Job ID = 6527992 SRX = SRX3632919 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:29:36 prefetch.2.10.7: 1) Downloading 'SRR6655571'... 2020-06-29T14:29:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:33:55 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:33:55 prefetch.2.10.7: 1) 'SRR6655571' was downloaded successfully 2020-06-29T14:33:55 prefetch.2.10.7: 'SRR6655571' has 0 unresolved dependencies Read 14570112 spots for SRR6655571/SRR6655571.sra Written 14570112 spots for SRR6655571/SRR6655571.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: 00:27:01 14570112 reads; of these: 14570112 (100.00%) were paired; of these: 1077741 (7.40%) aligned concordantly 0 times 10734265 (73.67%) aligned concordantly exactly 1 time 2758106 (18.93%) aligned concordantly >1 times ---- 1077741 pairs aligned concordantly 0 times; of these: 266421 (24.72%) aligned discordantly 1 time ---- 811320 pairs aligned 0 times concordantly or discordantly; of these: 1622640 mates make up the pairs; of these: 1124377 (69.29%) aligned 0 times 305897 (18.85%) aligned exactly 1 time 192366 (11.86%) aligned >1 times 96.14% overall alignment rate Time searching: 00:27:02 Overall time: 00:27:02 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] 730599 / 13711622 = 0.0533 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 00:16:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.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 00:16:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:16:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:16:16: 1000000 INFO @ Tue, 30 Jun 2020 00:16:21: 2000000 INFO @ Tue, 30 Jun 2020 00:16:27: 3000000 INFO @ Tue, 30 Jun 2020 00:16:32: 4000000 INFO @ Tue, 30 Jun 2020 00:16:37: 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 @ Tue, 30 Jun 2020 00:16:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.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 00:16:41: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:16:41: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:16:42: 6000000 INFO @ Tue, 30 Jun 2020 00:16:47: 1000000 INFO @ Tue, 30 Jun 2020 00:16:48: 7000000 INFO @ Tue, 30 Jun 2020 00:16:52: 2000000 INFO @ Tue, 30 Jun 2020 00:16:53: 8000000 INFO @ Tue, 30 Jun 2020 00:16:58: 3000000 INFO @ Tue, 30 Jun 2020 00:16:59: 9000000 INFO @ Tue, 30 Jun 2020 00:17:04: 4000000 INFO @ Tue, 30 Jun 2020 00:17:05: 10000000 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 00:17:10: 5000000 INFO @ Tue, 30 Jun 2020 00:17:10: 11000000 INFO @ Tue, 30 Jun 2020 00:17:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.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 00:17:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:17:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:17:15: 6000000 INFO @ Tue, 30 Jun 2020 00:17:16: 12000000 INFO @ Tue, 30 Jun 2020 00:17:17: 1000000 INFO @ Tue, 30 Jun 2020 00:17:21: 7000000 INFO @ Tue, 30 Jun 2020 00:17:22: 13000000 INFO @ Tue, 30 Jun 2020 00:17:23: 2000000 INFO @ Tue, 30 Jun 2020 00:17:27: 8000000 INFO @ Tue, 30 Jun 2020 00:17:27: 14000000 INFO @ Tue, 30 Jun 2020 00:17:29: 3000000 INFO @ Tue, 30 Jun 2020 00:17:33: 15000000 INFO @ Tue, 30 Jun 2020 00:17:33: 9000000 INFO @ Tue, 30 Jun 2020 00:17:35: 4000000 INFO @ Tue, 30 Jun 2020 00:17:39: 16000000 INFO @ Tue, 30 Jun 2020 00:17:39: 10000000 INFO @ Tue, 30 Jun 2020 00:17:41: 5000000 INFO @ Tue, 30 Jun 2020 00:17:44: 17000000 INFO @ Tue, 30 Jun 2020 00:17:45: 11000000 INFO @ Tue, 30 Jun 2020 00:17:47: 6000000 INFO @ Tue, 30 Jun 2020 00:17:50: 18000000 INFO @ Tue, 30 Jun 2020 00:17:51: 12000000 INFO @ Tue, 30 Jun 2020 00:17:53: 7000000 INFO @ Tue, 30 Jun 2020 00:17:56: 19000000 INFO @ Tue, 30 Jun 2020 00:17:57: 13000000 INFO @ Tue, 30 Jun 2020 00:17:59: 8000000 INFO @ Tue, 30 Jun 2020 00:18:02: 20000000 INFO @ Tue, 30 Jun 2020 00:18:03: 14000000 INFO @ Tue, 30 Jun 2020 00:18:04: 9000000 INFO @ Tue, 30 Jun 2020 00:18:07: 21000000 INFO @ Tue, 30 Jun 2020 00:18:09: 15000000 INFO @ Tue, 30 Jun 2020 00:18:10: 10000000 INFO @ Tue, 30 Jun 2020 00:18:13: 22000000 INFO @ Tue, 30 Jun 2020 00:18:15: 16000000 INFO @ Tue, 30 Jun 2020 00:18:16: 11000000 INFO @ Tue, 30 Jun 2020 00:18:19: 23000000 INFO @ Tue, 30 Jun 2020 00:18:21: 