Job ID = 6528132 SRX = SRX474593 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T15:03:40 prefetch.2.10.7: 1) Downloading 'SRR1174446'... 2020-06-29T15:03:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:08:59 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:08:59 prefetch.2.10.7: 1) 'SRR1174446' was downloaded successfully 2020-06-29T15:08:59 prefetch.2.10.7: 'SRR1174446' has 0 unresolved dependencies Read 17772248 spots for SRR1174446/SRR1174446.sra Written 17772248 spots for SRR1174446/SRR1174446.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: 00:53:40 17772248 reads; of these: 17772248 (100.00%) were paired; of these: 1141268 (6.42%) aligned concordantly 0 times 11201372 (63.03%) aligned concordantly exactly 1 time 5429608 (30.55%) aligned concordantly >1 times ---- 1141268 pairs aligned concordantly 0 times; of these: 121002 (10.60%) aligned discordantly 1 time ---- 1020266 pairs aligned 0 times concordantly or discordantly; of these: 2040532 mates make up the pairs; of these: 1526611 (74.81%) aligned 0 times 342672 (16.79%) aligned exactly 1 time 171249 (8.39%) aligned >1 times 95.71% overall alignment rate Time searching: 00:53:40 Overall time: 00:53:40 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] 1553844 / 16716051 = 0.0930 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 01:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.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 01:26:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:26:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:02: 1000000 INFO @ Tue, 30 Jun 2020 01:27:11: 2000000 INFO @ Tue, 30 Jun 2020 01:27:19: 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 01:27:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.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 01:27:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:27:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:28: 4000000 INFO @ Tue, 30 Jun 2020 01:27:33: 1000000 INFO @ Tue, 30 Jun 2020 01:27:36: 5000000 INFO @ Tue, 30 Jun 2020 01:27:41: 2000000 INFO @ Tue, 30 Jun 2020 01:27:45: 6000000 INFO @ Tue, 30 Jun 2020 01:27:50: 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 01:27:53: 7000000 INFO @ Tue, 30 Jun 2020 01:27:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.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 01:27:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:27:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:58: 4000000 INFO @ Tue, 30 Jun 2020 01:28:02: 8000000 INFO @ Tue, 30 Jun 2020 01:28:02: 1000000 INFO @ Tue, 30 Jun 2020 01:28:07: 5000000 INFO @ Tue, 30 Jun 2020 01:28:10: 2000000 INFO @ Tue, 30 Jun 2020 01:28:11: 9000000 INFO @ Tue, 30 Jun 2020 01:28:16: 6000000 INFO @ Tue, 30 Jun 2020 01:28:18: 3000000 INFO @ Tue, 30 Jun 2020 01:28:19: 10000000 INFO @ Tue, 30 Jun 2020 01:28:25: 7000000 INFO @ Tue, 30 Jun 2020 01:28:27: 4000000 INFO @ Tue, 30 Jun 2020 01:28:28: 11000000 INFO @ Tue, 30 Jun 2020 01:28:34: 8000000 INFO @ Tue, 30 Jun 2020 01:28:35: 5000000 INFO @ Tue, 30 Jun 2020 01:28:37: 12000000 INFO @ Tue, 30 Jun 2020 01:28:43: 9000000 INFO @ Tue, 30 Jun 2020 01:28:43: 6000000 INFO @ Tue, 30 Jun 2020 01:28:46: 13000000 INFO @ Tue, 30 Jun 2020 01:28:51: 7000000 INFO @ Tue, 30 Jun 2020 01:28:51: 10000000 INFO @ Tue, 30 Jun 2020 01:28:54: 14000000 INFO @ Tue, 30 Jun 2020 01:28:58: 8000000 INFO @ Tue, 30 Jun 2020 01:29:00: 11000000 INFO @ Tue, 30 Jun 2020 01:29:03: 15000000 INFO @ Tue, 30 Jun 2020 01:29:06: 9000000 INFO @ Tue, 30 Jun 2020 01:29:09: 12000000 INFO @ Tue, 30 Jun 2020 01:29:11: 16000000 INFO @ Tue, 30 Jun 2020 01:29:13: 10000000 INFO @ Tue, 30 Jun 2020 01:29:17: 13000000 INFO @ Tue, 30 Jun 2020 01:29:20: 17000000 INFO @ Tue, 30 Jun 2020 01:29:20: 11000000 INFO @ Tue, 30 Jun 2020 01:29:26: 14000000 INFO @ Tue, 30 Jun 2020 01:29:27: 12000000 INFO @ Tue, 30 Jun 2020 01:29:28: 18000000 INFO @ Tue, 30 Jun 2020 01:29:34: 15000000 INFO @ Tue, 30 Jun 2020 01:29:35: 13000000 INFO @ Tue, 30 Jun 2020 01:29:37: 19000000 INFO @ Tue, 30 Jun 2020 01:29:42: 14000000 INFO @ Tue, 30 Jun 2020 01:29:43: 16000000 INFO @ Tue, 30 Jun 2020 01:29:45: 20000000 INFO @ Tue, 30 Jun 2020 01:29:49: 15000000 INFO @ Tue, 30 Jun 2020 01:29:51: 17000000 INFO @ Tue, 30 Jun 2020 01:29:54: 21000000 INFO @ Tue, 30 Jun 2020 01:29:56: 16000000 INFO @ Tue, 30 Jun 2020 01:29:59: 18000000 INFO @ Tue, 30 Jun 2020 01:30:02: 22000000 INFO @ Tue, 30 