Job ID = 6527757 SRX = SRX2659833 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T13:26:48 prefetch.2.10.7: 1) Downloading 'SRR5364406'... 2020-06-29T13:26:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:35:26 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:35:26 prefetch.2.10.7: 1) 'SRR5364406' was downloaded successfully 2020-06-29T13:35:27 prefetch.2.10.7: 'SRR5364406' has 0 unresolved dependencies Read 36338650 spots for SRR5364406/SRR5364406.sra Written 36338650 spots for SRR5364406/SRR5364406.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: 01:09:07 36338650 reads; of these: 36338650 (100.00%) were paired; of these: 18688664 (51.43%) aligned concordantly 0 times 12176576 (33.51%) aligned concordantly exactly 1 time 5473410 (15.06%) aligned concordantly >1 times ---- 18688664 pairs aligned concordantly 0 times; of these: 1675164 (8.96%) aligned discordantly 1 time ---- 17013500 pairs aligned 0 times concordantly or discordantly; of these: 34027000 mates make up the pairs; of these: 31012537 (91.14%) aligned 0 times 1339851 (3.94%) aligned exactly 1 time 1674612 (4.92%) aligned >1 times 57.33% overall alignment rate Time searching: 01:09:07 Overall time: 01:09:07 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 20 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] 4176402 / 18841694 = 0.2217 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 00:23:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.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 00:23:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:23:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:23:18: 1000000 INFO @ Tue, 30 Jun 2020 00:23:25: 2000000 INFO @ Tue, 30 Jun 2020 00:23:31: 3000000 INFO @ Tue, 30 Jun 2020 00:23:37: 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 @ Tue, 30 Jun 2020 00:23:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.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 00:23:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:23:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:23:44: 5000000 INFO @ Tue, 30 Jun 2020 00:23:50: 1000000 INFO @ Tue, 30 Jun 2020 00:23:52: 6000000 INFO @ Tue, 30 Jun 2020 00:23:59: 2000000 INFO @ Tue, 30 Jun 2020 00:24:00: 7000000 INFO @ Tue, 30 Jun 2020 00:24:07: 3000000 INFO @ Tue, 30 Jun 2020 00:24:08: 8000000 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 00:24:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.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 00:24:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:24:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:24:15: 4000000 INFO @ Tue, 30 Jun 2020 00:24:16: 9000000 INFO @ Tue, 30 Jun 2020 00:24:20: 1000000 INFO @ Tue, 30 Jun 2020 00:24:23: 5000000 INFO @ Tue, 30 Jun 2020 00:24:25: 10000000 INFO @ Tue, 30 Jun 2020 00:24:28: 2000000 INFO @ Tue, 30 Jun 2020 00:24:31: 6000000 INFO @ Tue, 30 Jun 2020 00:24:32: 11000000 INFO @ Tue, 30 Jun 2020 00:24:36: 3000000 INFO @ Tue, 30 Jun 2020 00:24:40: 7000000 INFO @ Tue, 30 Jun 2020 00:24:40: 12000000 INFO @ Tue, 30 Jun 2020 00:24:45: 4000000 INFO @ Tue, 30 Jun 2020 00:24:47: 8000000 INFO @ Tue, 30 Jun 2020 00:24:48: 13000000 INFO @ Tue, 30 Jun 2020 00:24:53: 5000000 INFO @ Tue, 30 Jun 2020 00:24:56: 9000000 INFO @ Tue, 30 Jun 2020 00:24:56: 14000000 INFO @ Tue, 30 Jun 2020 00:25:01: 6000000 INFO @ Tue, 30 Jun 2020 00:25:04: 10000000 INFO @ Tue, 30 Jun 2020 00:25:04: 15000000 INFO @ Tue, 30 Jun 2020 00:25:10: 7000000 INFO @ Tue, 30 Jun 2020 00:25:12: 11000000 INFO @ Tue, 30 Jun 2020 00:25:12: 16000000 INFO @ Tue, 30 Jun 2020 00:25:18: 8000000 INFO @ Tue, 30 Jun 2020 00:25:19: 17000000 INFO @ Tue, 30 Jun 2020 00:25:20: 12000000 INFO @ Tue, 30 Jun 2020 00:25:26: 9000000 INFO @ Tue, 30 Jun 2020 00:25:28: 18000000 INFO @ Tue, 30 Jun 2020 00:25:28: 13000000 INFO @ Tue, 30 Jun 2020 00:25:34: 10000000 INFO @ Tue, 30 Jun 2020 00:25:35: 19000000 INFO @ Tue, 30 Jun 2020 00:25:36: 14000000 INFO @ Tue, 30 Jun 2020 00:25:42: 11000000 INFO @ Tue, 30 Jun 2020 00:25:43: 20000000 INFO @ Tue, 30 Jun 2020 00:25:44: 15000000 INFO @ Tue, 30 Jun 2020 00:25:51: 12000000 INFO @ Tue, 30 Jun 2020 00:25:51: 21000000 INFO @ Tue, 30 Jun 2020 00:25:52: 16000000 INFO @ Tue, 30 Jun 2020 00:25:59: 13000000 INFO @ Tue, 30 Jun 2020 00:26:00: 22000000 INFO @ Tue, 30 Jun 2020 00:26:01: 17000000 INFO @ Tue, 30 Jun 2020 00:26:07: 14000000 INFO @ Tue, 30 Jun 2020 00:26:08: 23000000 INFO @ Tue, 30 Jun 2020 00:26:09: 18000000 INFO @ Tue, 30 Jun 2020 00:26:15: 24000000 INFO @ Tue, 30 Jun 2020 00:26:16: 15000000 INFO @ Tue, 30 Jun 2020 00:26:17: 19000000 INFO @ Tue, 30 Jun 2020 00:26:23: 25000000 INFO @ Tue, 30 Jun 2020 00:26:24: 16000000 INFO @ Tue, 