Job ID = 14171534 SRX = SRX10386208 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17664347 spots for SRR14009273/SRR14009273.sra Written 17664347 spots for SRR14009273/SRR14009273.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172070 ("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: 00:21:49 17664347 reads; of these: 17664347 (100.00%) were paired; of these: 10590904 (59.96%) aligned concordantly 0 times 4872286 (27.58%) aligned concordantly exactly 1 time 2201157 (12.46%) aligned concordantly >1 times ---- 10590904 pairs aligned concordantly 0 times; of these: 234827 (2.22%) aligned discordantly 1 time ---- 10356077 pairs aligned 0 times concordantly or discordantly; of these: 20712154 mates make up the pairs; of these: 20137706 (97.23%) aligned 0 times 277073 (1.34%) aligned exactly 1 time 297375 (1.44%) aligned >1 times 43.00% overall alignment rate Time searching: 00:21:49 Overall time: 00:21:49 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] 935783 / 7259893 = 0.1289 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 @ Sat, 11 Dec 2021 12:25:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.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 @ Sat, 11 Dec 2021 12:25:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:25:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:25:42: 1000000 INFO @ Sat, 11 Dec 2021 12:25:48: 2000000 INFO @ Sat, 11 Dec 2021 12:25:55: 3000000 INFO @ Sat, 11 Dec 2021 12:26:02: 4000000 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 @ Sat, 11 Dec 2021 12:26:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.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 @ Sat, 11 Dec 2021 12:26:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:26:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:26:09: 5000000 INFO @ Sat, 11 Dec 2021 12:26:12: 1000000 INFO @ Sat, 11 Dec 2021 12:26:16: 6000000 INFO @ Sat, 11 Dec 2021 12:26:20: 2000000 INFO @ Sat, 11 Dec 2021 12:26:24: 7000000 INFO @ Sat, 11 Dec 2021 12:26:27: 3000000 INFO @ Sat, 11 Dec 2021 12:26:30: 8000000 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 @ Sat, 11 Dec 2021 12:26:33: 4000000 INFO @ Sat, 11 Dec 2021 12:26:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.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 @ Sat, 11 Dec 2021 12:26:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:26:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:26:38: 9000000 INFO @ Sat, 11 Dec 2021 12:26:41: 5000000 INFO @ Sat, 11 Dec 2021 12:26:42: 1000000 INFO @ Sat, 11 Dec 2021 12:26:46: 10000000 INFO @ Sat, 11 Dec 2021 12:26:48: 6000000 INFO @ Sat, 11 Dec 2021 12:26:49: 2000000 INFO @ Sat, 11 Dec 2021 12:26:53: 11000000 INFO @ Sat, 11 Dec 2021 12:26:55: 7000000 INFO @ Sat, 11 Dec 2021 12:26:57: 3000000 INFO @ Sat, 11 Dec 2021 12:27:01: 12000000 INFO @ Sat, 11 Dec 2021 12:27:02: 8000000 INFO @ Sat, 11 Dec 2021 12:27:05: 4000000 INFO @ Sat, 11 Dec 2021 12:27:09: 13000000 INFO @ Sat, 11 Dec 2021 12:27:10: 9000000 INFO @ Sat, 11 Dec 2021 12:27:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:27:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:27:11: #1 total tags in treatment: 6170779 INFO @ Sat, 11 Dec 2021 12:27:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:27:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:27:11: #1 tags after filtering in treatment: 5667845 INFO @ Sat, 11 Dec 2021 12:27:11: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 12:27:11: #1 finished! INFO @ Sat, 11 Dec 2021 12:27:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:27:12: #2 number of paired peaks: 356 WARNING @ Sat, 11 Dec 2021 12:27:12: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sat, 11 Dec 2021 12:27:12: start model_add_line... INFO @ Sat, 11 Dec 2021 12:27:12: start X-correlation... INFO @ Sat, 11 Dec 2021 12:27:12: end of X-cor INFO @ Sat, 11 Dec 2021 12:27:12: #2 finished! INFO @ Sat, 11 Dec 2021 12:27:12: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 12:27:12: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 12:27:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.05_model.r WARNING @ Sat, 11 Dec 2021 12:27:12: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:27:12: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 12:27:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:27:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:27:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:27:12: 5000000 INFO @ Sat, 11 Dec 2021 12:27:17: 10000000 INFO @ Sat, 11 Dec 2021 12:27:19: 6000000 INFO @ Sat, 11 Dec 2021 12:27:24: 11000000 INFO @ Sat, 11 Dec 2021 12:27:26: 7000000 INFO @ Sat, 11 Dec 2021 12:27:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:27:30: 12000000 INFO @ Sat, 11 Dec 2021 12:27:32: 8000000 INFO @ Sat, 11 Dec 2021 12:27:37: 13000000 INFO @ Sat, 11 Dec 2021 12:27:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:27:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:27:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.05_summits.bed INFO @ Sat, 11 Dec 2021 12:27:38: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1078 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:27:39: 9000000 INFO @ Sat, 11 Dec 2021 12:27:39: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:27:39: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:27:39: #1 total tags in treatment: 6170779 INFO @ Sat, 11 Dec 2021 12:27:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:27:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:27:40: #1 tags after filtering in treatment: 5667845 INFO @ Sat, 11 Dec 2021 12:27:40: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 12:27:40: #1 finished! INFO @ Sat, 11 Dec 2021 12:27:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:27:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:27:40: #2 number of paired peaks: 356 WARNING @ Sat, 11 Dec 2021 12:27:40: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sat, 11 Dec 2021 12:27:40: start model_add_line... INFO @ Sat, 11 Dec 2021 12:27:40: start X-correlation... INFO @ Sat, 11 Dec 2021 12:27:40: end of X-cor INFO @ Sat, 11 Dec 2021 12:27:40: #2 finished! INFO @ Sat, 11 Dec 2021 12:27:40: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 12:27:40: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 12:27:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.10_model.r WARNING @ Sat, 11 Dec 2021 12:27:40: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:27:40: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 12:27:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:27:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:27:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:27:45: 10000000 INFO @ Sat, 11 Dec 2021 12:27:52: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:27:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:27:58: 12000000 INFO @ Sat, 11 Dec 2021 12:28:05: 13000000 INFO @ Sat, 11 Dec 2021 12:28:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:28:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:28:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.10_summits.bed INFO @ Sat, 11 Dec 2021 12:28:06: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (788 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:28:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:28:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:28:07: #1 total tags in treatment: 6170779 INFO @ Sat, 11 Dec 2021 12:28:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:28:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:28:08: #1 tags after filtering in treatment: 5667845 INFO @ Sat, 11 Dec 2021 12:28:08: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 12:28:08: #1 finished! INFO @ Sat, 11 Dec 2021 12:28:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:28:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:28:08: #2 number of paired peaks: 356 WARNING @ Sat, 11 Dec 2021 12:28:08: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sat, 11 Dec 2021 12:28:08: start model_add_line... INFO @ Sat, 11 Dec 2021 12:28:08: start X-correlation... INFO @ Sat, 11 Dec 2021 12:28:08: end of X-cor INFO @ Sat, 11 Dec 2021 12:28:08: #2 finished! INFO @ Sat, 11 Dec 2021 12:28:08: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 12:28:08: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 12:28:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.20_model.r WARNING @ Sat, 11 Dec 2021 12:28:08: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:28:08: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 12:28:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:28:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:28:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:28:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:28:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:28:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:28:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386208/SRX10386208.20_summits.bed INFO @ Sat, 11 Dec 2021 12:28:34: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (501 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。