17000000 INFO @ Tue, 30 Jun 2020 00:18:22: 12000000 INFO @ Tue, 30 Jun 2020 00:18:25: 24000000 INFO @ Tue, 30 Jun 2020 00:18:26: 18000000 INFO @ Tue, 30 Jun 2020 00:18:28: 13000000 INFO @ Tue, 30 Jun 2020 00:18:31: 25000000 INFO @ Tue, 30 Jun 2020 00:18:32: 19000000 INFO @ Tue, 30 Jun 2020 00:18:34: 14000000 INFO @ Tue, 30 Jun 2020 00:18:37: 26000000 INFO @ Tue, 30 Jun 2020 00:18:38: 20000000 INFO @ Tue, 30 Jun 2020 00:18:40: 15000000 INFO @ Tue, 30 Jun 2020 00:18:40: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 00:18:40: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 00:18:40: #1 total tags in treatment: 12768664 INFO @ Tue, 30 Jun 2020 00:18:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:18:40: #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 00:18:41: #1 tags after filtering in treatment: 11563097 INFO @ Tue, 30 Jun 2020 00:18:41: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 30 Jun 2020 00:18:41: #1 finished! INFO @ Tue, 30 Jun 2020 00:18:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:18:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:18:41: #2 number of paired peaks: 21 WARNING @ Tue, 30 Jun 2020 00:18:41: Too few paired peaks (21) 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 00:18:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.05_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/SRX3632919/SRX3632919.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:18:44: 21000000 INFO @ Tue, 30 Jun 2020 00:18:46: 16000000 INFO @ Tue, 30 Jun 2020 00:18:50: 22000000 INFO @ Tue, 30 Jun 2020 00:18:52: 17000000 INFO @ Tue, 30 Jun 2020 00:18:56: 23000000 INFO @ Tue, 30 Jun 2020 00:18:57: 18000000 INFO @ Tue, 30 Jun 2020 00:19:02: 24000000 INFO @ Tue, 30 Jun 2020 00:19:03: 19000000 INFO @ Tue, 30 Jun 2020 00:19:08: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:19:09: 20000000 INFO @ Tue, 30 Jun 2020 00:19:14: 26000000 INFO @ Tue, 30 Jun 2020 00:19:15: 21000000 INFO @ Tue, 30 Jun 2020 00:19:17: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 00:19:17: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 00:19:17: #1 total tags in treatment: 12768664 INFO @ Tue, 30 Jun 2020 00:19:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:19:17: #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 00:19:17: #1 tags after filtering in treatment: 11563097 INFO @ Tue, 30 Jun 2020 00:19:17: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 30 Jun 2020 00:19:17: #1 finished! INFO @ Tue, 30 Jun 2020 00:19:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:19:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:19:18: #2 number of paired peaks: 21 WARNING @ Tue, 30 Jun 2020 00:19:18: Too few paired peaks (21) 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 00:19:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.10_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/SRX3632919/SRX3632919.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:19:21: 22000000 INFO @ Tue, 30 Jun 2020 00:19:26: 23000000 INFO @ Tue, 30 Jun 2020 00:19:32: 24000000 INFO @ Tue, 30 Jun 2020 00:19:37: 25000000 INFO @ Tue, 30 Jun 2020 00:19:43: 26000000 INFO @ Tue, 30 Jun 2020 00:19:46: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 00:19:46: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 00:19:46: #1 total tags in treatment: 12768664 INFO @ Tue, 30 Jun 2020 00:19:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:19:46: #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 00:19:46: #1 tags after filtering in treatment: 11563097 INFO @ Tue, 30 Jun 2020 00:19:46: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 30 Jun 2020 00:19:46: #1 finished! INFO @ Tue, 30 Jun 2020 00:19:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:19:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:19:47: #2 number of paired peaks: 21 WARNING @ Tue, 30 Jun 2020 00:19:47: Too few paired peaks (21) 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 00:19:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.20_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/SRX3632919/SRX3632919.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632919/SRX3632919.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。