Job ID = 12265178 SRX = SRX3282112 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36984564 spots for SRR6171263/SRR6171263.sra Written 36984564 spots for SRR6171263/SRR6171263.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265775 ("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: 01:22:28 36984564 reads; of these: 36984564 (100.00%) were paired; of these: 13235983 (35.79%) aligned concordantly 0 times 7024543 (18.99%) aligned concordantly exactly 1 time 16724038 (45.22%) aligned concordantly >1 times ---- 13235983 pairs aligned concordantly 0 times; of these: 1057672 (7.99%) aligned discordantly 1 time ---- 12178311 pairs aligned 0 times concordantly or discordantly; of these: 24356622 mates make up the pairs; of these: 18877092 (77.50%) aligned 0 times 408920 (1.68%) aligned exactly 1 time 5070610 (20.82%) aligned >1 times 74.48% overall alignment rate Time searching: 01:22:28 Overall time: 01:22:28 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 24 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] 14481541 / 24637033 = 0.5878 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:17:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.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, 03 Apr 2021 08:17:33: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:17:33: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:17:39: 1000000 INFO @ Sat, 03 Apr 2021 08:17:45: 2000000 INFO @ Sat, 03 Apr 2021 08:17:51: 3000000 INFO @ Sat, 03 Apr 2021 08:17:57: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.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, 03 Apr 2021 08:18:03: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:18:03: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:18:03: 5000000 INFO @ Sat, 03 Apr 2021 08:18:10: 6000000 INFO @ Sat, 03 Apr 2021 08:18:10: 1000000 INFO @ Sat, 03 Apr 2021 08:18:16: 7000000 INFO @ Sat, 03 Apr 2021 08:18:17: 2000000 INFO @ Sat, 03 Apr 2021 08:18:23: 8000000 INFO @ Sat, 03 Apr 2021 08:18:23: 3000000 INFO @ Sat, 03 Apr 2021 08:18:29: 9000000 INFO @ Sat, 03 Apr 2021 08:18:30: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:18:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.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, 03 Apr 2021 08:18:33: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:18:33: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:18:36: 10000000 INFO @ Sat, 03 Apr 2021 08:18:36: 5000000 INFO @ Sat, 03 Apr 2021 08:18:40: 1000000 INFO @ Sat, 03 Apr 2021 08:18:44: 11000000 INFO @ Sat, 03 Apr 2021 08:18:44: 6000000 INFO @ Sat, 03 Apr 2021 08:18:46: 2000000 INFO @ Sat, 03 Apr 2021 08:18:51: 12000000 INFO @ Sat, 03 Apr 2021 08:18:51: 7000000 INFO @ Sat, 03 Apr 2021 08:18:53: 3000000 INFO @ Sat, 03 Apr 2021 08:18:57: 13000000 INFO @ Sat, 03 Apr 2021 08:18:58: 8000000 INFO @ Sat, 03 Apr 2021 08:18:59: 4000000 INFO @ Sat, 03 Apr 2021 08:19:03: 14000000 INFO @ Sat, 03 Apr 2021 08:19:04: 9000000 INFO @ Sat, 03 Apr 2021 08:19:05: 5000000 INFO @ Sat, 03 Apr 2021 08:19:09: 15000000 INFO @ Sat, 03 Apr 2021 08:19:11: 6000000 INFO @ Sat, 03 Apr 2021 08:19:11: 10000000 INFO @ Sat, 03 Apr 2021 08:19:15: 16000000 INFO @ Sat, 03 Apr 2021 08:19:17: 7000000 INFO @ Sat, 03 Apr 2021 08:19:18: 11000000 INFO @ Sat, 03 Apr 2021 08:19:21: 17000000 INFO @ Sat, 03 Apr 2021 08:19:23: 8000000 INFO @ Sat, 03 Apr 2021 08:19:25: 12000000 INFO @ Sat, 03 Apr 2021 08:19:28: 18000000 INFO @ Sat, 03 Apr 2021 08:19:29: 9000000 INFO @ Sat, 03 Apr 2021 08:19:31: 13000000 INFO @ Sat, 03 Apr 2021 08:19:34: 19000000 INFO @ Sat, 03 Apr 2021 08:19:35: 10000000 INFO @ Sat, 03 Apr 2021 08:19:37: 14000000 INFO @ Sat, 03 Apr 2021 08:19:40: 20000000 INFO @ Sat, 03 Apr 2021 08:19:41: 11000000 INFO @ Sat, 03 Apr 2021 08:19:43: 15000000 INFO @ Sat, 03 Apr 2021 08:19:47: 21000000 INFO @ Sat, 03 Apr 2021 08:19:47: 12000000 INFO @ Sat, 03 Apr 2021 08:19:50: 16000000 INFO @ Sat, 03 Apr 2021 08:19:53: 13000000 INFO @ Sat, 03 Apr 2021 08:19:54: 22000000 INFO @ Sat, 03 Apr 2021 08:19:56: 17000000 INFO @ Sat, 03 Apr 2021 08:19:58: 14000000 INFO @ Sat, 03 Apr 2021 08:20:01: 23000000 INFO @ Sat, 03 Apr 2021 08:20:03: 18000000 INFO @ Sat, 03 Apr 2021 08:20:04: 15000000 INFO @ Sat, 03 Apr 2021 08:20:07: 24000000 INFO @ Sat, 03 Apr 2021 08:20:09: 19000000 INFO @ Sat, 03 Apr 2021 08:20:09: 16000000 INFO @ Sat, 03 Apr 2021 08:20:14: 25000000 INFO @ Sat, 03 Apr 2021 08:20:15: 20000000 INFO @ Sat, 03 Apr 2021 08:20:15: 17000000 INFO @ Sat, 03 Apr 2021 08:20:21: 18000000 INFO @ Sat, 03 Apr 2021 08:20:22: 21000000 INFO @ Sat, 03 Apr 2021 08:20:22: 26000000 INFO @ Sat, 03 Apr 2021 08:20:23: #1 tag size is determined as 100 bps INFO @ Sat, 03 Apr 2021 08:20:23: #1 tag size = 100 INFO @ Sat, 03 Apr 2021 08:20:23: #1 total tags in treatment: 9419169 INFO @ Sat, 03 Apr 2021 08:20:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:20:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:20:23: #1 tags after filtering in treatment: 6957647 INFO @ Sat, 03 Apr 2021 08:20:23: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 08:20:23: #1 finished! INFO @ Sat, 03 Apr 2021 08:20:23: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:20:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:20:24: #2 number of paired peaks: 457 WARNING @ Sat, 03 Apr 2021 08:20:24: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Sat, 03 Apr 2021 