Jun 2020 01:30:03: 17000000 INFO @ Tue, 30 Jun 2020 01:30:07: 19000000 INFO @ Tue, 30 Jun 2020 01:30:10: 23000000 INFO @ Tue, 30 Jun 2020 01:30:10: 18000000 INFO @ Tue, 30 Jun 2020 01:30:15: 20000000 INFO @ Tue, 30 Jun 2020 01:30:18: 19000000 INFO @ Tue, 30 Jun 2020 01:30:18: 24000000 INFO @ Tue, 30 Jun 2020 01:30:23: 21000000 INFO @ Tue, 30 Jun 2020 01:30:25: 20000000 INFO @ Tue, 30 Jun 2020 01:30:26: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:30:31: 22000000 INFO @ Tue, 30 Jun 2020 01:30:33: 21000000 INFO @ Tue, 30 Jun 2020 01:30:34: 26000000 INFO @ Tue, 30 Jun 2020 01:30:39: 23000000 INFO @ Tue, 30 Jun 2020 01:30:41: 22000000 INFO @ Tue, 30 Jun 2020 01:30:42: 27000000 INFO @ Tue, 30 Jun 2020 01:30:47: 24000000 INFO @ Tue, 30 Jun 2020 01:30:48: 23000000 INFO @ Tue, 30 Jun 2020 01:30:49: 28000000 INFO @ Tue, 30 Jun 2020 01:30:54: 25000000 INFO @ Tue, 30 Jun 2020 01:30:55: 24000000 INFO @ Tue, 30 Jun 2020 01:30:57: 29000000 INFO @ Tue, 30 Jun 2020 01:31:02: 26000000 INFO @ Tue, 30 Jun 2020 01:31:02: 25000000 INFO @ Tue, 30 Jun 2020 01:31:04: 30000000 INFO @ Tue, 30 Jun 2020 01:31:10: 26000000 INFO @ Tue, 30 Jun 2020 01:31:10: 27000000 INFO @ Tue, 30 Jun 2020 01:31:11: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:31:11: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:31:11: #1 total tags in treatment: 15080075 INFO @ Tue, 30 Jun 2020 01:31:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:31:11: #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 01:31:12: #1 tags after filtering in treatment: 12979667 INFO @ Tue, 30 Jun 2020 01:31:12: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 30 Jun 2020 01:31:12: #1 finished! INFO @ Tue, 30 Jun 2020 01:31:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:31:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:31:13: #2 number of paired peaks: 85 WARNING @ Tue, 30 Jun 2020 01:31:13: Too few paired peaks (85) 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 01:31:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.05_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/SRX474593/SRX474593.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:31:17: 28000000 INFO @ Tue, 30 Jun 2020 01:31:17: 27000000 INFO @ Tue, 30 Jun 2020 01:31:24: 29000000 INFO @ Tue, 30 Jun 2020 01:31:25: 28000000 INFO @ Tue, 30 Jun 2020 01:31:31: 30000000 INFO @ Tue, 30 Jun 2020 01:31:32: 29000000 INFO @ Tue, 30 Jun 2020 01:31:38: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:31:38: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:31:38: #1 total tags in treatment: 15080075 INFO @ Tue, 30 Jun 2020 01:31:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:31:38: #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 01:31:38: #1 tags after filtering in treatment: 12979667 INFO @ Tue, 30 Jun 2020 01:31:38: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 30 Jun 2020 01:31:38: #1 finished! INFO @ Tue, 30 Jun 2020 01:31:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:31:39: #2 number of paired peaks: 85 WARNING @ Tue, 30 Jun 2020 01:31:39: Too few paired peaks (85) 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 01:31:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.10_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/SRX474593/SRX474593.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:31:39: 30000000 INFO @ Tue, 30 Jun 2020 01:31:45: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:31:45: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:31:45: #1 total tags in treatment: 15080075 INFO @ Tue, 30 Jun 2020 01:31:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:31:45: #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 01:31:45: #1 tags after filtering in treatment: 12979667 INFO @ Tue, 30 Jun 2020 01:31:45: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 30 Jun 2020 01:31:45: #1 finished! INFO @ Tue, 30 Jun 2020 01:31:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:31:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:31:46: #2 number of paired peaks: 85 WARNING @ Tue, 30 Jun 2020 01:31:46: Too few paired peaks (85) 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 01:31:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.20_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/SRX474593/SRX474593.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474593/SRX474593.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。