Job ID = 6528131 SRX = SRX474592 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:20:20 prefetch.2.10.7: 1) Downloading 'SRR1174445'... 2020-06-29T14:20:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:22:59 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:22:59 prefetch.2.10.7: 1) 'SRR1174445' was downloaded successfully 2020-06-29T14:22:59 prefetch.2.10.7: 'SRR1174445' has 0 unresolved dependencies Read 12859401 spots for SRR1174445/SRR1174445.sra Written 12859401 spots for SRR1174445/SRR1174445.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: 00:26:55 12859401 reads; of these: 12859401 (100.00%) were paired; of these: 639606 (4.97%) aligned concordantly 0 times 8468017 (65.85%) aligned concordantly exactly 1 time 3751778 (29.18%) aligned concordantly >1 times ---- 639606 pairs aligned concordantly 0 times; of these: 76163 (11.91%) aligned discordantly 1 time ---- 563443 pairs aligned 0 times concordantly or discordantly; of these: 1126886 mates make up the pairs; of these: 722014 (64.07%) aligned 0 times 267369 (23.73%) aligned exactly 1 time 137503 (12.20%) aligned >1 times 97.19% overall alignment rate Time searching: 00:26:55 Overall time: 00:26:55 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] 805128 / 12256930 = 0.0657 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 00:04:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.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 00:04:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:04:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:05:00: 1000000 INFO @ Tue, 30 Jun 2020 00:05:07: 2000000 INFO @ Tue, 30 Jun 2020 00:05:14: 3000000 INFO @ Tue, 30 Jun 2020 00:05:21: 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 00:05:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.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 00:05:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:05:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:05:28: 5000000 INFO @ Tue, 30 Jun 2020 00:05:31: 1000000 INFO @ Tue, 30 Jun 2020 00:05:36: 6000000 INFO @ Tue, 30 Jun 2020 00:05:38: 2000000 INFO @ Tue, 30 Jun 2020 00:05:44: 7000000 INFO @ Tue, 30 Jun 2020 00:05:47: 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 00:05:52: 8000000 INFO @ Tue, 30 Jun 2020 00:05:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.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 00:05:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:05:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:05:55: 4000000 INFO @ Tue, 30 Jun 2020 00:05:59: 9000000 INFO @ Tue, 30 Jun 2020 00:06:00: 1000000 INFO @ Tue, 30 Jun 2020 00:06:03: 5000000 INFO @ Tue, 30 Jun 2020 00:06:07: 2000000 INFO @ Tue, 30 Jun 2020 00:06:07: 10000000 INFO @ Tue, 30 Jun 2020 00:06:11: 6000000 INFO @ Tue, 30 Jun 2020 00:06:14: 3000000 INFO @ Tue, 30 Jun 2020 00:06:15: 11000000 INFO @ Tue, 30 Jun 2020 00:06:19: 7000000 INFO @ Tue, 30 Jun 2020 00:06:22: 4000000 INFO @ Tue, 30 Jun 2020 00:06:23: 12000000 INFO @ Tue, 30 Jun 2020 00:06:27: 8000000 INFO @ Tue, 30 Jun 2020 00:06:29: 5000000 INFO @ Tue, 30 Jun 2020 00:06:31: 13000000 INFO @ Tue, 30 Jun 2020 00:06:35: 9000000 INFO @ Tue, 30 Jun 2020 00:06:36: 6000000 INFO @ Tue, 30 Jun 2020 00:06:39: 14000000 INFO @ Tue, 30 Jun 2020 00:06:43: 7000000 INFO @ Tue, 30 Jun 2020 00:06:43: 10000000 INFO @ Tue, 30 Jun 2020 00:06:47: 15000000 INFO @ Tue, 30 Jun 2020 00:06:50: 8000000 INFO @ Tue, 30 Jun 2020 00:06:51: 11000000 INFO @ Tue, 30 Jun 2020 00:06:54: 16000000 INFO @ Tue, 30 Jun 2020 00:06:57: 9000000 INFO @ Tue, 30 Jun 2020 00:06:59: 12000000 INFO @ Tue, 30 Jun 2020 00:07:02: 17000000 INFO @ Tue, 30 Jun 2020 00:07:05: 10000000 INFO @ Tue, 30 Jun 2020 00:07:07: 13000000 INFO @ Tue, 30 Jun 2020 00:07:10: 18000000 INFO @ Tue, 30 Jun 2020 00:07:12: 11000000 INFO @ Tue, 30 Jun 2020 00:07:15: 14000000 INFO @ Tue, 30 Jun 2020 00:07:18: 19000000 INFO @ Tue, 30 Jun 2020 00:07:19: 12000000 INFO @ Tue, 30 Jun 2020 00:07:23: 15000000 INFO @ Tue, 30 Jun 2020 00:07:26: 20000000 INFO @ Tue, 30 Jun 2020 00:07:26: 13000000 INFO @ Tue, 30 Jun 2020 00:07:30: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:07:33: 14000000 INFO @ Tue, 30 Jun 2020 00:07:33: 21000000 INFO @ Tue, 30 Jun 2020 00:07:38: 17000000 INFO @ Tue, 30 Jun 2020 00:07:40: 15000000 INFO @ Tue, 30 Jun 2020 00:07:41: 22000000 INFO @ Tue, 30 Jun 2020 00:07:46: 18000000 INFO @ Tue, 30 Jun 2020 00:07:47: 16000000 INFO @ Tue, 30 Jun 2020 00:07:49: 23000000 INFO @ Tue, 30 Jun 2020 00:07:52: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:07:52: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:07:52: #1 total tags in treatment: 11415324 INFO @ Tue, 30 Jun 2020 00:07:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:07:52: #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 00:07:52: #1 tags after filtering in treatment: 10175448 INFO @ Tue, 30 Jun 2020 00:07:52: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 30 Jun 2020 00:07:52: #1 finished! INFO @ Tue, 30 Jun 2020 00:07:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:07:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:07:52: #2 number of paired peaks: 79 WARNING @ Tue, 30 Jun 2020 00:07:52: Too few paired peaks (79) 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 00:07:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.05_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/SRX474592/SRX474592.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:07:54: 17000000 INFO @ Tue, 30 Jun 2020 00:07:54: 19000000 INFO @ Tue, 30 Jun 2020 00:08:01: 18000000 INFO @ Tue, 30 Jun 2020 00:08:02: 20000000 INFO @ Tue, 30 Jun 2020 00:08:08: 19000000 INFO @ Tue, 30 Jun 2020 00:08:10: 21000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:08:15: 20000000 INFO @ Tue, 30 Jun 2020 00:08:18: 22000000 INFO @ Tue, 30 Jun 2020 00:08:22: 21000000 INFO @ Tue, 30 Jun 2020 00:08:25: 23000000 INFO @ Tue, 30 Jun 2020 00:08:28: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:08:28: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:08:28: #1 total tags in treatment: 11415324 INFO @ Tue, 30 Jun 2020 00:08:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:08:28: #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 00:08:28: #1 tags after filtering in treatment: 10175448 INFO @ Tue, 30 Jun 2020 00:08:28: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 30 Jun 2020 00:08:28: #1 finished! INFO @ Tue, 30 Jun 2020 00:08:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:08:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:08:29: 22000000 INFO @ Tue, 30 Jun 2020 00:08:29: #2 number of paired peaks: 79 WARNING @ Tue, 30 Jun 2020 00:08:29: Too few paired peaks (79) 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 00:08:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.10_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/SRX474592/SRX474592.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:08:34: 23000000 INFO @ Tue, 30 Jun 2020 00:08:36: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:08:36: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:08:36: #1 total tags in treatment: 11415324 INFO @ Tue, 30 Jun 2020 00:08:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:08:36: #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 00:08:36: #1 tags after filtering in treatment: 10175448 INFO @ Tue, 30 Jun 2020 00:08:36: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 30 Jun 2020 00:08:36: #1 finished! INFO @ Tue, 30 Jun 2020 00:08:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:08:37: #2 number of paired peaks: 79 WARNING @ Tue, 30 Jun 2020 00:08:37: Too few paired peaks (79) 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 00:08:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.20_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/SRX474592/SRX474592.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474592/SRX474592.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling