Job ID = 14168927 SRX = SRX9217375 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34440073 spots for SRR12744930/SRR12744930.sra Written 34440073 spots for SRR12744930/SRR12744930.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170004 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:29:10 34440073 reads; of these: 34440073 (100.00%) were paired; of these: 9079563 (26.36%) aligned concordantly 0 times 14236438 (41.34%) aligned concordantly exactly 1 time 11124072 (32.30%) aligned concordantly >1 times ---- 9079563 pairs aligned concordantly 0 times; of these: 1379462 (15.19%) aligned discordantly 1 time ---- 7700101 pairs aligned 0 times concordantly or discordantly; of these: 15400202 mates make up the pairs; of these: 13627564 (88.49%) aligned 0 times 478949 (3.11%) aligned exactly 1 time 1293689 (8.40%) aligned >1 times 80.22% overall alignment rate Time searching: 00:29:11 Overall time: 00:29:11 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 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] 16073637 / 23689073 = 0.6785 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 22:26:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.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 22:26:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:26:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:26:29: 1000000 INFO @ Fri, 10 Dec 2021 22:26:35: 2000000 INFO @ Fri, 10 Dec 2021 22:26:42: 3000000 INFO @ Fri, 10 Dec 2021 22:26:48: 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 @ Fri, 10 Dec 2021 22:26:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.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 22:26:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:26:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:26:54: 5000000 INFO @ Fri, 10 Dec 2021 22:26:59: 1000000 INFO @ Fri, 10 Dec 2021 22:27:01: 6000000 INFO @ Fri, 10 Dec 2021 22:27:06: 2000000 INFO @ Fri, 10 Dec 2021 22:27:08: 7000000 INFO @ Fri, 10 Dec 2021 22:27:12: 3000000 INFO @ Fri, 10 Dec 2021 22:27:15: 8000000 INFO @ Fri, 10 Dec 2021 22:27:18: 4000000 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 22:27:21: 9000000 INFO @ Fri, 10 Dec 2021 22:27:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.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 22:27:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:27:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:27:25: 5000000 INFO @ Fri, 10 Dec 2021 22:27:28: 10000000 INFO @ Fri, 10 Dec 2021 22:27:29: 1000000 INFO @ Fri, 10 Dec 2021 22:27:31: 6000000 INFO @ Fri, 10 Dec 2021 22:27:35: 11000000 INFO @ Fri, 10 Dec 2021 22:27:36: 2000000 INFO @ Fri, 10 Dec 2021 22:27:37: 7000000 INFO @ Fri, 10 Dec 2021 22:27:42: 12000000 INFO @ Fri, 10 Dec 2021 22:27:42: 3000000 INFO @ Fri, 10 Dec 2021 22:27:44: 8000000 INFO @ Fri, 10 Dec 2021 22:27:49: 13000000 INFO @ Fri, 10 Dec 2021 22:27:49: 4000000 INFO @ Fri, 10 Dec 2021 22:27:50: 9000000 INFO @ Fri, 10 Dec 2021 22:27:55: 5000000 INFO @ Fri, 10 Dec 2021 22:27:56: 14000000 INFO @ Fri, 10 Dec 2021 22:27:56: 10000000 INFO @ Fri, 10 Dec 2021 22:28:02: 6000000 INFO @ Fri, 10 Dec 2021 22:28:03: 15000000 INFO @ Fri, 10 Dec 2021 22:28:03: 11000000 INFO @ Fri, 10 Dec 2021 22:28:08: 7000000 INFO @ Fri, 10 Dec 2021 22:28:09: 12000000 INFO @ Fri, 10 Dec 2021 22:28:10: 16000000 INFO @ Fri, 10 Dec 2021 22:28:15: 8000000 INFO @ Fri, 10 Dec 2021 22:28:16: 13000000 INFO @ Fri, 10 Dec 2021 22:28:17: 17000000 INFO @ Fri, 10 Dec 2021 22:28:21: 9000000 INFO @ Fri, 10 Dec 2021 22:28:22: 14000000 INFO @ Fri, 10 Dec 2021 22:28:24: 18000000 INFO @ Fri, 10 Dec 2021 22:28:27: 10000000 INFO @ Fri, 10 Dec 2021 22:28:28: 15000000 INFO @ Fri, 10 Dec 2021 22:28:31: 19000000 INFO @ Fri, 10 Dec 2021 22:28:34: 11000000 INFO @ Fri, 10 Dec 2021 22:28:35: 16000000 INFO @ Fri, 10 Dec 2021 22:28:37: 20000000 INFO @ Fri, 10 Dec 2021 22:28:40: 12000000 INFO @ Fri, 10 Dec 2021 22:28:41: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 22:28:44: 21000000 INFO @ Fri, 10 Dec 2021 22:28:47: 13000000 INFO @ Fri, 10 Dec 2021 22:28:47: 18000000 INFO @ Fri, 10 Dec 2021 22:28:51: 22000000 INFO @ Fri, 10 Dec 2021 22:28:53: 14000000 INFO @ Fri, 10 Dec 2021 22:28:54: 19000000 INFO @ Fri, 10 Dec 2021 22:28:58: 23000000 INFO @ Fri, 10 Dec 2021 22:28:59: #1 tag size is determined as 47 bps INFO @ Fri, 10 Dec 2021 22:28:59: #1 tag size = 47 INFO @ Fri, 10 Dec 2021 22:28:59: #1 total tags in treatment: 9897336 INFO @ Fri, 10 Dec 2021 22:28:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:28:59: #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 22:28:59: #1 tags after filtering in treatment: 5292066 INFO @ Fri, 10 Dec 2021 22:28:59: #1 Redundant rate of treatment: 0.47 INFO @ Fri, 10 Dec 2021 22:28:59: #1 finished! INFO @ Fri, 10 Dec 2021 22:28:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:28:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:28:59: #2 number of paired peaks: 1809 INFO @ Fri, 10 Dec 2021 22:28:59: start model_add_line... INFO @ Fri, 10 Dec 2021 22:28:59: start X-correlation... INFO @ Fri, 10 Dec 2021 22:28:59: end of X-cor INFO @ Fri, 10 Dec 2021 22:28:59: #2 finished! INFO @ Fri, 10 Dec 2021 22:28:59: #2 predicted fragment length is 77 bps INFO @ Fri, 10 Dec 2021 22:28:59: #2 alternative fragment length(s) may be 77 bps INFO @ Fri, 10 Dec 2021 22:28:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.05_model.r WARNING @ Fri, 10 Dec 2021 22:28:59: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:28:59: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Fri, 10 Dec 2021 22:28:59: #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 22:28:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:28:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:29:00: 15000000 INFO @ Fri, 10 Dec 2021 22:29:00: 20000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 22:29:06: 16000000 INFO @ Fri, 10 Dec 2021 22:29:07: 21000000 INFO @ Fri, 10 Dec 2021 22:29:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:29:12: 17000000 INFO @ Fri, 10 Dec 2021 22:29:13: 22000000 INFO @ Fri, 10 Dec 2021 22:29:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.05_peaks.xls INFO @ Fri, 10 Dec 2021 22:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.05_summits.bed INFO @ Fri, 10 Dec 2021 22:29:16: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12607 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:29:19: 18000000 INFO @ Fri, 10 Dec 2021 22:29:19: 23000000 INFO @ Fri, 10 Dec 2021 22:29:20: #1 tag size is determined as 47 bps INFO @ Fri, 10 Dec 2021 22:29:20: #1 tag size = 47 INFO @ Fri, 10 Dec 2021 22:29:20: #1 total tags in treatment: 9897336 INFO @ Fri, 10 Dec 2021 22:29:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:29:20: #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 22:29:20: #1 tags after filtering in treatment: 5292066 INFO @ Fri, 10 Dec 2021 22:29:20: #1 Redundant rate of treatment: 0.47 INFO @ Fri, 10 Dec 2021 22:29:20: #1 finished! INFO @ Fri, 10 Dec 2021 22:29:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:29:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:29:21: #2 number of paired peaks: 1809 INFO @ Fri, 10 Dec 2021 22:29:21: start model_add_line... INFO @ Fri, 10 Dec 2021 22:29:21: start X-correlation... INFO @ Fri, 10 Dec 2021 22:29:21: end of X-cor INFO @ Fri, 10 Dec 2021 22:29:21: #2 finished! INFO @ Fri, 10 Dec 2021 22:29:21: #2 predicted fragment length is 77 bps INFO @ Fri, 10 Dec 2021 22:29:21: #2 alternative fragment length(s) may be 77 bps INFO @ Fri, 10 Dec 2021 22:29:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.10_model.r WARNING @ Fri, 10 Dec 2021 22:29:21: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:29:21: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Fri, 10 Dec 2021 22:29:21: #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 22:29:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:29:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:29:25: 19000000 INFO @ Fri, 10 Dec 2021 22:29:31: 20000000 INFO @ Fri, 10 Dec 2021 22:29:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:29:37: 21000000 INFO @ Fri, 10 Dec 2021 22:29:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.10_peaks.xls INFO @ Fri, 10 Dec 2021 22:29:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:29:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.10_summits.bed INFO @ Fri, 10 Dec 2021 22:29:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4551 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:29:43: 22000000 INFO @ Fri, 10 Dec 2021 22:29:48: 23000000 INFO @ Fri, 10 Dec 2021 22:29:49: #1 tag size is determined as 47 bps INFO @ Fri, 10 Dec 2021 22:29:49: #1 tag size = 47 INFO @ Fri, 10 Dec 2021 22:29:49: #1 total tags in treatment: 9897336 INFO @ Fri, 10 Dec 2021 22:29:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:29:49: #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 22:29:49: #1 tags after filtering in treatment: 5292066 INFO @ Fri, 10 Dec 2021 22:29:49: #1 Redundant rate of treatment: 0.47 INFO @ Fri, 10 Dec 2021 22:29:49: #1 finished! INFO @ Fri, 10 Dec 2021 22:29:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:29:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:29:50: #2 number of paired peaks: 1809 INFO @ Fri, 10 Dec 2021 22:29:50: start model_add_line... INFO @ Fri, 10 Dec 2021 22:29:50: start X-correlation... INFO @ Fri, 10 Dec 2021 22:29:50: end of X-cor INFO @ Fri, 10 Dec 2021 22:29:50: #2 finished! INFO @ Fri, 10 Dec 2021 22:29:50: #2 predicted fragment length is 77 bps INFO @ Fri, 10 Dec 2021 22:29:50: #2 alternative fragment length(s) may be 77 bps INFO @ Fri, 10 Dec 2021 22:29:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.20_model.r WARNING @ Fri, 10 Dec 2021 22:29:50: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:29:50: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Fri, 10 Dec 2021 22:29:50: #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 22:29:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:29:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:30:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:30:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.20_peaks.xls INFO @ Fri, 10 Dec 2021 22:30:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:30:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9217375/SRX9217375.20_summits.bed INFO @ Fri, 10 Dec 2021 22:30:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (463 records, 4 fields): 1 millis CompletedMACS2peakCalling