Job ID = 6528141 SRX = SRX474599 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:36:36 prefetch.2.10.7: 1) Downloading 'SRR1174452'... 2020-06-29T14:36:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:40:40 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:40:40 prefetch.2.10.7: 1) 'SRR1174452' was downloaded successfully 2020-06-29T14:40:40 prefetch.2.10.7: 'SRR1174452' has 0 unresolved dependencies Read 13328170 spots for SRR1174452/SRR1174452.sra Written 13328170 spots for SRR1174452/SRR1174452.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:29:23 13328170 reads; of these: 13328170 (100.00%) were paired; of these: 788438 (5.92%) aligned concordantly 0 times 8588829 (64.44%) aligned concordantly exactly 1 time 3950903 (29.64%) aligned concordantly >1 times ---- 788438 pairs aligned concordantly 0 times; of these: 71268 (9.04%) aligned discordantly 1 time ---- 717170 pairs aligned 0 times concordantly or discordantly; of these: 1434340 mates make up the pairs; of these: 1035873 (72.22%) aligned 0 times 268797 (18.74%) aligned exactly 1 time 129670 (9.04%) aligned >1 times 96.11% overall alignment rate Time searching: 00:29:24 Overall time: 00:29:24 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] 944236 / 12583864 = 0.0750 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 00:25:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.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 00:25:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:25:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:25:51: 1000000 INFO @ Tue, 30 Jun 2020 00:25:58: 2000000 INFO @ Tue, 30 Jun 2020 00:26:05: 3000000 INFO @ Tue, 30 Jun 2020 00:26:11: 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 00:26:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.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 00:26:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:26:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:26:19: 5000000 INFO @ Tue, 30 Jun 2020 00:26:22: 1000000 INFO @ Tue, 30 Jun 2020 00:26:27: 6000000 INFO @ Tue, 30 Jun 2020 00:26:30: 2000000 INFO @ Tue, 30 Jun 2020 00:26:35: 7000000 INFO @ Tue, 30 Jun 2020 00:26:38: 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 00:26:42: 8000000 INFO @ Tue, 30 Jun 2020 00:26:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.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 00:26:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:26:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:26:46: 4000000 INFO @ Tue, 30 Jun 2020 00:26:50: 9000000 INFO @ Tue, 30 Jun 2020 00:26:52: 1000000 INFO @ Tue, 30 Jun 2020 00:26:54: 5000000 INFO @ Tue, 30 Jun 2020 00:26:57: 10000000 INFO @ Tue, 30 Jun 2020 00:26:59: 2000000 INFO @ Tue, 30 Jun 2020 00:27:02: 6000000 INFO @ Tue, 30 Jun 2020 00:27:05: 11000000 INFO @ Tue, 30 Jun 2020 00:27:07: 3000000 INFO @ Tue, 30 Jun 2020 00:27:10: 7000000 INFO @ Tue, 30 Jun 2020 00:27:12: 12000000 INFO @ Tue, 30 Jun 2020 00:27:15: 4000000 INFO @ Tue, 30 Jun 2020 00:27:18: 8000000 INFO @ Tue, 30 Jun 2020 00:27:20: 13000000 INFO @ Tue, 30 Jun 2020 00:27:23: 5000000 INFO @ Tue, 30 Jun 2020 00:27:26: 9000000 INFO @ Tue, 30 Jun 2020 00:27:28: 14000000 INFO @ Tue, 30 Jun 2020 00:27:31: 6000000 INFO @ Tue, 30 Jun 2020 00:27:34: 10000000 INFO @ Tue, 30 Jun 2020 00:27:35: 15000000 INFO @ Tue, 30 Jun 2020 00:27:39: 7000000 INFO @ Tue, 30 Jun 2020 00:27:42: 11000000 INFO @ Tue, 30 Jun 2020 00:27:43: 16000000 INFO @ Tue, 30 Jun 2020 00:27:47: 8000000 INFO @ Tue, 30 Jun 2020 00:27:50: 12000000 INFO @ Tue, 30 Jun 2020 00:27:51: 17000000 INFO @ Tue, 30 Jun 2020 00:27:55: 9000000 INFO @ Tue, 30 Jun 2020 00:27:58: 13000000 INFO @ Tue, 30 Jun 2020 00:27:58: 18000000 INFO @ Tue, 30 Jun 2020 00:28:03: 10000000 INFO @ Tue, 30 Jun 2020 00:28:06: 14000000 INFO @ Tue, 30 Jun 2020 00:28:06: 19000000 INFO @ Tue, 30 Jun 2020 00:28:11: 11000000 INFO @ Tue, 30 Jun 2020 00:28:14: 20000000 INFO @ Tue, 30 Jun 2020 00:28:14: 15000000 INFO @ Tue, 30 Jun 2020 00:28:19: 12000000 INFO @ Tue, 30 Jun 2020 00:28:22: 21000000 INFO @ Tue, 30 Jun 2020 00:28:22: 16000000 INFO @ Tue, 30 Jun 2020 00:28:27: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:28:29: 22000000 INFO @ Tue, 30 Jun 2020 00:28:30: 17000000 INFO @ Tue, 30 Jun 2020 00:28:35: 14000000 INFO @ Tue, 30 Jun 2020 00:28:37: 23000000 INFO @ Tue, 30 Jun 2020 00:28:39: 18000000 INFO @ Tue, 30 Jun 2020 00:28:42: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:28:42: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:28:42: #1 total tags in treatment: 11596538 INFO @ Tue, 30 Jun 2020 00:28:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:28:42: #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 00:28:43: #1 tags after filtering in treatment: 10274260 INFO @ Tue, 30 Jun 2020 00:28:43: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 30 Jun 2020 00:28:43: #1 finished! INFO @ Tue, 30 Jun 2020 00:28:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:28:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:28:43: 15000000 INFO @ Tue, 30 Jun 2020 00:28:43: #2 number of paired peaks: 91 WARNING @ Tue, 30 Jun 2020 00:28:43: Too few paired peaks (91) 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 00:28:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.05_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/SRX474599/SRX474599.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:28:46: 19000000 INFO @ Tue, 30 Jun 2020 00:28:50: 16000000 INFO @ Tue, 30 Jun 2020 00:28:54: 20000000 INFO @ Tue, 30 Jun 2020 00:28:58: 17000000 INFO @ Tue, 30 Jun 2020 00:29:02: 21000000 INFO @ Tue, 30 Jun 2020 00:29:06: 18000000 INFO @ Tue, 30 Jun 2020 00:29:10: 22000000 INFO @ Tue, 30 Jun 2020 00:29:14: 19000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:29:17: 23000000 INFO @ Tue, 30 Jun 2020 00:29:21: 20000000 INFO @ Tue, 30 Jun 2020 00:29:23: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:29:23: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:29:23: #1 total tags in treatment: 11596538 INFO @ Tue, 30 Jun 2020 00:29:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:29:23: #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 00:29:23: #1 tags after filtering in treatment: 10274260 INFO @ Tue, 30 Jun 2020 00:29:23: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 30 Jun 2020 00:29:23: #1 finished! INFO @ Tue, 30 Jun 2020 00:29:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:29:24: #2 number of paired peaks: 91 WARNING @ Tue, 30 Jun 2020 00:29:24: Too few paired peaks (91) 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 00:29:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.10_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/SRX474599/SRX474599.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:29:29: 21000000 INFO @ Tue, 30 Jun 2020 00:29:35: 22000000 INFO @ Tue, 30 Jun 2020 00:29:42: 23000000 INFO @ Tue, 30 Jun 2020 00:29:47: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:29:47: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:29:47: #1 total tags in treatment: 11596538 INFO @ Tue, 30 Jun 2020 00:29:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:29:47: #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 00:29:48: #1 tags after filtering in treatment: 10274260 INFO @ Tue, 30 Jun 2020 00:29:48: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 30 Jun 2020 00:29:48: #1 finished! INFO @ Tue, 30 Jun 2020 00:29:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:29:48: #2 number of paired peaks: 91 WARNING @ Tue, 30 Jun 2020 00:29:48: Too few paired peaks (91) 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 00:29:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.20_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/SRX474599/SRX474599.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474599/SRX474599.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling