Job ID = 14168706 SRX = ERX3978765 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18836645 spots for ERR3975780/ERR3975780.sra Written 18836645 spots for ERR3975780/ERR3975780.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169819 ("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: 00:32:18 18836645 reads; of these: 18836645 (100.00%) were paired; of these: 7632935 (40.52%) aligned concordantly 0 times 5850343 (31.06%) aligned concordantly exactly 1 time 5353367 (28.42%) aligned concordantly >1 times ---- 7632935 pairs aligned concordantly 0 times; of these: 1645227 (21.55%) aligned discordantly 1 time ---- 5987708 pairs aligned 0 times concordantly or discordantly; of these: 11975416 mates make up the pairs; of these: 7609486 (63.54%) aligned 0 times 380395 (3.18%) aligned exactly 1 time 3985535 (33.28%) aligned >1 times 79.80% overall alignment rate Time searching: 00:32:18 Overall time: 00:32:18 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 20 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] 4190431 / 12749270 = 0.3287 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 20:10:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.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 20:10:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:10:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:10:16: 1000000 INFO @ Fri, 10 Dec 2021 20:10:22: 2000000 INFO @ Fri, 10 Dec 2021 20:10:28: 3000000 INFO @ Fri, 10 Dec 2021 20:10:34: 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 20:10:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.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 20:10:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:10:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:10:40: 5000000 INFO @ Fri, 10 Dec 2021 20:10:47: 6000000 INFO @ Fri, 10 Dec 2021 20:10:47: 1000000 INFO @ Fri, 10 Dec 2021 20:10:53: 7000000 INFO @ Fri, 10 Dec 2021 20:10:54: 2000000 INFO @ Fri, 10 Dec 2021 20:11:00: 8000000 INFO @ Fri, 10 Dec 2021 20:11:02: 3000000 INFO @ Fri, 10 Dec 2021 20:11:06: 9000000 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 20:11:09: 4000000 INFO @ Fri, 10 Dec 2021 20:11:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.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 20:11:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:11:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:11:13: 10000000 INFO @ Fri, 10 Dec 2021 20:11:17: 1000000 INFO @ Fri, 10 Dec 2021 20:11:17: 5000000 INFO @ Fri, 10 Dec 2021 20:11:20: 11000000 INFO @ Fri, 10 Dec 2021 20:11:24: 6000000 INFO @ Fri, 10 Dec 2021 20:11:24: 2000000 INFO @ Fri, 10 Dec 2021 20:11:26: 12000000 INFO @ Fri, 10 Dec 2021 20:11:32: 7000000 INFO @ Fri, 10 Dec 2021 20:11:32: 3000000 INFO @ Fri, 10 Dec 2021 20:11:33: 13000000 INFO @ Fri, 10 Dec 2021 20:11:39: 14000000 INFO @ Fri, 10 Dec 2021 20:11:39: 8000000 INFO @ Fri, 10 Dec 2021 20:11:39: 4000000 INFO @ Fri, 10 Dec 2021 20:11:44: 15000000 INFO @ Fri, 10 Dec 2021 20:11:47: 9000000 INFO @ Fri, 10 Dec 2021 20:11:47: 5000000 INFO @ Fri, 10 Dec 2021 20:11:50: 16000000 INFO @ Fri, 10 Dec 2021 20:11:54: 10000000 INFO @ Fri, 10 Dec 2021 20:11:55: 6000000 INFO @ Fri, 10 Dec 2021 20:11:56: 17000000 INFO @ Fri, 10 Dec 2021 20:12:02: 11000000 INFO @ Fri, 10 Dec 2021 20:12:02: 18000000 INFO @ Fri, 10 Dec 2021 20:12:03: 7000000 INFO @ Fri, 10 Dec 2021 20:12:09: 19000000 INFO @ Fri, 10 Dec 2021 20:12:09: 12000000 INFO @ Fri, 10 Dec 2021 20:12:10: 8000000 INFO @ Fri, 10 Dec 2021 20:12:15: 20000000 INFO @ Fri, 10 Dec 2021 20:12:17: 13000000 INFO @ Fri, 10 Dec 2021 20:12:18: 9000000 INFO @ Fri, 10 Dec 2021 20:12:22: 21000000 INFO @ Fri, 10 Dec 2021 20:12:24: 14000000 INFO @ Fri, 10 Dec 2021 20:12:26: 10000000 INFO @ Fri, 10 Dec 2021 20:12:27: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:12:27: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:12:27: #1 total tags in treatment: 7116395 INFO @ Fri, 10 Dec 2021 20:12:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:12:27: #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 20:12:27: #1 tags after filtering in treatment: 5165769 INFO @ Fri, 10 Dec 2021 20:12:27: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 10 Dec 2021 20:12:27: #1 finished! INFO @ Fri, 10 Dec 2021 20:12:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:12:27: #2 number of paired peaks: 4866 INFO @ Fri, 10 Dec 2021 20:12:27: start model_add_line... INFO @ Fri, 10 Dec 2021 20:12:27: start X-correlation... INFO @ Fri, 10 Dec 2021 20:12:27: end of X-cor INFO @ Fri, 10 Dec 2021 20:12:27: #2 finished! INFO @ Fri, 10 Dec 2021 20:12:27: #2 predicted fragment length is 207 bps INFO @ Fri, 10 Dec 2021 20:12:27: #2 alternative fragment length(s) may be 207 bps INFO @ Fri, 10 Dec 2021 20:12:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.05_model.r WARNING @ Fri, 10 Dec 2021 20:12:27: #2 Since the d (207) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:12:27: #2 You may need to consider one of the other alternative d(s): 207 WARNING @ Fri, 10 Dec 2021 20:12:27: #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 20:12:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:12:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:12:30: 15000000 INFO @ Fri, 10 Dec 2021 20:12:33: 11000000 INFO @ Fri, 10 Dec 2021 20:12:37: 16000000 INFO @ Fri, 10 Dec 2021 20:12:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:12:41: 12000000 INFO @ Fri, 10 Dec 2021 20:12:43: 17000000 INFO @ Fri, 10 Dec 2021 20:12:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:12:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:12:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.05_summits.bed INFO @ Fri, 10 Dec 2021 20:12:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11214 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:12:48: 13000000 INFO @ Fri, 10 Dec 2021 20:12:51: 18000000 INFO @ Fri, 10 Dec 2021 20:12:55: 14000000 INFO @ Fri, 10 Dec 2021 20:12:58: 19000000 INFO @ Fri, 10 Dec 2021 20:13:02: 15000000 INFO @ Fri, 10 Dec 2021 20:13:06: 20000000 INFO @ Fri, 10 Dec 2021 20:13:09: 16000000 INFO @ Fri, 10 Dec 2021 20:13:13: 21000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:13:16: 17000000 INFO @ Fri, 10 Dec 2021 20:13:19: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:13:19: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:13:19: #1 total tags in treatment: 7116395 INFO @ Fri, 10 Dec 2021 20:13:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:13:19: #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 20:13:19: #1 tags after filtering in treatment: 5165769 INFO @ Fri, 10 Dec 2021 20:13:19: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 10 Dec 2021 20:13:19: #1 finished! INFO @ Fri, 10 Dec 2021 20:13:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:13:19: #2 number of paired peaks: 4866 INFO @ Fri, 10 Dec 2021 20:13:19: start model_add_line... INFO @ Fri, 10 Dec 2021 20:13:19: start X-correlation... INFO @ Fri, 10 Dec 2021 20:13:19: end of X-cor INFO @ Fri, 10 Dec 2021 20:13:19: #2 finished! INFO @ Fri, 10 Dec 2021 20:13:19: #2 predicted fragment length is 207 bps INFO @ Fri, 10 Dec 2021 20:13:19: #2 alternative fragment length(s) may be 207 bps INFO @ Fri, 10 Dec 2021 20:13:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.10_model.r WARNING @ Fri, 10 Dec 2021 20:13:19: #2 Since the d (207) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:13:19: #2 You may need to consider one of the other alternative d(s): 207 WARNING @ Fri, 10 Dec 2021 20:13:19: #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 20:13:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:13:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:13:23: 18000000 INFO @ Fri, 10 Dec 2021 20:13:30: 19000000 INFO @ Fri, 10 Dec 2021 20:13:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:13:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:13:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:13:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.10_summits.bed INFO @ Fri, 10 Dec 2021 20:13:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6608 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:13:38: 20000000 INFO @ Fri, 10 Dec 2021 20:13:45: 21000000 INFO @ Fri, 10 Dec 2021 20:13:50: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:13:50: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:13:50: #1 total tags in treatment: 7116395 INFO @ Fri, 10 Dec 2021 20:13:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:13:50: #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 20:13:50: #1 tags after filtering in treatment: 5165769 INFO @ Fri, 10 Dec 2021 20:13:50: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 10 Dec 2021 20:13:50: #1 finished! INFO @ Fri, 10 Dec 2021 20:13:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:13:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:13:51: #2 number of paired peaks: 4866 INFO @ Fri, 10 Dec 2021 20:13:51: start model_add_line... INFO @ Fri, 10 Dec 2021 20:13:51: start X-correlation... INFO @ Fri, 10 Dec 2021 20:13:51: end of X-cor INFO @ Fri, 10 Dec 2021 20:13:51: #2 finished! INFO @ Fri, 10 Dec 2021 20:13:51: #2 predicted fragment length is 207 bps INFO @ Fri, 10 Dec 2021 20:13:51: #2 alternative fragment length(s) may be 207 bps INFO @ Fri, 10 Dec 2021 20:13:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.20_model.r WARNING @ Fri, 10 Dec 2021 20:13:51: #2 Since the d (207) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:13:51: #2 You may need to consider one of the other alternative d(s): 207 WARNING @ Fri, 10 Dec 2021 20:13:51: #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 20:13:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:13:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:14:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:14:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:14:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:14:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978765/ERX3978765.20_summits.bed INFO @ Fri, 10 Dec 2021 20:14:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2530 records, 4 fields): 4 millis CompletedMACS2peakCalling