Job ID = 6527983 SRX = SRX3632900 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:27:37 prefetch.2.10.7: 1) Downloading 'SRR6655540'... 2020-06-29T14:27:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:32:22 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:32:22 prefetch.2.10.7: 1) 'SRR6655540' was downloaded successfully 2020-06-29T14:32:22 prefetch.2.10.7: 'SRR6655540' has 0 unresolved dependencies Read 15946053 spots for SRR6655540/SRR6655540.sra Written 15946053 spots for SRR6655540/SRR6655540.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:28:31 15946053 reads; of these: 15946053 (100.00%) were paired; of these: 1140826 (7.15%) aligned concordantly 0 times 12168918 (76.31%) aligned concordantly exactly 1 time 2636309 (16.53%) aligned concordantly >1 times ---- 1140826 pairs aligned concordantly 0 times; of these: 321278 (28.16%) aligned discordantly 1 time ---- 819548 pairs aligned 0 times concordantly or discordantly; of these: 1639096 mates make up the pairs; of these: 1065151 (64.98%) aligned 0 times 377434 (23.03%) aligned exactly 1 time 196511 (11.99%) aligned >1 times 96.66% overall alignment rate Time searching: 00:28:32 Overall time: 00:28:32 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 16 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] 718528 / 15067979 = 0.0477 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 00:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.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 00:17:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:17:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:17:49: 1000000 INFO @ Tue, 30 Jun 2020 00:17:57: 2000000 INFO @ Tue, 30 Jun 2020 00:18:04: 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 00:18:11: 4000000 INFO @ Tue, 30 Jun 2020 00:18:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.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 00:18:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:18:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:18:20: 5000000 INFO @ Tue, 30 Jun 2020 00:18:21: 1000000 INFO @ Tue, 30 Jun 2020 00:18:30: 6000000 INFO @ Tue, 30 Jun 2020 00:18:30: 2000000 INFO @ Tue, 30 Jun 2020 00:18:39: 7000000 INFO @ Tue, 30 Jun 2020 00:18:39: 3000000 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 00:18:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.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 00:18:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:18:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:18:48: 8000000 INFO @ Tue, 30 Jun 2020 00:18:49: 4000000 INFO @ Tue, 30 Jun 2020 00:18:51: 1000000 INFO @ Tue, 30 Jun 2020 00:18:57: 9000000 INFO @ Tue, 30 Jun 2020 00:18:58: 5000000 INFO @ Tue, 30 Jun 2020 00:18:59: 2000000 INFO @ Tue, 30 Jun 2020 00:19:06: 10000000 INFO @ Tue, 30 Jun 2020 00:19:07: 6000000 INFO @ Tue, 30 Jun 2020 00:19:08: 3000000 INFO @ Tue, 30 Jun 2020 00:19:14: 11000000 INFO @ Tue, 30 Jun 2020 00:19:16: 7000000 INFO @ Tue, 30 Jun 2020 00:19:17: 4000000 INFO @ Tue, 30 Jun 2020 00:19:23: 12000000 INFO @ Tue, 30 Jun 2020 00:19:25: 5000000 INFO @ Tue, 30 Jun 2020 00:19:26: 8000000 INFO @ Tue, 30 Jun 2020 00:19:31: 13000000 INFO @ Tue, 30 Jun 2020 00:19:34: 6000000 INFO @ Tue, 30 Jun 2020 00:19:35: 9000000 INFO @ Tue, 30 Jun 2020 00:19:40: 14000000 INFO @ Tue, 30 Jun 2020 00:19:42: 7000000 INFO @ Tue, 30 Jun 2020 00:19:44: 10000000 INFO @ Tue, 30 Jun 2020 00:19:49: 15000000 INFO @ Tue, 30 Jun 2020 00:19:51: 8000000 INFO @ Tue, 30 Jun 2020 00:19:53: 11000000 INFO @ Tue, 30 Jun 2020 00:19:57: 16000000 INFO @ Tue, 30 Jun 2020 00:19:59: 9000000 INFO @ Tue, 30 Jun 2020 00:20:02: 12000000 INFO @ Tue, 30 Jun 2020 00:20:06: 17000000 INFO @ Tue, 30 Jun 2020 00:20:08: 10000000 INFO @ Tue, 30 Jun 2020 00:20:11: 13000000 INFO @ Tue, 30 Jun 2020 00:20:15: 18000000 INFO @ Tue, 30 Jun 2020 00:20:17: 11000000 INFO @ Tue, 30 Jun 2020 00:20:20: 14000000 INFO @ Tue, 30 Jun 2020 00:20:24: 19000000 INFO @ Tue, 30 Jun 2020 00:20:26: 12000000 INFO @ Tue, 30 Jun 2020 00:20:29: 15000000 INFO @ Tue, 30 Jun 2020 00:20:33: 20000000 INFO @ Tue, 30 Jun 2020 00:20:35: 13000000 INFO @ Tue, 30 Jun 2020 00:20:38: 16000000 INFO @ Tue, 30 Jun 2020 00:20:42: 21000000 INFO @ Tue, 30 Jun 2020 00:20:44: 14000000 INFO @ Tue, 30 Jun 2020 00:20:47: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:20:50: 22000000 INFO @ Tue, 30 Jun 2020 00:20:52: 15000000 INFO @ Tue, 30 Jun 2020 00:20:56: 18000000 INFO @ Tue, 30 Jun 2020 00:20:59: 23000000 INFO @ Tue, 30 Jun 2020 00:21:01: 16000000 INFO @ Tue, 30 Jun 2020 00:21:05: 19000000 INFO @ Tue, 30 Jun 2020 00:21:08: 24000000 INFO @ Tue, 30 Jun 2020 00:21:10: 17000000 INFO @ Tue, 30 Jun 2020 00:21:14: 20000000 INFO @ Tue, 30 Jun 2020 00:21:17: 25000000 INFO @ Tue, 30 Jun 2020 00:21:19: 18000000 INFO @ Tue, 30 Jun 2020 00:21:23: 21000000 INFO @ Tue, 30 Jun 2020 00:21:26: 26000000 INFO @ Tue, 30 Jun 2020 00:21:27: 19000000 INFO @ Tue, 30 Jun 2020 00:21:32: 22000000 INFO @ Tue, 30 Jun 2020 00:21:34: 27000000 INFO @ Tue, 30 Jun 2020 00:21:36: 20000000 INFO @ Tue, 30 Jun 2020 00:21:41: 23000000 INFO @ Tue, 30 Jun 2020 00:21:43: 28000000 INFO @ Tue, 30 Jun 2020 00:21:45: 21000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:21:51: 24000000 INFO @ Tue, 30 Jun 2020 00:21:51: 29000000 INFO @ Tue, 30 Jun 2020 00:21:53: 22000000 INFO @ Tue, 30 Jun 2020 00:21:54: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 00:21:54: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 00:21:54: #1 total tags in treatment: 14094535 INFO @ Tue, 30 Jun 2020 00:21:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:21:54: #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 00:21:55: #1 tags after filtering in treatment: 12709920 INFO @ Tue, 30 Jun 2020 00:21:55: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 30 Jun 2020 00:21:55: #1 finished! INFO @ Tue, 30 Jun 2020 00:21:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:21:55: #2 number of paired peaks: 5 WARNING @ Tue, 30 Jun 2020 00:21:55: Too few paired peaks (5) 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 00:21:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.05_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/SRX3632900/SRX3632900.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:22:00: 25000000 INFO @ Tue, 30 Jun 2020 00:22:02: 23000000 INFO @ Tue, 30 Jun 2020 00:22:09: 26000000 INFO @ Tue, 30 Jun 2020 00:22:10: 24000000 INFO @ Tue, 30 Jun 2020 00:22:19: 25000000 INFO @ Tue, 30 Jun 2020 00:22:19: 27000000 INFO @ Tue, 30 Jun 2020 00:22:27: 26000000 INFO @ Tue, 30 Jun 2020 00:22:28: 28000000 INFO @ Tue, 30 Jun 2020 00:22:35: 27000000 INFO @ Tue, 30 Jun 2020 00:22:37: 29000000 INFO @ Tue, 30 Jun 2020 00:22:41: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 00:22:41: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 00:22:41: #1 total tags in treatment: 14094535 INFO @ Tue, 30 Jun 2020 00:22:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:22:41: #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 00:22:41: #1 tags after filtering in treatment: 12709920 INFO @ Tue, 30 Jun 2020 00:22:41: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 30 Jun 2020 00:22:41: #1 finished! INFO @ Tue, 30 Jun 2020 00:22:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:22:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:22:42: #2 number of paired peaks: 5 WARNING @ Tue, 30 Jun 2020 00:22:42: Too few paired peaks (5) 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 00:22:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.10_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/SRX3632900/SRX3632900.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:22:43: 28000000 INFO @ Tue, 30 Jun 2020 00:22:50: 29000000 INFO @ Tue, 30 Jun 2020 00:22:53: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 00:22:53: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 00:22:53: #1 total tags in treatment: 14094535 INFO @ Tue, 30 Jun 2020 00:22:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:22:53: #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 00:22:53: #1 tags after filtering in treatment: 12709920 INFO @ Tue, 30 Jun 2020 00:22:53: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 30 Jun 2020 00:22:53: #1 finished! INFO @ Tue, 30 Jun 2020 00:22:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:22:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:22:54: #2 number of paired peaks: 5 WARNING @ Tue, 30 Jun 2020 00:22:54: Too few paired peaks (5) 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 00:22:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.20_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/SRX3632900/SRX3632900.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632900/SRX3632900.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling