Job ID = 12266647 SRX = SRX7806721 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17691152 spots for SRR11186387/SRR11186387.sra Written 17691152 spots for SRR11186387/SRR11186387.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267104 ("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: 00:31:51 17691152 reads; of these: 17691152 (100.00%) were paired; of these: 8809375 (49.80%) aligned concordantly 0 times 6031338 (34.09%) aligned concordantly exactly 1 time 2850439 (16.11%) aligned concordantly >1 times ---- 8809375 pairs aligned concordantly 0 times; of these: 1624825 (18.44%) aligned discordantly 1 time ---- 7184550 pairs aligned 0 times concordantly or discordantly; of these: 14369100 mates make up the pairs; of these: 11886332 (82.72%) aligned 0 times 1301320 (9.06%) aligned exactly 1 time 1181448 (8.22%) aligned >1 times 66.41% overall alignment rate Time searching: 00:31:51 Overall time: 00:31:51 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 12 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] 1822098 / 10450386 = 0.1744 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 09:45:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.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 09:45:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:45:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:45:46: 1000000 INFO @ Sat, 03 Apr 2021 09:45:54: 2000000 INFO @ Sat, 03 Apr 2021 09:46:01: 3000000 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 09:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.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 09:46:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:46:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:46:09: 4000000 INFO @ Sat, 03 Apr 2021 09:46:17: 1000000 INFO @ Sat, 03 Apr 2021 09:46:18: 5000000 INFO @ Sat, 03 Apr 2021 09:46:27: 2000000 INFO @ Sat, 03 Apr 2021 09:46:27: 6000000 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 09:46:36: 7000000 INFO @ Sat, 03 Apr 2021 09:46:37: 3000000 INFO @ Sat, 03 Apr 2021 09:46:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.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 09:46:38: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:46:38: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:46:45: 8000000 INFO @ Sat, 03 Apr 2021 09:46:47: 4000000 INFO @ Sat, 03 Apr 2021 09:46:49: 1000000 INFO @ Sat, 03 Apr 2021 09:46:54: 9000000 INFO @ Sat, 03 Apr 2021 09:46:57: 5000000 INFO @ Sat, 03 Apr 2021 09:46:59: 2000000 INFO @ Sat, 03 Apr 2021 09:47:04: 10000000 INFO @ Sat, 03 Apr 2021 09:47:08: 6000000 INFO @ Sat, 03 Apr 2021 09:47:10: 3000000 INFO @ Sat, 03 Apr 2021 09:47:13: 11000000 INFO @ Sat, 03 Apr 2021 09:47:18: 7000000 INFO @ Sat, 03 Apr 2021 09:47:20: 4000000 INFO @ Sat, 03 Apr 2021 09:47:22: 12000000 INFO @ Sat, 03 Apr 2021 09:47:27: 8000000 INFO @ Sat, 03 Apr 2021 09:47:30: 5000000 INFO @ Sat, 03 Apr 2021 09:47:31: 13000000 INFO @ Sat, 03 Apr 2021 09:47:37: 9000000 INFO @ Sat, 03 Apr 2021 09:47:40: 6000000 INFO @ Sat, 03 Apr 2021 09:47:40: 14000000 INFO @ Sat, 03 Apr 2021 09:47:47: 10000000 INFO @ Sat, 03 Apr 2021 09:47:49: 15000000 INFO @ Sat, 03 Apr 2021 09:47:50: 7000000 INFO @ Sat, 03 Apr 2021 09:47:57: 11000000 INFO @ Sat, 03 Apr 2021 09:47:58: 16000000 INFO @ Sat, 03 Apr 2021 09:48:00: 8000000 INFO @ Sat, 03 Apr 2021 09:48:07: 12000000 INFO @ Sat, 03 Apr 2021 09:48:08: 17000000 INFO @ Sat, 03 Apr 2021 09:48:10: 9000000 INFO @ Sat, 03 Apr 2021 09:48:17: 13000000 INFO @ Sat, 03 Apr 2021 09:48:17: 18000000 INFO @ Sat, 03 Apr 2021 09:48:19: 10000000 INFO @ Sat, 03 Apr 2021 09:48:26: 19000000 INFO @ Sat, 03 Apr 2021 09:48:26: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:48:28: 11000000 INFO @ Sat, 03 Apr 2021 09:48:34: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:48:34: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:48:34: #1 total tags in treatment: 7198191 INFO @ Sat, 03 Apr 2021 09:48:34: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:48:34: #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 09:48:34: #1 tags after filtering in treatment: 6006327 INFO @ Sat, 03 Apr 2021 09:48:34: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 09:48:34: #1 finished! INFO @ Sat, 03 Apr 2021 09:48:34: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:48:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:48:34: #2 number of paired peaks: 641 WARNING @ Sat, 03 Apr 2021 09:48:34: Fewer paired peaks (641) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 641 pairs to build model! INFO @ Sat, 03 Apr 2021 09:48:34: start model_add_line... INFO @ Sat, 03 Apr 2021 09:48:34: start X-correlation... INFO @ Sat, 03 Apr 2021 09:48:34: end of X-cor INFO @ Sat, 03 Apr 2021 09:48:34: #2 finished! INFO @ Sat, 03 Apr 2021 09:48:34: #2 predicted fragment length is 132 bps INFO @ Sat, 03 Apr 2021 09:48:34: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 03 Apr 2021 09:48:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.05_model.r