Job ID = 6528145 SRX = SRX474611 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:26:06 prefetch.2.10.7: 1) Downloading 'SRR1174464'... 2020-06-29T14:26:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:31:17 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:31:17 prefetch.2.10.7: 1) 'SRR1174464' was downloaded successfully 2020-06-29T14:31:17 prefetch.2.10.7: 'SRR1174464' has 0 unresolved dependencies Read 15264105 spots for SRR1174464/SRR1174464.sra Written 15264105 spots for SRR1174464/SRR1174464.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: 00:31:02 15264105 reads; of these: 15264105 (100.00%) were paired; of these: 1278925 (8.38%) aligned concordantly 0 times 9735081 (63.78%) aligned concordantly exactly 1 time 4250099 (27.84%) aligned concordantly >1 times ---- 1278925 pairs aligned concordantly 0 times; of these: 76057 (5.95%) aligned discordantly 1 time ---- 1202868 pairs aligned 0 times concordantly or discordantly; of these: 2405736 mates make up the pairs; of these: 1966540 (81.74%) aligned 0 times 298216 (12.40%) aligned exactly 1 time 140980 (5.86%) aligned >1 times 93.56% overall alignment rate Time searching: 00:31:02 Overall time: 00:31:02 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] 1043015 / 14037189 = 0.0743 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 00:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.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 00:19:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:19:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:19:44: 1000000 INFO @ Tue, 30 Jun 2020 00:19:49: 2000000 INFO @ Tue, 30 Jun 2020 00:19:54: 3000000 INFO @ Tue, 30 Jun 2020 00:19:58: 4000000 INFO @ Tue, 30 Jun 2020 00:20:03: 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 00:20:08: 6000000 INFO @ Tue, 30 Jun 2020 00:20:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.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 00:20:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:20:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:20:13: 7000000 INFO @ Tue, 30 Jun 2020 00:20:15: 1000000 INFO @ Tue, 30 Jun 2020 00:20:18: 8000000 INFO @ Tue, 30 Jun 2020 00:20:20: 2000000 INFO @ Tue, 30 Jun 2020 00:20:22: 9000000 INFO @ Tue, 30 Jun 2020 00:20:26: 3000000 INFO @ Tue, 30 Jun 2020 00:20:27: 10000000 INFO @ Tue, 30 Jun 2020 00:20:31: 4000000 INFO @ Tue, 30 Jun 2020 00:20:32: 11000000 INFO @ Tue, 30 Jun 2020 00:20:37: 5000000 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 00:20:37: 12000000 INFO @ Tue, 30 Jun 2020 00:20:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.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 00:20:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:20:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:20:42: 13000000 INFO @ Tue, 30 Jun 2020 00:20:43: 6000000 INFO @ Tue, 30 Jun 2020 00:20:44: 1000000 INFO @ Tue, 30 Jun 2020 00:20:47: 14000000 INFO @ Tue, 30 Jun 2020 00:20:48: 7000000 INFO @ Tue, 30 Jun 2020 00:20:49: 2000000 INFO @ Tue, 30 Jun 2020 00:20:53: 15000000 INFO @ Tue, 30 Jun 2020 00:20:54: 8000000 INFO @ Tue, 30 Jun 2020 00:20:54: 3000000 INFO @ Tue, 30 Jun 2020 00:20:58: 16000000 INFO @ Tue, 30 Jun 2020 00:20:59: 4000000 INFO @ Tue, 30 Jun 2020 00:21:00: 9000000 INFO @ Tue, 30 Jun 2020 00:21:03: 17000000 INFO @ Tue, 30 Jun 2020 00:21:05: 5000000 INFO @ Tue, 30 Jun 2020 00:21:05: 10000000 INFO @ Tue, 30 Jun 2020 00:21:08: 18000000 INFO @ Tue, 30 Jun 2020 00:21:10: 6000000 INFO @ Tue, 30 Jun 2020 00:21:11: 11000000 INFO @ Tue, 30 Jun 2020 00:21:13: 19000000 INFO @ Tue, 30 Jun 2020 00:21:15: 7000000 INFO @ Tue, 30 Jun 2020 00:21:16: 12000000 INFO @ Tue, 30 Jun 2020 00:21:18: 20000000 INFO @ Tue, 30 Jun 2020 00:21:20: 8000000 INFO @ Tue, 30 Jun 2020 00:21:22: 13000000 INFO @ Tue, 30 Jun 2020 00:21:23: 21000000 INFO @ Tue, 30 Jun 2020 00:21:25: 9000000 INFO @ Tue, 30 Jun 2020 00:21:28: 14000000 INFO @ Tue, 30 Jun 2020 00:21:28: 22000000 INFO @ Tue, 30 Jun 2020 00:21:31: 10000000 INFO @ Tue, 30 Jun 2020 00:21:33: 23000000 INFO @ Tue, 30 Jun 2020 00:21:33: 15000000 INFO @ Tue, 30 Jun 2020 