30 Jun 2020 00:26:25: 20000000 INFO @ Tue, 30 Jun 2020 00:26:32: 26000000 INFO @ Tue, 30 Jun 2020 00:26:32: 17000000 INFO @ Tue, 30 Jun 2020 00:26:34: 21000000 INFO @ Tue, 30 Jun 2020 00:26:40: 27000000 INFO @ Tue, 30 Jun 2020 00:26:41: 18000000 INFO @ Tue, 30 Jun 2020 00:26:42: 22000000 INFO @ Tue, 30 Jun 2020 00:26:48: 28000000 INFO @ Tue, 30 Jun 2020 00:26:49: 19000000 INFO @ Tue, 30 Jun 2020 00:26:50: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:26:56: 29000000 INFO @ Tue, 30 Jun 2020 00:26:57: 20000000 INFO @ Tue, 30 Jun 2020 00:26:59: 24000000 INFO @ Tue, 30 Jun 2020 00:27:03: 30000000 INFO @ Tue, 30 Jun 2020 00:27:05: 21000000 INFO @ Tue, 30 Jun 2020 00:27:07: 25000000 INFO @ Tue, 30 Jun 2020 00:27:11: 31000000 INFO @ Tue, 30 Jun 2020 00:27:13: 22000000 INFO @ Tue, 30 Jun 2020 00:27:16: 26000000 INFO @ Tue, 30 Jun 2020 00:27:19: 32000000 INFO @ Tue, 30 Jun 2020 00:27:22: 23000000 INFO @ Tue, 30 Jun 2020 00:27:24: 27000000 INFO @ Tue, 30 Jun 2020 00:27:27: 33000000 INFO @ Tue, 30 Jun 2020 00:27:30: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 00:27:30: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 00:27:30: #1 total tags in treatment: 13855711 INFO @ Tue, 30 Jun 2020 00:27:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:27:30: #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 00:27:30: #1 tags after filtering in treatment: 12748415 INFO @ Tue, 30 Jun 2020 00:27:30: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 30 Jun 2020 00:27:30: #1 finished! INFO @ Tue, 30 Jun 2020 00:27:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:27:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:27:30: 24000000 INFO @ Tue, 30 Jun 2020 00:27:31: #2 number of paired peaks: 36 WARNING @ Tue, 30 Jun 2020 00:27:31: Too few paired peaks (36) 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 00:27:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.05_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/SRX2659833/SRX2659833.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:27:33: 28000000 INFO @ Tue, 30 Jun 2020 00:27:38: 25000000 INFO @ Tue, 30 Jun 2020 00:27:41: 29000000 INFO @ Tue, 30 Jun 2020 00:27:47: 26000000 INFO @ Tue, 30 Jun 2020 00:27:49: 30000000 INFO @ Tue, 30 Jun 2020 00:27:55: 27000000 INFO @ Tue, 30 Jun 2020 00:27:58: 31000000 INFO @ Tue, 30 Jun 2020 00:28:04: 28000000 INFO @ Tue, 30 Jun 2020 00:28:06: 32000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:28:12: 29000000 INFO @ Tue, 30 Jun 2020 00:28:14: 33000000 INFO @ Tue, 30 Jun 2020 00:28:16: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 00:28:16: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 00:28:16: #1 total tags in treatment: 13855711 INFO @ Tue, 30 Jun 2020 00:28:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:28:16: #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 00:28:17: #1 tags after filtering in treatment: 12748415 INFO @ Tue, 30 Jun 2020 00:28:17: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 30 Jun 2020 00:28:17: #1 finished! INFO @ Tue, 30 Jun 2020 00:28:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:28:18: #2 number of paired peaks: 36 WARNING @ Tue, 30 Jun 2020 00:28:18: Too few paired peaks (36) 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 00:28:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.10_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/SRX2659833/SRX2659833.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:28:20: 30000000 INFO @ Tue, 30 Jun 2020 00:28:27: 31000000 INFO @ Tue, 30 Jun 2020 00:28:34: 32000000 INFO @ Tue, 30 Jun 2020 00:28:41: 33000000 INFO @ Tue, 30 Jun 2020 00:28:44: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 00:28:44: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 00:28:44: #1 total tags in treatment: 13855711 INFO @ Tue, 30 Jun 2020 00:28:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:28:44: #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 00:28:44: #1 tags after filtering in treatment: 12748415 INFO @ Tue, 30 Jun 2020 00:28:44: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 30 Jun 2020 00:28:44: #1 finished! INFO @ Tue, 30 Jun 2020 00:28:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:28:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:28:45: #2 number of paired peaks: 36 WARNING @ Tue, 30 Jun 2020 00:28:45: Too few paired peaks (36) 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 00:28:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.20_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/SRX2659833/SRX2659833.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2659833/SRX2659833.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling