Job ID = 6527986 SRX = SRX3632910 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:28:06 prefetch.2.10.7: 1) Downloading 'SRR6655555'... 2020-06-29T14:28:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:29:50 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:29:50 prefetch.2.10.7: 'SRR6655555' is valid 2020-06-29T14:29:50 prefetch.2.10.7: 1) 'SRR6655555' was downloaded successfully 2020-06-29T14:29:50 prefetch.2.10.7: 'SRR6655555' has 0 unresolved dependencies Read 4599383 spots for SRR6655555/SRR6655555.sra Written 4599383 spots for SRR6655555/SRR6655555.sra 2020-06-29T14:30:35 prefetch.2.10.7: 1) Downloading 'SRR6655556'... 2020-06-29T14:30:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:36:37 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:36:37 prefetch.2.10.7: 1) 'SRR6655556' was downloaded successfully 2020-06-29T14:36:37 prefetch.2.10.7: 'SRR6655556' has 0 unresolved dependencies Read 21754087 spots for SRR6655556/SRR6655556.sra Written 21754087 spots for SRR6655556/SRR6655556.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: 01:05:06 26353470 reads; of these: 26353470 (100.00%) were paired; of these: 6033808 (22.90%) aligned concordantly 0 times 15786412 (59.90%) aligned concordantly exactly 1 time 4533250 (17.20%) aligned concordantly >1 times ---- 6033808 pairs aligned concordantly 0 times; of these: 861000 (14.27%) aligned discordantly 1 time ---- 5172808 pairs aligned 0 times concordantly or discordantly; of these: 10345616 mates make up the pairs; of these: 8998439 (86.98%) aligned 0 times 745992 (7.21%) aligned exactly 1 time 601185 (5.81%) aligned >1 times 82.93% overall alignment rate Time searching: 01:05:06 Overall time: 01:05:06 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] 5631303 / 21068003 = 0.2673 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 01:12:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.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 01:12:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:12:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:13:05: 1000000 INFO @ Tue, 30 Jun 2020 01:13:11: 2000000 INFO @ Tue, 30 Jun 2020 01:13:16: 3000000 INFO @ Tue, 30 Jun 2020 01:13:22: 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 01:13:28: 5000000 INFO @ Tue, 30 Jun 2020 01:13:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.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 01:13:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:13:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:13:34: 6000000 INFO @ Tue, 30 Jun 2020 01:13:35: 1000000 INFO @ Tue, 30 Jun 2020 01:13:40: 7000000 INFO @ Tue, 30 Jun 2020 01:13:42: 2000000 INFO @ Tue, 30 Jun 2020 01:13:46: 8000000 INFO @ Tue, 30 Jun 2020 01:13:48: 3000000 INFO @ Tue, 30 Jun 2020 01:13:53: 9000000 INFO @ Tue, 30 Jun 2020 01:13:55: 4000000 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 01:13:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.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 01:13:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:13:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:14:00: 10000000 INFO @ Tue, 30 Jun 2020 01:14:02: 5000000 INFO @ Tue, 30 Jun 2020 01:14:07: 1000000 INFO @ Tue, 30 Jun 2020 01:14:07: 11000000 INFO @ Tue, 30 Jun 2020 01:14:09: 6000000 INFO @ Tue, 30 Jun 2020 01:14:14: 2000000 INFO @ Tue, 30 Jun 2020 01:14:14: 12000000 INFO @ Tue, 30 Jun 2020 01:14:16: 7000000 INFO @ Tue, 30 Jun 2020 01:14:21: 3000000 INFO @ Tue, 30 Jun 2020 01:14:21: 13000000 INFO @ Tue, 30 Jun 2020 01:14:23: 8000000 INFO @ Tue, 30 Jun 2020 01:14:28: 4000000 INFO @ Tue, 30 Jun 2020 01:14:28: 14000000 INFO @ Tue, 30 Jun 2020 01:14:30: 9000000 INFO @ Tue, 30 Jun 2020 01:14:35: 5000000 INFO @ Tue, 30 Jun 2020 01:14:35: 15000000 INFO @ Tue, 30 Jun 2020 01:14:37: 10000000 INFO @ Tue, 30 Jun 2020 01:14:42: 16000000 INFO @ Tue, 30 Jun 2020 01:14:42: 6000000 INFO @ Tue, 30 Jun 2020 01:14:44: 11000000 INFO @ Tue, 30 Jun 2020 01:14:49: 17000000 INFO @ Tue, 30 Jun 2020 01:14:49: 7000000 INFO @ Tue, 30 Jun 2020 01:14:51: 12000000 INFO @ Tue, 30 Jun 2020 01:14:56: 18000000 INFO @ Tue, 30 Jun 2020 01:14:56: 8000000 INFO @ Tue, 30 Jun 2020 01:14:58: 13000000 INFO @ Tue, 30 Jun 2020 01:15:03: 19000000 INFO @ Tue, 30 Jun 2020 01:15:03: 9000000 INFO @ Tue, 30 Jun 2020 01:15:05: 14000000 INFO @ Tue, 30 Jun 2020 01:15:10: 20000000 INFO @ Tue, 30 Jun 2020 01:15:10: 10000000 INFO @ Tue, 30 Jun 2020 01:15:12: 15000000 INFO @ Tue, 30 Jun 2020 01:15:17: 21000000 INFO @ Tue, 30 Jun 2020 01:15:17: 11000000 INFO @ Tue, 30 Jun 2020 01:15:19: 16000000 INFO @ Tue, 30 Jun 2020 01:15:24: 22000000 INFO @ Tue, 30 Jun 2020 01:15:24: 12000000 INFO @ Tue, 30 Jun 2020 01:15:26: 17000000 INFO @ Tue, 30 Jun 2020 01:15:31: 23000000 INFO @ Tue, 30 Jun 2020 01:15:31: 13000000 INFO @ Tue, 30 Jun 2020 01:15:32: 18000000 INFO @ Tue, 30 Jun 2020 01:15:38: 24000000 INFO @ Tue, 30 Jun 2020 01:15:38: 14000000 INFO @ Tue, 30 Jun 2020 01:15:39: 19000000 INFO @ Tue, 30 Jun 2020 01:15:45: 25000000 INFO @ Tue, 30 Jun 2020 01:15:45: 15000000 INFO @ Tue, 30 Jun 2020 01:15:46: 20000000 INFO @ Tue, 30 Jun 2020 01:15:52: 16000000 INFO @ Tue, 30 Jun 2020 01:15:53: 26000000 INFO @ Tue, 30 Jun 2020 01:15:53: 21000000 INFO @ Tue, 30 Jun 2020 01:15:59: 17000000 INFO @ Tue, 30 Jun 2020 01:16:00: 22000000 INFO @ Tue, 30 Jun 2020 01:16:00: 27000000 INFO @ Tue, 30 Jun 2020 01:16:06: 18000000 INFO @ Tue, 30 Jun 2020 01:16:07: 23000000 INFO @ Tue, 30 Jun 2020 01:16:08: 28000000 INFO @ Tue, 30 Jun 2020 01:16:12: 19000000 INFO @ Tue, 30 Jun 2020 01:16:14: 24000000 INFO @ Tue, 30 Jun 2020 01:16:15: 29000000 INFO @ Tue, 30 Jun 2020 01:16:19: 20000000 INFO @ Tue, 30 Jun 2020 01:16:21: 25000000 INFO @ Tue, 30 Jun 2020 01:16:23: 30000000 INFO @ Tue, 30 Jun 2020 01:16:26: 21000000 INFO @ Tue, 30 Jun 2020 01:16:28: 26000000 INFO @ Tue, 30 Jun 2020 01:16:30: 31000000 INFO @ Tue, 30 Jun 2020 01:16:33: 22000000 INFO @ Tue, 30 Jun 2020 01:16:36: 27000000 INFO @ Tue, 30 Jun 2020 01:16:38: 32000000 INFO @ Tue, 30 Jun 2020 01:16:40: 23000000 INFO @ Tue, 30 Jun 2020 01:16:41: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 01:16:41: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 01:16:41: #1 total tags in treatment: 14813381 INFO @ Tue, 30 Jun 2020 01:16:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:16:41: #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 01:16:42: #1 tags after filtering in treatment: 12991461 INFO @ Tue, 30 Jun 2020 01:16:42: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 30 Jun 2020 01:16:42: #1 finished! INFO @ Tue, 30 Jun 2020 01:16:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:16:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:16:42: #2 number of paired peaks: 50 WARNING @ Tue, 30 Jun 2020 01:16:43: Too few paired peaks (50) 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 01:16:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.05_peaks.narrowPeak: No such file or directory INFO @ Tue, 30 Jun 2020 01:16:43: 28000000 pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:16:46: 24000000 INFO @ Tue, 30 Jun 2020 01:16:49: 29000000 INFO @ Tue, 30 Jun 2020 01:16:52: 25000000 INFO @ Tue, 30 Jun 2020 01:16:56: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:16:59: 26000000 INFO @ Tue, 30 Jun 2020 01:17:02: 31000000 INFO @ Tue, 30 Jun 2020 01:17:05: 27000000 INFO @ Tue, 30 Jun 2020 01:17:09: 32000000 INFO @ Tue, 30 Jun 2020 01:17:12: 28000000 INFO @ Tue, 30 Jun 2020 01:17:12: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 01:17:12: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 01:17:12: #1 total tags in treatment: 14813381 INFO @ Tue, 30 Jun 2020 01:17:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:17:12: #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 01:17:12: #1 tags after filtering in treatment: 12991461 INFO @ Tue, 30 Jun 2020 01:17:12: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 30 Jun 2020 01:17:12: #1 finished! INFO @ Tue, 30 Jun 2020 01:17:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:17:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:17:13: #2 number of paired peaks: 50 WARNING @ Tue, 30 Jun 2020 01:17:13: Too few paired peaks (50) 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 01:17:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.10_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/SRX3632910/SRX3632910.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:17:17: 29000000 INFO @ Tue, 30 Jun 2020 01:17:23: 30000000 INFO @ Tue, 30 Jun 2020 01:17:29: 31000000 INFO @ Tue, 30 Jun 2020 01:17:35: 32000000 INFO @ Tue, 30 Jun 2020 01:17:37: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 01:17:37: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 01:17:37: #1 total tags in treatment: 14813381 INFO @ Tue, 30 Jun 2020 01:17:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:17:37: #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 01:17:38: #1 tags after filtering in treatment: 12991461 INFO @ Tue, 30 Jun 2020 01:17:38: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 30 Jun 2020 01:17:38: #1 finished! INFO @ Tue, 30 Jun 2020 01:17:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:17:39: #2 number of paired peaks: 50 WARNING @ Tue, 30 Jun 2020 01:17:39: Too few paired peaks (50) 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 01:17:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.20_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/SRX3632910/SRX3632910.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3632910/SRX3632910.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。