Job ID = 14166949 SRX = SRX7541110 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15471109 spots for SRR10871160/SRR10871160.sra Written 15471109 spots for SRR10871160/SRR10871160.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167308 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:04 Time loading mirror index: 00:00:05 Multiseed full-index search: 00:23:01 15471109 reads; of these: 15471109 (100.00%) were paired; of these: 10520322 (68.00%) aligned concordantly 0 times 4182010 (27.03%) aligned concordantly exactly 1 time 768777 (4.97%) aligned concordantly >1 times ---- 10520322 pairs aligned concordantly 0 times; of these: 654539 (6.22%) aligned discordantly 1 time ---- 9865783 pairs aligned 0 times concordantly or discordantly; of these: 19731566 mates make up the pairs; of these: 18611345 (94.32%) aligned 0 times 647880 (3.28%) aligned exactly 1 time 472341 (2.39%) aligned >1 times 39.85% overall alignment rate Time searching: 00:23:11 Overall time: 00:23:11 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] 2723748 / 5599218 = 0.4865 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:37:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.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 @ Fri, 10 Dec 2021 08:37:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:37:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:37:29: 1000000 INFO @ Fri, 10 Dec 2021 08:37:38: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:37:47: 3000000 INFO @ Fri, 10 Dec 2021 08:37:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.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 @ Fri, 10 Dec 2021 08:37:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:37:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:37:55: 4000000 INFO @ Fri, 10 Dec 2021 08:38:00: 1000000 INFO @ Fri, 10 Dec 2021 08:38:03: 5000000 INFO @ Fri, 10 Dec 2021 08:38:08: 2000000 INFO @ Fri, 10 Dec 2021 08:38:12: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:38:17: 3000000 INFO @ Fri, 10 Dec 2021 08:38:19: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:38:19: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:38:19: #1 total tags in treatment: 2403697 INFO @ Fri, 10 Dec 2021 08:38:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:38:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:38:19: #1 tags after filtering in treatment: 2312986 INFO @ Fri, 10 Dec 2021 08:38:19: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 08:38:19: #1 finished! INFO @ Fri, 10 Dec 2021 08:38:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:38:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:38:20: #2 number of paired peaks: 538 WARNING @ Fri, 10 Dec 2021 08:38:20: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Fri, 10 Dec 2021 08:38:20: start model_add_line... INFO @ Fri, 10 Dec 2021 08:38:20: start X-correlation... INFO @ Fri, 10 Dec 2021 08:38:20: end of X-cor INFO @ Fri, 10 Dec 2021 08:38:20: #2 finished! INFO @ Fri, 10 Dec 2021 08:38:20: #2 predicted fragment length is 140 bps INFO @ Fri, 10 Dec 2021 08:38:20: #2 alternative fragment length(s) may be 140 bps INFO @ Fri, 10 Dec 2021 08:38:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.05_model.r WARNING @ Fri, 10 Dec 2021 08:38:20: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:38:20: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Fri, 10 Dec 2021 08:38:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:38:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:38:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:38:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.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 @ Fri, 10 Dec 2021 08:38:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:38:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:38:24: 4000000 INFO @ Fri, 10 Dec 2021 08:38:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:38:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:38:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:38:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.05_summits.bed INFO @ Fri, 10 Dec 2021 08:38:29: Done! INFO @ Fri, 10 Dec 2021 08:38:29: 1000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (873 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:38:32: 5000000 INFO @ Fri, 10 Dec 2021 08:38:37: 2000000 INFO @ Fri, 10 Dec 2021 08:38:40: 6000000 INFO @ Fri, 10 Dec 2021 08:38:46: 3000000 INFO @ Fri, 10 Dec 2021 08:38:48: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:38:48: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:38:48: #1 total tags in treatment: 2403697 INFO @ Fri, 10 Dec 2021 08:38:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:38:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:38:48: #1 tags after filtering in treatment: 2312986 INFO @ Fri, 10 Dec 2021 08:38:48: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 08:38:48: #1 finished! INFO @ Fri, 10 Dec 2021 08:38:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:38:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:38:48: #2 number of paired peaks: 538 WARNING @ Fri, 10 Dec 2021 08:38:48: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Fri, 10 Dec 2021 08:38:48: start model_add_line... INFO @ Fri, 10 Dec 2021 08:38:48: start X-correlation... INFO @ Fri, 10 Dec 2021 08:38:49: end of X-cor INFO @ Fri, 10 Dec 2021 08:38:49: #2 finished! INFO @ Fri, 10 Dec 2021 08:38:49: #2 predicted fragment length is 140 bps INFO @ Fri, 10 Dec 2021 08:38:49: #2 alternative fragment length(s) may be 140 bps INFO @ Fri, 10 Dec 2021 08:38:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.10_model.r WARNING @ Fri, 10 Dec 2021 08:38:49: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:38:49: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Fri, 10 Dec 2021 08:38:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:38:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:38:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:38:54: 4000000 INFO @ Fri, 10 Dec 2021 08:38:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:38:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:38:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:38:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.10_summits.bed INFO @ Fri, 10 Dec 2021 08:38:57: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (312 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:39:02: 5000000 INFO @ Fri, 10 Dec 2021 08:39:10: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:39:18: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:39:18: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:39:18: #1 total tags in treatment: 2403697 INFO @ Fri, 10 Dec 2021 08:39:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:39:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:39:18: #1 tags after filtering in treatment: 2312986 INFO @ Fri, 10 Dec 2021 08:39:18: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 08:39:18: #1 finished! INFO @ Fri, 10 Dec 2021 08:39:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:39:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:39:18: #2 number of paired peaks: 538 WARNING @ Fri, 10 Dec 2021 08:39:18: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Fri, 10 Dec 2021 08:39:18: start model_add_line... INFO @ Fri, 10 Dec 2021 08:39:18: start X-correlation... INFO @ Fri, 10 Dec 2021 08:39:18: end of X-cor INFO @ Fri, 10 Dec 2021 08:39:18: #2 finished! INFO @ Fri, 10 Dec 2021 08:39:18: #2 predicted fragment length is 140 bps INFO @ Fri, 10 Dec 2021 08:39:18: #2 alternative fragment length(s) may be 140 bps INFO @ Fri, 10 Dec 2021 08:39:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.20_model.r WARNING @ Fri, 10 Dec 2021 08:39:19: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:39:19: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Fri, 10 Dec 2021 08:39:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:39:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:39:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:39:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:39:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:39:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:39:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541110/SRX7541110.20_summits.bed INFO @ Fri, 10 Dec 2021 08:39:28: Done! pass1 - making usageList (7 chroms): 7 millis pass2 - checking and writing primary data (154 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。