Job ID = 6627043 SRX = SRX8325350 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4702795 spots for SRR11772156/SRR11772156.sra Written 4702795 spots for SRR11772156/SRR11772156.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627278 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:27 4702795 reads; of these: 4702795 (100.00%) were paired; of these: 1425460 (30.31%) aligned concordantly 0 times 2507401 (53.32%) aligned concordantly exactly 1 time 769934 (16.37%) aligned concordantly >1 times ---- 1425460 pairs aligned concordantly 0 times; of these: 559920 (39.28%) aligned discordantly 1 time ---- 865540 pairs aligned 0 times concordantly or discordantly; of these: 1731080 mates make up the pairs; of these: 809205 (46.75%) aligned 0 times 463778 (26.79%) aligned exactly 1 time 458097 (26.46%) aligned >1 times 91.40% overall alignment rate Time searching: 00:14:27 Overall time: 00:14:27 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 8 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] 1637956 / 3731106 = 0.4390 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, 14 Jul 2020 09:53:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.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, 14 Jul 2020 09:53:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:53:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:54:04: 1000000 INFO @ Tue, 14 Jul 2020 09:54:12: 2000000 INFO @ Tue, 14 Jul 2020 09:54:19: 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, 14 Jul 2020 09:54:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.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, 14 Jul 2020 09:54:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:54:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:54:27: 4000000 INFO @ Tue, 14 Jul 2020 09:54:34: 1000000 INFO @ Tue, 14 Jul 2020 09:54:35: 5000000 INFO @ Tue, 14 Jul 2020 09:54:38: #1 tag size is determined as 149 bps INFO @ Tue, 14 Jul 2020 09:54:38: #1 tag size = 149 INFO @ Tue, 14 Jul 2020 09:54:38: #1 total tags in treatment: 1853460 INFO @ Tue, 14 Jul 2020 09:54:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:54:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:54:38: #1 tags after filtering in treatment: 1763876 INFO @ Tue, 14 Jul 2020 09:54:38: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 09:54:38: #1 finished! INFO @ Tue, 14 Jul 2020 09:54:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:54:38: #2 number of paired peaks: 445 WARNING @ Tue, 14 Jul 2020 09:54:38: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Tue, 14 Jul 2020 09:54:38: start model_add_line... INFO @ Tue, 14 Jul 2020 09:54:38: start X-correlation... INFO @ Tue, 14 Jul 2020 09:54:38: end of X-cor INFO @ Tue, 14 Jul 2020 09:54:38: #2 finished! INFO @ Tue, 14 Jul 2020 09:54:38: #2 predicted fragment length is 172 bps INFO @ Tue, 14 Jul 2020 09:54:38: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 14 Jul 2020 09:54:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.05_model.r WARNING @ Tue, 14 Jul 2020 09:54:38: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:54:38: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Tue, 14 Jul 2020 09:54:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:54:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:54:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:54:42: 2000000 INFO @ Tue, 14 Jul 2020 09:54:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:54:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:54:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:54:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.05_summits.bed INFO @ Tue, 14 Jul 2020 09:54:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (682 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:54:49: 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, 14 Jul 2020 09:54:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.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, 14 Jul 2020 09:54:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:54:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:54:57: 4000000 INFO @ Tue, 14 Jul 2020 09:55:04: 1000000 INFO @ Tue, 14 Jul 2020 09:55:05: 5000000 INFO @ Tue, 14 Jul 2020 09:55:07: #1 tag size is determined as 149 bps INFO @ Tue, 14 Jul 2020 09:55:07: #1 tag size = 149 INFO @ Tue, 14 Jul 2020 09:55:07: #1 total tags in treatment: 1853460 INFO @ Tue, 14 Jul 2020 09:55:07: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:55:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:55:07: #1 tags after filtering in treatment: 1763876 INFO @ Tue, 14 Jul 2020 09:55:07: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 09:55:07: #1 finished! INFO @ Tue, 14 Jul 2020 09:55:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:55:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:55:07: #2 number of paired peaks: 445 WARNING @ Tue, 14 Jul 2020 09:55:07: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Tue, 14 Jul 2020 09:55:07: start model_add_line... INFO @ Tue, 14 Jul 2020 09:55:07: start X-correlation... INFO @ Tue, 14 Jul 2020 09:55:07: end of X-cor INFO @ Tue, 14 Jul 2020 09:55:07: #2 finished! INFO @ Tue, 14 Jul 2020 09:55:07: #2 predicted fragment length is 172 bps INFO @ Tue, 14 Jul 2020 09:55:07: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 14 Jul 2020 09:55:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.10_model.r WARNING @ Tue, 14 Jul 2020 09:55:07: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:55:07: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Tue, 14 Jul 2020 09:55:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:55:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:55:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:55:12: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:55:12: 2000000 INFO @ Tue, 14 Jul 2020 09:55:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:55:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:55:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.10_summits.bed INFO @ Tue, 14 Jul 2020 09:55:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:55:19: 3000000 INFO @ Tue, 14 Jul 2020 09:55:27: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:55:34: 5000000 INFO @ Tue, 14 Jul 2020 09:55:37: #1 tag size is determined as 149 bps INFO @ Tue, 14 Jul 2020 09:55:37: #1 tag size = 149 INFO @ Tue, 14 Jul 2020 09:55:37: #1 total tags in treatment: 1853460 INFO @ Tue, 14 Jul 2020 09:55:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:55:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:55:37: #1 tags after filtering in treatment: 1763876 INFO @ Tue, 14 Jul 2020 09:55:37: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 09:55:37: #1 finished! INFO @ Tue, 14 Jul 2020 09:55:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:55:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:55:37: #2 number of paired peaks: 445 WARNING @ Tue, 14 Jul 2020 09:55:37: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Tue, 14 Jul 2020 09:55:37: start model_add_line... INFO @ Tue, 14 Jul 2020 09:55:37: start X-correlation... INFO @ Tue, 14 Jul 2020 09:55:37: end of X-cor INFO @ Tue, 14 Jul 2020 09:55:37: #2 finished! INFO @ Tue, 14 Jul 2020 09:55:37: #2 predicted fragment length is 172 bps INFO @ Tue, 14 Jul 2020 09:55:37: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 14 Jul 2020 09:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.20_model.r WARNING @ Tue, 14 Jul 2020 09:55:37: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:55:37: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Tue, 14 Jul 2020 09:55:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:55:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:55:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:55:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:55:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:55:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:55:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325350/SRX8325350.20_summits.bed INFO @ Tue, 14 Jul 2020 09:55:43: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (192 records, 4 fields): 2 millis CompletedMACS2peakCalling