WARNING @ Sat, 03 Apr 2021 09:48:34: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:48:34: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Sat, 03 Apr 2021 09:48:34: #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 09:48:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:48:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:48:36: 15000000 INFO @ Sat, 03 Apr 2021 09:48:38: 12000000 INFO @ Sat, 03 Apr 2021 09:48:45: 16000000 INFO @ Sat, 03 Apr 2021 09:48:47: 13000000 INFO @ Sat, 03 Apr 2021 09:48:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:48:55: 17000000 INFO @ Sat, 03 Apr 2021 09:48:56: 14000000 INFO @ Sat, 03 Apr 2021 09:48:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:48:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:48:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.05_summits.bed INFO @ Sat, 03 Apr 2021 09:48:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4800 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:49:04: 18000000 INFO @ Sat, 03 Apr 2021 09:49:05: 15000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:49:13: 19000000 INFO @ Sat, 03 Apr 2021 09:49:14: 16000000 INFO @ Sat, 03 Apr 2021 09:49:21: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:49:21: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:49:21: #1 total tags in treatment: 7198191 INFO @ Sat, 03 Apr 2021 09:49:21: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:49:21: #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 09:49:21: #1 tags after filtering in treatment: 6006327 INFO @ Sat, 03 Apr 2021 09:49:21: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 09:49:21: #1 finished! INFO @ Sat, 03 Apr 2021 09:49:21: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:49:21: #2 number of paired peaks: 641 WARNING @ Sat, 03 Apr 2021 09:49:21: Fewer paired peaks (641) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 641 pairs to build model! INFO @ Sat, 03 Apr 2021 09:49:21: start model_add_line... INFO @ Sat, 03 Apr 2021 09:49:21: start X-correlation... INFO @ Sat, 03 Apr 2021 09:49:21: end of X-cor INFO @ Sat, 03 Apr 2021 09:49:21: #2 finished! INFO @ Sat, 03 Apr 2021 09:49:21: #2 predicted fragment length is 132 bps INFO @ Sat, 03 Apr 2021 09:49:21: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 03 Apr 2021 09:49:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.10_model.r WARNING @ Sat, 03 Apr 2021 09:49:21: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:49:21: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Sat, 03 Apr 2021 09:49:21: #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 09:49:21: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:49:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:49:23: 17000000 INFO @ Sat, 03 Apr 2021 09:49:32: 18000000 INFO @ Sat, 03 Apr 2021 09:49:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:49:41: 19000000 INFO @ Sat, 03 Apr 2021 09:49:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:49:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:49:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.10_summits.bed INFO @ Sat, 03 Apr 2021 09:49:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1886 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:49:48: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:49:48: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:49:48: #1 total tags in treatment: 7198191 INFO @ Sat, 03 Apr 2021 09:49:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:49:48: #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 09:49:48: #1 tags after filtering in treatment: 6006327 INFO @ Sat, 03 Apr 2021 09:49:48: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 09:49:48: #1 finished! INFO @ Sat, 03 Apr 2021 09:49:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:49:48: #2 number of paired peaks: 641 WARNING @ Sat, 03 Apr 2021 09:49:48: Fewer paired peaks (641) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 641 pairs to build model! INFO @ Sat, 03 Apr 2021 09:49:48: start model_add_line... INFO @ Sat, 03 Apr 2021 09:49:48: start X-correlation... INFO @ Sat, 03 Apr 2021 09:49:48: end of X-cor INFO @ Sat, 03 Apr 2021 09:49:48: #2 finished! INFO @ Sat, 03 Apr 2021 09:49:48: #2 predicted fragment length is 132 bps INFO @ Sat, 03 Apr 2021 09:49:48: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 03 Apr 2021 09:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.20_model.r WARNING @ Sat, 03 Apr 2021 09:49:48: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:49:48: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Sat, 03 Apr 2021 09:49:48: #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 09:49:48: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:50:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806721/SRX7806721.20_summits.bed INFO @ Sat, 03 Apr 2021 09:50:12: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (473 records, 4 fields): 3 millis CompletedMACS2peakCalling