08:20:24: start model_add_line... INFO @ Sat, 03 Apr 2021 08:20:24: start X-correlation... INFO @ Sat, 03 Apr 2021 08:20:24: end of X-cor INFO @ Sat, 03 Apr 2021 08:20:24: #2 finished! INFO @ Sat, 03 Apr 2021 08:20:24: #2 predicted fragment length is 138 bps INFO @ Sat, 03 Apr 2021 08:20:24: #2 alternative fragment length(s) may be 138 bps INFO @ Sat, 03 Apr 2021 08:20:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.05_model.r WARNING @ Sat, 03 Apr 2021 08:20:24: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:20:24: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Sat, 03 Apr 2021 08:20:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:20:24: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:20:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:20:26: 19000000 INFO @ Sat, 03 Apr 2021 08:20:28: 22000000 INFO @ Sat, 03 Apr 2021 08:20:32: 20000000 INFO @ Sat, 03 Apr 2021 08:20:34: 23000000 INFO @ Sat, 03 Apr 2021 08:20:37: 21000000 INFO @ Sat, 03 Apr 2021 08:20:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:20:40: 24000000 INFO @ Sat, 03 Apr 2021 08:20:43: 22000000 INFO @ Sat, 03 Apr 2021 08:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.05_summits.bed INFO @ Sat, 03 Apr 2021 08:20:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3156 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:20:46: 25000000 INFO @ Sat, 03 Apr 2021 08:20:49: 23000000 INFO @ Sat, 03 Apr 2021 08:20:52: 26000000 INFO @ Sat, 03 Apr 2021 08:20:53: #1 tag size is determined as 100 bps INFO @ Sat, 03 Apr 2021 08:20:53: #1 tag size = 100 INFO @ Sat, 03 Apr 2021 08:20:53: #1 total tags in treatment: 9419169 INFO @ Sat, 03 Apr 2021 08:20:53: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:20:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:20:53: #1 tags after filtering in treatment: 6957647 INFO @ Sat, 03 Apr 2021 08:20:53: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 08:20:53: #1 finished! INFO @ Sat, 03 Apr 2021 08:20:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:20:54: #2 number of paired peaks: 457 WARNING @ Sat, 03 Apr 2021 08:20:54: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Sat, 03 Apr 2021 08:20:54: start model_add_line... INFO @ Sat, 03 Apr 2021 08:20:54: start X-correlation... INFO @ Sat, 03 Apr 2021 08:20:54: end of X-cor INFO @ Sat, 03 Apr 2021 08:20:54: #2 finished! INFO @ Sat, 03 Apr 2021 08:20:54: #2 predicted fragment length is 138 bps INFO @ Sat, 03 Apr 2021 08:20:54: #2 alternative fragment length(s) may be 138 bps INFO @ Sat, 03 Apr 2021 08:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.10_model.r WARNING @ Sat, 03 Apr 2021 08:20:54: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:20:54: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Sat, 03 Apr 2021 08:20:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:20:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:20:55: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:21:01: 25000000 INFO @ Sat, 03 Apr 2021 08:21:07: 26000000 INFO @ Sat, 03 Apr 2021 08:21:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:21:08: #1 tag size is determined as 100 bps INFO @ Sat, 03 Apr 2021 08:21:08: #1 tag size = 100 INFO @ Sat, 03 Apr 2021 08:21:08: #1 total tags in treatment: 9419169 INFO @ Sat, 03 Apr 2021 08:21:08: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:21:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:21:08: #1 tags after filtering in treatment: 6957647 INFO @ Sat, 03 Apr 2021 08:21:08: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 08:21:08: #1 finished! INFO @ Sat, 03 Apr 2021 08:21:08: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:21:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:21:09: #2 number of paired peaks: 457 WARNING @ Sat, 03 Apr 2021 08:21:09: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Sat, 03 Apr 2021 08:21:09: start model_add_line... INFO @ Sat, 03 Apr 2021 08:21:09: start X-correlation... INFO @ Sat, 03 Apr 2021 08:21:09: end of X-cor INFO @ Sat, 03 Apr 2021 08:21:09: #2 finished! INFO @ Sat, 03 Apr 2021 08:21:09: #2 predicted fragment length is 138 bps INFO @ Sat, 03 Apr 2021 08:21:09: #2 alternative fragment length(s) may be 138 bps INFO @ Sat, 03 Apr 2021 08:21:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.20_model.r WARNING @ Sat, 03 Apr 2021 08:21:09: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:21:09: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Sat, 03 Apr 2021 08:21:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:21:09: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:21:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:21:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:21:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:21:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.10_summits.bed INFO @ Sat, 03 Apr 2021 08:21:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1554 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:21:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:21:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:21:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:21:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3282112/SRX3282112.20_summits.bed INFO @ Sat, 03 Apr 2021 08:21:29: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (589 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。