Job ID = 6527932 SRX = SRX3293423 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T13:42:29 prefetch.2.10.7: 1) Downloading 'SRR6183249'... 2020-06-29T13:42:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:43:54 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:43:55 prefetch.2.10.7: 'SRR6183249' is valid 2020-06-29T13:43:55 prefetch.2.10.7: 1) 'SRR6183249' was downloaded successfully 2020-06-29T13:43:55 prefetch.2.10.7: 'SRR6183249' has 0 unresolved dependencies Read 18020459 spots for SRR6183249/SRR6183249.sra Written 18020459 spots for SRR6183249/SRR6183249.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: 00:25:04 18020459 reads; of these: 18020459 (100.00%) were paired; of these: 5450904 (30.25%) aligned concordantly 0 times 8638066 (47.93%) aligned concordantly exactly 1 time 3931489 (21.82%) aligned concordantly >1 times ---- 5450904 pairs aligned concordantly 0 times; of these: 828330 (15.20%) aligned discordantly 1 time ---- 4622574 pairs aligned 0 times concordantly or discordantly; of these: 9245148 mates make up the pairs; of these: 6818578 (73.75%) aligned 0 times 1192412 (12.90%) aligned exactly 1 time 1234158 (13.35%) aligned >1 times 81.08% overall alignment rate Time searching: 00:25:04 Overall time: 00:25:04 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] 850458 / 12819175 = 0.0663 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 23:20:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.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 23:20:24: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:20:24: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:20:28: 1000000 INFO @ Mon, 29 Jun 2020 23:20:32: 2000000 INFO @ Mon, 29 Jun 2020 23:20:36: 3000000 INFO @ Mon, 29 Jun 2020 23:20:40: 4000000 INFO @ Mon, 29 Jun 2020 23:20:44: 5000000 INFO @ Mon, 29 Jun 2020 23:20:47: 6000000 INFO @ Mon, 29 Jun 2020 23:20:51: 7000000 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 23:20:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.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 23:20:53: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:20:53: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:20:55: 8000000 INFO @ Mon, 29 Jun 2020 23:20:58: 1000000 INFO @ Mon, 29 Jun 2020 23:20:59: 9000000 INFO @ Mon, 29 Jun 2020 23:21:02: 2000000 INFO @ Mon, 29 Jun 2020 23:21:03: 10000000 INFO @ Mon, 29 Jun 2020 23:21:06: 3000000 INFO @ Mon, 29 Jun 2020 23:21:07: 11000000 INFO @ Mon, 29 Jun 2020 23:21:11: 4000000 INFO @ Mon, 29 Jun 2020 23:21:11: 12000000 INFO @ Mon, 29 Jun 2020 23:21:15: 5000000 INFO @ Mon, 29 Jun 2020 23:21:15: 13000000 INFO @ Mon, 29 Jun 2020 23:21:19: 14000000 INFO @ Mon, 29 Jun 2020 23:21:19: 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 @ Mon, 29 Jun 2020 23:21:23: 15000000 INFO @ Mon, 29 Jun 2020 23:21:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.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 23:21:23: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:21:23: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:21:24: 7000000 INFO @ Mon, 29 Jun 2020 23:21:27: 16000000 INFO @ Mon, 29 Jun 2020 23:21:28: 1000000 INFO @ Mon, 29 Jun 2020 23:21:28: 8000000 INFO @ Mon, 29 Jun 2020 23:21:31: 17000000 INFO @ Mon, 29 Jun 2020 23:21:32: 2000000 INFO @ Mon, 29 Jun 2020 23:21:32: 9000000 INFO @ Mon, 29 Jun 2020 23:21:35: 18000000 INFO @ Mon, 29 Jun 2020 23:21:36: 3000000 INFO @ Mon, 29 Jun 2020 23:21:37: 10000000 INFO @ Mon, 29 Jun 2020 23:21:39: 19000000 INFO @ Mon, 29 Jun 2020 23:21:41: 4000000 INFO @ Mon, 29 Jun 2020 23:21:41: 11000000 INFO @ Mon, 29 Jun 2020 23:21:43: 20000000 INFO @ Mon, 29 Jun 2020 23:21:45: 5000000 INFO @ Mon, 29 Jun 2020 23:21:46: 12000000 INFO @ Mon, 29 Jun 2020 23:21:47: 21000000 INFO @ Mon, 29 Jun 2020 23:21:50: 6000000 INFO @ Mon, 29 Jun 2020 23:21:50: 13000000 INFO @ Mon, 29 Jun 2020 23:21:51: 22000000 INFO @ Mon, 29 Jun 2020 23:21:54: 7000000 INFO @ Mon, 29 Jun 2020 23:21:54: 14000000 INFO @ Mon, 29 Jun 2020 23:21:55: 23000000 INFO @ Mon, 29 Jun 2020 23:21:58: 8000000 INFO @ Mon, 29 Jun 2020 23:21:58: 15000000 INFO @ Mon, 29 Jun 2020 23:21:59: 24000000 INFO @ Mon, 29 Jun 2020 23:22:03: 9000000 INFO @ Mon, 29 Jun 2020 23:22:03: 16000000 INFO @ Mon, 29 Jun 2020 23:22:03: 25000000 INFO @ Mon, 29 Jun 2020 23:22:07: 10000000 INFO @ Mon, 29 Jun 2020 23:22:07: 17000000 INFO @ Mon, 29 Jun 2020 23:22:07: 26000000 INFO @ Mon, 29 Jun 2020 23:22:11: 27000000 INFO @ Mon, 29 Jun 2020 23:22:11: 11000000 INFO @ Mon, 29 Jun 2020 23:22:11: 18000000 INFO @ Mon, 29 Jun 2020 23:22:13: #1 tag size is determined as 25 bps INFO @ Mon, 29 Jun 2020 23:22:13: #1 tag size = 25 INFO @ Mon, 29 Jun 2020 23:22:13: #1 total tags in treatment: 11721442 INFO @ Mon, 29 Jun 2020 23:22:13: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:22:13: #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 23:22:14: #1 tags after filtering in treatment: 10239556 INFO @ Mon, 29 Jun 2020 23:22:14: #1 Redundant rate of treatment: 0.13 INFO @ Mon, 29 Jun 2020 23:22:14: #1 finished! INFO @ Mon, 29 Jun 2020 23:22:14: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:22:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:22:14: #2 number of paired peaks: 33 WARNING @ Mon, 29 Jun 2020 23:22:14: Too few paired peaks (33) 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 23:22:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.05_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/SRX3293423/SRX3293423.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:22:15: 12000000 INFO @ Mon, 29 Jun 2020 23:22:16: 19000000 INFO @ Mon, 29 Jun 2020 23:22:20: 13000000 INFO @ Mon, 29 Jun 2020 23:22:20: 20000000 INFO @ Mon, 29 Jun 2020 23:22:24: 14000000 INFO @ Mon, 29 Jun 2020 23:22:25: 21000000 INFO @ Mon, 29 Jun 2020 23:22:28: 15000000 INFO @ Mon, 29 Jun 2020 23:22:29: 22000000 INFO @ Mon, 29 Jun 2020 23:22:33: 16000000 INFO @ Mon, 29 Jun 2020 23:22:33: 23000000 INFO @ Mon, 29 Jun 2020 23:22:37: 17000000 INFO @ Mon, 29 Jun 2020 23:22:38: 24000000 INFO @ Mon, 29 Jun 2020 23:22:41: 18000000 INFO @ Mon, 29 Jun 2020 23:22:42: 25000000 INFO @ Mon, 29 Jun 2020 23:22:46: 19000000 INFO @ Mon, 29 Jun 2020 23:22:47: 26000000 INFO @ Mon, 29 Jun 2020 23:22:50: 20000000 INFO @ Mon, 29 Jun 2020 23:22:51: 27000000 INFO @ Mon, 29 Jun 2020 23:22:54: #1 tag size is determined as 25 bps INFO @ Mon, 29 Jun 2020 23:22:54: #1 tag size = 25 INFO @ Mon, 29 Jun 2020 23:22:54: #1 total tags in treatment: 11721442 INFO @ Mon, 29 Jun 2020 23:22:54: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:22:54: #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 23:22:54: #1 tags after filtering in treatment: 10239556 INFO @ Mon, 29 Jun 2020 23:22:54: #1 Redundant rate of treatment: 0.13 INFO @ Mon, 29 Jun 2020 23:22:54: #1 finished! INFO @ Mon, 29 Jun 2020 23:22:54: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:22:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:22:54: 21000000 INFO @ Mon, 29 Jun 2020 23:22:55: #2 number of paired peaks: 33 WARNING @ Mon, 29 Jun 2020 23:22:55: Too few paired peaks (33) 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 23:22:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.10_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/SRX3293423/SRX3293423.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:22:59: 22000000 INFO @ Mon, 29 Jun 2020 23:23:03: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:23:07: 24000000 INFO @ Mon, 29 Jun 2020 23:23:12: 25000000 INFO @ Mon, 29 Jun 2020 23:23:16: 26000000 INFO @ Mon, 29 Jun 2020 23:23:20: 27000000 INFO @ Mon, 29 Jun 2020 23:23:23: #1 tag size is determined as 25 bps INFO @ Mon, 29 Jun 2020 23:23:23: #1 tag size = 25 INFO @ Mon, 29 Jun 2020 23:23:23: #1 total tags in treatment: 11721442 INFO @ Mon, 29 Jun 2020 23:23:23: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:23:23: #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 23:23:23: #1 tags after filtering in treatment: 10239556 INFO @ Mon, 29 Jun 2020 23:23:23: #1 Redundant rate of treatment: 0.13 INFO @ Mon, 29 Jun 2020 23:23:23: #1 finished! INFO @ Mon, 29 Jun 2020 23:23:23: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:23:23: #2 number of paired peaks: 33 WARNING @ Mon, 29 Jun 2020 23:23:23: Too few paired peaks (33) 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 23:23:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.20_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/SRX3293423/SRX3293423.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3293423/SRX3293423.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。