00:21:36: 11000000 INFO @ Tue, 30 Jun 2020 00:21:38: 24000000 INFO @ Tue, 30 Jun 2020 00:21:39: 16000000 INFO @ Tue, 30 Jun 2020 00:21:41: 12000000 INFO @ Tue, 30 Jun 2020 00:21:43: 25000000 INFO @ Tue, 30 Jun 2020 00:21:44: 17000000 INFO @ Tue, 30 Jun 2020 00:21:47: 13000000 INFO @ Tue, 30 Jun 2020 00:21:48: 26000000 INFO @ Tue, 30 Jun 2020 00:21:50: 18000000 INFO @ Tue, 30 Jun 2020 00:21:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:21:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:21:50: #1 total tags in treatment: 12943759 INFO @ Tue, 30 Jun 2020 00:21:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:21:50: #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 00:21:51: #1 tags after filtering in treatment: 11402613 INFO @ Tue, 30 Jun 2020 00:21:51: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 30 Jun 2020 00:21:51: #1 finished! INFO @ Tue, 30 Jun 2020 00:21:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:21:51: #2 number of paired peaks: 55 WARNING @ Tue, 30 Jun 2020 00:21:51: Too few paired peaks (55) 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 00:21:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.05_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/SRX474611/SRX474611.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:21:52: 14000000 INFO @ Tue, 30 Jun 2020 00:21:56: 19000000 INFO @ Tue, 30 Jun 2020 00:21:57: 15000000 INFO @ Tue, 30 Jun 2020 00:22:01: 20000000 INFO @ Tue, 30 Jun 2020 00:22:02: 16000000 INFO @ Tue, 30 Jun 2020 00:22:06: 21000000 INFO @ Tue, 30 Jun 2020 00:22:07: 17000000 INFO @ Tue, 30 Jun 2020 00:22:12: 22000000 INFO @ Tue, 30 Jun 2020 00:22:12: 18000000 INFO @ Tue, 30 Jun 2020 00:22:17: 19000000 INFO @ Tue, 30 Jun 2020 00:22:17: 23000000 INFO @ Tue, 30 Jun 2020 00:22:22: 20000000 INFO @ Tue, 30 Jun 2020 00:22:23: 24000000 INFO @ Tue, 30 Jun 2020 00:22:27: 21000000 INFO @ Tue, 30 Jun 2020 00:22:28: 25000000 INFO @ Tue, 30 Jun 2020 00:22:32: 22000000 INFO @ Tue, 30 Jun 2020 00:22:33: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:22:36: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:22:36: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:22:36: #1 total tags in treatment: 12943759 INFO @ Tue, 30 Jun 2020 00:22:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:22:36: #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 00:22:36: #1 tags after filtering in treatment: 11402613 INFO @ Tue, 30 Jun 2020 00:22:36: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 30 Jun 2020 00:22:36: #1 finished! INFO @ Tue, 30 Jun 2020 00:22:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:22:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:22:37: 23000000 INFO @ Tue, 30 Jun 2020 00:22:37: #2 number of paired peaks: 55 WARNING @ Tue, 30 Jun 2020 00:22:37: Too few paired peaks (55) 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 00:22:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.10_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/SRX474611/SRX474611.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:22:41: 24000000 INFO @ Tue, 30 Jun 2020 00:22:46: 25000000 INFO @ Tue, 30 Jun 2020 00:22:51: 26000000 INFO @ Tue, 30 Jun 2020 00:22:53: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:22:53: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:22:53: #1 total tags in treatment: 12943759 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 00:22:54: #1 tags after filtering in treatment: 11402613 INFO @ Tue, 30 Jun 2020 00:22:54: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 30 Jun 2020 00:22:54: #1 finished! INFO @ Tue, 30 Jun 2020 00:22:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:22:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:22:54: #2 number of paired peaks: 55 WARNING @ Tue, 30 Jun 2020 00:22:54: Too few paired peaks (55) 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/SRX474611/SRX474611.20_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/SRX474611/SRX474611.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474611/SRX474611.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。