Job ID = 6528133 SRX = SRX474594 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:15:20 prefetch.2.10.7: 1) Downloading 'SRR1174447'... 2020-06-29T14:15:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:19:15 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:19:15 prefetch.2.10.7: 1) 'SRR1174447' was downloaded successfully 2020-06-29T14:19:15 prefetch.2.10.7: 'SRR1174447' has 0 unresolved dependencies Read 21772566 spots for SRR1174447/SRR1174447.sra Written 21772566 spots for SRR1174447/SRR1174447.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: 00:42:19 21772566 reads; of these: 21772566 (100.00%) were paired; of these: 2205939 (10.13%) aligned concordantly 0 times 14123200 (64.87%) aligned concordantly exactly 1 time 5443427 (25.00%) aligned concordantly >1 times ---- 2205939 pairs aligned concordantly 0 times; of these: 85175 (3.86%) aligned discordantly 1 time ---- 2120764 pairs aligned 0 times concordantly or discordantly; of these: 4241528 mates make up the pairs; of these: 3706590 (87.39%) aligned 0 times 381835 (9.00%) aligned exactly 1 time 153103 (3.61%) aligned >1 times 91.49% overall alignment rate Time searching: 00:42:19 Overall time: 00:42:19 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] 3874703 / 19629046 = 0.1974 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 00:26:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.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 00:26:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:26:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:26:57: 1000000 INFO @ Tue, 30 Jun 2020 00:27:02: 2000000 INFO @ Tue, 30 Jun 2020 00:27:08: 3000000 INFO @ Tue, 30 Jun 2020 00:27:14: 4000000 INFO @ Tue, 30 Jun 2020 00:27:19: 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 00:27:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.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 00:27:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:27:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:27:25: 6000000 INFO @ Tue, 30 Jun 2020 00:27:27: 1000000 INFO @ Tue, 30 Jun 2020 00:27:31: 7000000 INFO @ Tue, 30 Jun 2020 00:27:33: 2000000 INFO @ Tue, 30 Jun 2020 00:27:37: 8000000 INFO @ Tue, 30 Jun 2020 00:27:39: 3000000 INFO @ Tue, 30 Jun 2020 00:27:42: 9000000 INFO @ Tue, 30 Jun 2020 00:27:45: 4000000 INFO @ Tue, 30 Jun 2020 00:27:48: 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 00:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.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 00:27:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:27:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:27:51: 5000000 INFO @ Tue, 30 Jun 2020 00:27:54: 11000000 INFO @ Tue, 30 Jun 2020 00:27:57: 1000000 INFO @ Tue, 30 Jun 2020 00:27:57: 6000000 INFO @ Tue, 30 Jun 2020 00:28:00: 12000000 INFO @ Tue, 30 Jun 2020 00:28:03: 2000000 INFO @ Tue, 30 Jun 2020 00:28:03: 7000000 INFO @ Tue, 30 Jun 2020 00:28:06: 13000000 INFO @ Tue, 30 Jun 2020 00:28:09: 3000000 INFO @ Tue, 30 Jun 2020 00:28:10: 8000000 INFO @ Tue, 30 Jun 2020 00:28:12: 14000000 INFO @ Tue, 30 Jun 2020 00:28:15: 4000000 INFO @ Tue, 30 Jun 2020 00:28:16: 9000000 INFO @ Tue, 30 Jun 2020 00:28:18: 15000000 INFO @ Tue, 30 Jun 2020 00:28:21: 5000000 INFO @ Tue, 30 Jun 2020 00:28:22: 10000000 INFO @ Tue, 30 Jun 2020 00:28:24: 16000000 INFO @ Tue, 30 Jun 2020 00:28:27: 6000000 INFO @ Tue, 30 Jun 2020 00:28:28: 11000000 INFO @ Tue, 30 Jun 2020 00:28:30: 17000000 INFO @ Tue, 30 Jun 2020 00:28:33: 7000000 INFO @ Tue, 30 Jun 2020 00:28:34: 12000000 INFO @ Tue, 30 Jun 2020 00:28:36: 18000000 INFO @ Tue, 30 Jun 2020 00:28:38: 8000000 INFO @ Tue, 30 Jun 2020 00:28:40: 13000000 INFO @ Tue, 30 Jun 2020 00:28:42: 19000000 INFO @ Tue, 30 Jun 2020 00:28:44: 9000000 INFO @ Tue, 30 Jun 2020 00:28:46: 14000000 INFO @ Tue, 30 Jun 2020 00:28:48: 20000000 INFO @ Tue, 30 Jun 2020 00:28:50: 10000000 INFO @ Tue, 30 Jun 2020 00:28:52: 15000000 INFO @ Tue, 30 Jun 2020 00:28:54: 21000000 INFO @ Tue, 30 Jun 2020 00:28:56: 11000000 INFO @ Tue, 30 Jun 2020 00:28:58: 16000000 INFO @ Tue, 30 Jun 2020 00:29:00: 22000000 INFO @ Tue, 30 Jun 2020 00:29:02: 12000000 INFO @ Tue, 30 Jun 2020 00:29:04: 17000000 INFO @ Tue, 30 Jun 2020 00:29:06: 23000000 INFO @ Tue, 30 Jun 2020 00:29:07: 13000000 INFO @ Tue, 30 Jun 2020 00:29:10: 18000000 INFO @ Tue, 30 Jun 2020 00:29:12: 24000000 INFO @ Tue, 30 Jun 2020 00:29:13: 14000000 INFO @ Tue, 30 Jun 2020 00:29:16: 19000000 INFO @ Tue, 30 Jun 2020 00:29:17: 25000000 INFO @ Tue, 30 Jun 2020 00:29:19: 15000000 INFO @ Tue, 30 Jun 2020 00:29:22: 20000000 INFO @ Tue, 30 Jun 2020 00:29:23: 26000000 INFO @ Tue, 30 Jun 2020 00:29:25: 16000000 INFO @ Tue, 30 Jun 2020 00:29:28: 21000000 INFO @ Tue, 30 Jun 2020 00:29:29: 27000000 INFO @ Tue, 30 Jun 2020 00:29:31: 17000000 INFO @ Tue, 30 Jun 2020 00:29:34: 22000000 INFO @ Tue, 30 Jun 2020 00:29:35: 28000000 INFO @ Tue, 30 Jun 2020 00:29:37: 18000000 INFO @ Tue, 30 Jun 2020 00:29:40: 23000000 INFO @ Tue, 30 Jun 2020 00:29:41: 29000000 INFO @ Tue, 30 Jun 2020 00:29:43: 19000000 INFO @ Tue, 30 Jun 2020 00:29:47: 24000000 INFO @ Tue, 30 Jun 2020 00:29:47: 30000000 INFO @ Tue, 30 Jun 2020 00:29:49: 20000000 INFO @ Tue, 30 Jun 2020 00:29:53: 25000000 INFO @ Tue, 30 Jun 2020 00:29:53: 31000000 INFO @ Tue, 30 Jun 2020 00:29:55: 21000000 INFO @ Tue, 30 Jun 2020 00:29:59: 26000000 INFO @ Tue, 30 Jun 2020 00:29:59: 32000000 INFO @ Tue, 30 Jun 2020 00:30:00: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:30:00: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:30:00: #1 total tags in treatment: 15700224 INFO @ Tue, 30 Jun 2020 00:30:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:30:00: #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 00:30:00: #1 tags after filtering in treatment: 13716846 INFO @ Tue, 30 Jun 2020 00:30:00: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 30 Jun 2020 00:30:00: #1 finished! INFO @ Tue, 30 Jun 2020 00:30:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:30:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:30:01: 22000000 INFO @ Tue, 30 Jun 2020 00:30:01: #2 number of paired peaks: 65 WARNING @ Tue, 30 Jun 2020 00:30:01: Too few paired peaks (65) 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 00:30:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.05_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/SRX474594/SRX474594.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:30:05: 27000000 INFO @ Tue, 30 Jun 2020 00:30:07: 23000000 INFO @ Tue, 30 Jun 2020 00:30:11: 28000000 INFO @ Tue, 30 Jun 2020 00:30:13: 24000000 INFO @ Tue, 30 Jun 2020 00:30:17: 29000000 INFO @ Tue, 30 Jun 2020 00:30:18: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:30:23: 30000000 INFO @ Tue, 30 Jun 2020 00:30:24: 26000000 INFO @ Tue, 30 Jun 2020 00:30:30: 31000000 INFO @ Tue, 30 Jun 2020 00:30:30: 27000000 INFO @ Tue, 30 Jun 2020 00:30:35: 32000000 INFO @ Tue, 30 Jun 2020 00:30:36: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:30:36: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:30:36: #1 total tags in treatment: 15700224 INFO @ Tue, 30 Jun 2020 00:30:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:30:36: #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 00:30:36: 28000000 INFO @ Tue, 30 Jun 2020 00:30:36: #1 tags after filtering in treatment: 13716846 INFO @ Tue, 30 Jun 2020 00:30:36: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 30 Jun 2020 00:30:36: #1 finished! INFO @ Tue, 30 Jun 2020 00:30:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:30:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:30:37: #2 number of paired peaks: 65 WARNING @ Tue, 30 Jun 2020 00:30:37: Too few paired peaks (65) 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 00:30:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.10_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/SRX474594/SRX474594.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:30:42: 29000000 INFO @ Tue, 30 Jun 2020 00:30:48: 30000000 INFO @ Tue, 30 Jun 2020 00:30:53: 31000000 INFO @ Tue, 30 Jun 2020 00:30:59: 32000000 INFO @ Tue, 30 Jun 2020 00:30:59: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:30:59: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:30:59: #1 total tags in treatment: 15700224 INFO @ Tue, 30 Jun 2020 00:30:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:30:59: #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 00:31:00: #1 tags after filtering in treatment: 13716846 INFO @ Tue, 30 Jun 2020 00:31:00: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 30 Jun 2020 00:31:00: #1 finished! INFO @ Tue, 30 Jun 2020 00:31:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:31:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:31:01: #2 number of paired peaks: 65 WARNING @ Tue, 30 Jun 2020 00:31:01: Too few paired peaks (65) 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 00:31:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.20_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/SRX474594/SRX474594.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474594/SRX474594.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。