Job ID = 6528236 SRX = SRX4940246 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:56:13 prefetch.2.10.7: 1) Downloading 'SRR8113879'... 2020-06-29T14:56:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:57:27 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:57:28 prefetch.2.10.7: 'SRR8113879' is valid 2020-06-29T14:57:28 prefetch.2.10.7: 1) 'SRR8113879' was downloaded successfully 2020-06-29T14:57:28 prefetch.2.10.7: 'SRR8113879' has 0 unresolved dependencies Read 4976245 spots for SRR8113879/SRR8113879.sra Written 4976245 spots for SRR8113879/SRR8113879.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: 00:11:14 4976245 reads; of these: 4976245 (100.00%) were paired; of these: 373684 (7.51%) aligned concordantly 0 times 3824220 (76.85%) aligned concordantly exactly 1 time 778341 (15.64%) aligned concordantly >1 times ---- 373684 pairs aligned concordantly 0 times; of these: 112851 (30.20%) aligned discordantly 1 time ---- 260833 pairs aligned 0 times concordantly or discordantly; of these: 521666 mates make up the pairs; of these: 336512 (64.51%) aligned 0 times 123748 (23.72%) aligned exactly 1 time 61406 (11.77%) aligned >1 times 96.62% overall alignment rate Time searching: 00:11:14 Overall time: 00:11:14 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_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] 185294 / 4676919 = 0.0396 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 00:18:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.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 00:18:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:18:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:19:02: 1000000 INFO @ Tue, 30 Jun 2020 00:19:11: 2000000 INFO @ Tue, 30 Jun 2020 00:19:19: 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 00:19:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.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 00:19:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:19:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:19:27: 4000000 INFO @ Tue, 30 Jun 2020 00:19:36: 1000000 INFO @ Tue, 30 Jun 2020 00:19:36: 5000000 INFO @ Tue, 30 Jun 2020 00:19:44: 6000000 INFO @ Tue, 30 Jun 2020 00:19:47: 2000000 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 00:19:53: 7000000 INFO @ Tue, 30 Jun 2020 00:19:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.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 00:19:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:19:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:19:58: 3000000 INFO @ Tue, 30 Jun 2020 00:20:01: 8000000 INFO @ Tue, 30 Jun 2020 00:20:03: 1000000 INFO @ Tue, 30 Jun 2020 00:20:08: 4000000 INFO @ Tue, 30 Jun 2020 00:20:10: 9000000 INFO @ Tue, 30 Jun 2020 00:20:12: 2000000 INFO @ Tue, 30 Jun 2020 00:20:12: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 00:20:12: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 00:20:12: #1 total tags in treatment: 4418587 INFO @ Tue, 30 Jun 2020 00:20:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:20:12: #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 00:20:12: #1 tags after filtering in treatment: 4271027 INFO @ Tue, 30 Jun 2020 00:20:12: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 30 Jun 2020 00:20:12: #1 finished! INFO @ Tue, 30 Jun 2020 00:20:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:20:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:20:12: #2 number of paired peaks: 95 WARNING @ Tue, 30 Jun 2020 00:20:12: Too few paired peaks (95) 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 00:20:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.05_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/SRX4940246/SRX4940246.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:20:18: 5000000 INFO @ Tue, 30 Jun 2020 00:20:21: 3000000 INFO @ Tue, 30 Jun 2020 00:20:27: 6000000 INFO @ Tue, 30 Jun 2020 00:20:29: 4000000 INFO @ Tue, 30 Jun 2020 00:20:37: 7000000 INFO @ Tue, 30 Jun 2020 00:20:38: 5000000 INFO @ Tue, 30 Jun 2020 00:20:46: 6000000 INFO @ Tue, 30 Jun 2020 00:20:46: 8000000 INFO @ Tue, 30 Jun 2020 00:20:54: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:20:55: 9000000 INFO @ Tue, 30 Jun 2020 00:20:58: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 00:20:58: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 00:20:58: #1 total tags in treatment: 4418587 INFO @ Tue, 30 Jun 2020 00:20:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:20:58: #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 00:20:58: #1 tags after filtering in treatment: 4271027 INFO @ Tue, 30 Jun 2020 00:20:58: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 30 Jun 2020 00:20:58: #1 finished! INFO @ Tue, 30 Jun 2020 00:20:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:20:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:20:58: #2 number of paired peaks: 95 WARNING @ Tue, 30 Jun 2020 00:20:58: Too few paired peaks (95) 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 00:20:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.10_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/SRX4940246/SRX4940246.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:21:02: 8000000 INFO @ Tue, 30 Jun 2020 00:21:09: 9000000 INFO @ Tue, 30 Jun 2020 00:21:11: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 00:21:11: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 00:21:11: #1 total tags in treatment: 4418587 INFO @ Tue, 30 Jun 2020 00:21:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:21:11: #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 00:21:11: #1 tags after filtering in treatment: 4271027 INFO @ Tue, 30 Jun 2020 00:21:11: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 30 Jun 2020 00:21:11: #1 finished! INFO @ Tue, 30 Jun 2020 00:21:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:21:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:21:12: #2 number of paired peaks: 95 WARNING @ Tue, 30 Jun 2020 00:21:12: Too few paired peaks (95) 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 00:21:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.20_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/SRX4940246/SRX4940246.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4940246/SRX4940246.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。