jun 2020 23:38:05: 2000000 INFO @ Mon, 29 Jun 2020 23:38:11: 8000000 INFO @ Mon, 29 Jun 2020 23:38:12: 3000000 INFO @ Mon, 29 Jun 2020 23:38:18: 9000000 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 @ Mon, 29 Jun 2020 23:38:19: 4000000 INFO @ Mon, 29 Jun 2020 23:38:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.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 @ Mon, 29 Jun 2020 23:38:20: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:38:20: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:38:25: 10000000 INFO @ Mon, 29 Jun 2020 23:38:26: 5000000 INFO @ Mon, 29 Jun 2020 23:38:29: 1000000 INFO @ Mon, 29 Jun 2020 23:38:33: 11000000 INFO @ Mon, 29 Jun 2020 23:38:34: 6000000 INFO @ Mon, 29 Jun 2020 23:38:38: 2000000 INFO @ Mon, 29 Jun 2020 23:38:41: 12000000 INFO @ Mon, 29 Jun 2020 23:38:42: 7000000 INFO @ Mon, 29 Jun 2020 23:38:47: 3000000 INFO @ Mon, 29 Jun 2020 23:38:49: 13000000 INFO @ Mon, 29 Jun 2020 23:38:49: 8000000 INFO @ Mon, 29 Jun 2020 23:38:56: 4000000 INFO @ Mon, 29 Jun 2020 23:38:56: 14000000 INFO @ Mon, 29 Jun 2020 23:38:57: 9000000 INFO @ Mon, 29 Jun 2020 23:39:04: 15000000 INFO @ Mon, 29 Jun 2020 23:39:05: 5000000 INFO @ Mon, 29 Jun 2020 23:39:05: 10000000 INFO @ Mon, 29 Jun 2020 23:39:12: 16000000 INFO @ Mon, 29 Jun 2020 23:39:12: 11000000 INFO @ Mon, 29 Jun 2020 23:39:13: 6000000 INFO @ Mon, 29 Jun 2020 23:39:19: 17000000 INFO @ Mon, 29 Jun 2020 23:39:20: 12000000 INFO @ Mon, 29 Jun 2020 23:39:22: 7000000 INFO @ Mon, 29 Jun 2020 23:39:27: 18000000 INFO @ Mon, 29 Jun 2020 23:39:28: 13000000 INFO @ Mon, 29 Jun 2020 23:39:31: 8000000 INFO @ Mon, 29 Jun 2020 23:39:35: 19000000 INFO @ Mon, 29 Jun 2020 23:39:35: 14000000 INFO @ Mon, 29 Jun 2020 23:39:39: 9000000 INFO @ Mon, 29 Jun 2020 23:39:43: 15000000 INFO @ Mon, 29 Jun 2020 23:39:43: 20000000 INFO @ Mon, 29 Jun 2020 23:39:47: 10000000 INFO @ Mon, 29 Jun 2020 23:39:50: 16000000 INFO @ Mon, 29 Jun 2020 23:39:51: 21000000 INFO @ Mon, 29 Jun 2020 23:39:56: 11000000 INFO @ Mon, 29 Jun 2020 23:39:58: 17000000 INFO @ Mon, 29 Jun 2020 23:39:59: 22000000 INFO @ Mon, 29 Jun 2020 23:40:04: 12000000 INFO @ Mon, 29 Jun 2020 23:40:06: 18000000 INFO @ Mon, 29 Jun 2020 23:40:06: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:40:09: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 23:40:09: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 23:40:09: #1 total tags in treatment: 11124116 INFO @ Mon, 29 Jun 2020 23:40:09: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:40:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:40:09: #1 tags after filtering in treatment: 10089870 INFO @ Mon, 29 Jun 2020 23:40:09: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 29 Jun 2020 23:40:09: #1 finished! INFO @ Mon, 29 Jun 2020 23:40:09: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:40:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:40:10: #2 number of paired peaks: 65 WARNING @ Mon, 29 Jun 2020 23:40:10: Too few paired peaks (65) 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 @ Mon, 29 Jun 2020 23:40:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.05_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/dm3/SRX3632917/SRX3632917.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:40:13: 13000000 INFO @ Mon, 29 Jun 2020 23:40:13: 19000000 INFO @ Mon, 29 Jun 2020 23:40:21: 20000000 INFO @ Mon, 29 Jun 2020 23:40:21: 14000000 INFO @ Mon, 29 Jun 2020 23:40:28: 21000000 INFO @ Mon, 29 Jun 2020 23:40:29: 15000000 INFO @ Mon, 29 Jun 2020 23:40:36: 22000000 INFO @ Mon, 29 Jun 2020 23:40:38: 16000000 INFO @ Mon, 29 Jun 2020 23:40:44: 23000000 INFO @ Mon, 29 Jun 2020 23:40:46: 17000000 INFO @ Mon, 29 Jun 2020 23:40:46: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 23:40:46: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 23:40:46: #1 total tags in treatment: 11124116 INFO @ Mon, 29 Jun 2020 23:40:46: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:40:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:40:46: #1 tags after filtering in treatment: 10089870 INFO @ Mon, 29 Jun 2020 23:40:46: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 29 Jun 2020 23:40:46: #1 finished! INFO @ Mon, 29 Jun 2020 23:40:46: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:40:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:40:47: #2 number of paired peaks: 65 WARNING @ Mon, 29 Jun 2020 23:40:47: Too few paired peaks (65) 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 @ Mon, 29 Jun 2020 23:40:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.10_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/SRX3632917/SRX3632917.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:40:53: 18000000 INFO @ Mon, 29 Jun 2020 23:41:00: 19000000 INFO @ Mon, 29 Jun 2020 23:41:07: 20000000 INFO @ Mon, 29 Jun 2020 23:41:15: 21000000 INFO @ Mon, 29 Jun 2020 23:41:22: 22000000 INFO @ Mon, 29 Jun 2020 23:41:29: 23000000 INFO @ Mon, 29 Jun 2020 23:41:32: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 23:41:32: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 23:41:32: #1 total tags in treatment: 11124116 INFO @ Mon, 29 Jun 2020 23:41:32: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:41:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:41:32: #1 tags after filtering in treatment: 10089870 INFO @ Mon, 29 Jun 2020 23:41:32: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 29 Jun 2020 23:41:32: #1 finished! INFO @ Mon, 29 Jun 2020 23:41:32: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:41:32: #2 number of paired peaks: 65 WARNING @ Mon, 29 Jun 2020 23:41:32: Too few paired peaks (65) 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 @ Mon, 29 Jun 2020 23:41:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.20_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/SRX3632917/SRX3632917.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632917/SRX3632917.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling