Job ID = 14168518 SRX = ERX3978751 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18350126 spots for ERR3975763/ERR3975763.sra Written 18350126 spots for ERR3975763/ERR3975763.sra Read 19524972 spots for ERR3975813/ERR3975813.sra Written 19524972 spots for ERR3975813/ERR3975813.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169805 ("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: 01:04:30 37875098 reads; of these: 37875098 (100.00%) were paired; of these: 11099338 (29.31%) aligned concordantly 0 times 4818784 (12.72%) aligned concordantly exactly 1 time 21956976 (57.97%) aligned concordantly >1 times ---- 11099338 pairs aligned concordantly 0 times; of these: 1935284 (17.44%) aligned discordantly 1 time ---- 9164054 pairs aligned 0 times concordantly or discordantly; of these: 18328108 mates make up the pairs; of these: 7758838 (42.33%) aligned 0 times 465081 (2.54%) aligned exactly 1 time 10104189 (55.13%) aligned >1 times 89.76% overall alignment rate Time searching: 01:04:30 Overall time: 01:04:30 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 48 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] 19479909 / 28507015 = 0.6833 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 20:08:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.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 20:08:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:08:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:08:32: 1000000 INFO @ Fri, 10 Dec 2021 20:08:39: 2000000 INFO @ Fri, 10 Dec 2021 20:08:47: 3000000 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 20:08:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.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 20:08:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:08:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:08:55: 4000000 INFO @ Fri, 10 Dec 2021 20:09:02: 1000000 INFO @ Fri, 10 Dec 2021 20:09:03: 5000000 INFO @ Fri, 10 Dec 2021 20:09:10: 2000000 INFO @ Fri, 10 Dec 2021 20:09:11: 6000000 INFO @ Fri, 10 Dec 2021 20:09:18: 3000000 INFO @ Fri, 10 Dec 2021 20:09:19: 7000000 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 20:09:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.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 20:09:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:09:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:09:26: 4000000 INFO @ Fri, 10 Dec 2021 20:09:27: 8000000 INFO @ Fri, 10 Dec 2021 20:09:31: 1000000 INFO @ Fri, 10 Dec 2021 20:09:34: 5000000 INFO @ Fri, 10 Dec 2021 20:09:35: 9000000 INFO @ Fri, 10 Dec 2021 20:09:39: 2000000 INFO @ Fri, 10 Dec 2021 20:09:42: 6000000 INFO @ Fri, 10 Dec 2021 20:09:43: 10000000 INFO @ Fri, 10 Dec 2021 20:09:46: 3000000 INFO @ Fri, 10 Dec 2021 20:09:51: 7000000 INFO @ Fri, 10 Dec 2021 20:09:51: 11000000 INFO @ Fri, 10 Dec 2021 20:09:53: 4000000 INFO @ Fri, 10 Dec 2021 20:09:59: 12000000 INFO @ Fri, 10 Dec 2021 20:09:59: 8000000 INFO @ Fri, 10 Dec 2021 20:10:00: 5000000 INFO @ Fri, 10 Dec 2021 20:10:06: 13000000 INFO @ Fri, 10 Dec 2021 20:10:07: 9000000 INFO @ Fri, 10 Dec 2021 20:10:07: 6000000 INFO @ Fri, 10 Dec 2021 20:10:14: 14000000 INFO @ Fri, 10 Dec 2021 20:10:14: 7000000 INFO @ Fri, 10 Dec 2021 20:10:15: 10000000 INFO @ Fri, 10 Dec 2021 20:10:21: 15000000 INFO @ Fri, 10 Dec 2021 20:10:21: 8000000 INFO @ Fri, 10 Dec 2021 20:10:23: 11000000 INFO @ Fri, 10 Dec 2021 20:10:28: 9000000 INFO @ Fri, 10 Dec 2021 20:10:29: 16000000 INFO @ Fri, 10 Dec 2021 20:10:30: 12000000 INFO @ Fri, 10 Dec 2021 20:10:35: 10000000 INFO @ Fri, 10 Dec 2021 20:10:36: 17000000 INFO @ Fri, 10 Dec 2021 20:10:38: 13000000 INFO @ Fri, 10 Dec 2021 20:10:42: 11000000 INFO @ Fri, 10 Dec 2021 20:10:44: 18000000 INFO @ Fri, 10 Dec 2021 20:10:45: 14000000 INFO @ Fri, 10 Dec 2021 20:10:49: 12000000 INFO @ Fri, 10 Dec 2021 20:10:52: 19000000 INFO @ Fri, 10 Dec 2021 20:10:52: 15000000 INFO @ Fri, 10 Dec 2021 20:10:56: 13000000 INFO @ Fri, 10 Dec 2021 20:10:59: 20000000 INFO @ Fri, 10 Dec 2021 20:11:00: 16000000 INFO @ Fri, 10 Dec 2021 20:11:02: 14000000 INFO @ Fri, 10 Dec 2021 20:11:07: 21000000 INFO @ Fri, 10 Dec 2021 20:11:07: 17000000 INFO @ Fri, 10 Dec 2021 20:11:09: 15000000 INFO @ Fri, 10 Dec 2021 20:11:14: 18000000 INFO @ Fri, 10 Dec 2021 20:11:15: 22000000 INFO @ Fri, 10 Dec 2021 20:11:15: 16000000 INFO @ Fri, 10 Dec 2021 20:11:22: 17000000 INFO @ Fri, 10 Dec 2021 20:11:22: 19000000 INFO @ Fri, 10 Dec 2021 20:11:22: 23000000 INFO @ Fri, 10 Dec 2021 20:11:28: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:11:29: 20000000 INFO @ Fri, 10 Dec 2021 20:11:30: 24000000 INFO @ Fri, 10 Dec 2021 20:11:35: 19000000 INFO @ Fri, 10 Dec 2021 20:11:37: 21000000 INFO @ Fri, 10 Dec 2021 20:11:38: 25000000 INFO @ Fri, 10 Dec 2021 20:11:41: 20000000 INFO @ Fri, 10 Dec 2021 20:11:44: 22000000 INFO @ Fri, 10 Dec 2021 20:11:46: 26000000 INFO @ Fri, 10 Dec 2021 20:11:48: 21000000 INFO @ Fri, 10 Dec 2021 20:11:51: 23000000 INFO @ Fri, 10 Dec 2021 20:11:54: 27000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:11:54: 22000000 INFO @ Fri, 10 Dec 2021 20:11:59: 24000000 INFO @ Fri, 10 Dec 2021 20:12:01: 23000000 INFO @ Fri, 10 Dec 2021 20:12:02: 28000000 INFO @ Fri, 10 Dec 2021 20:12:06: 25000000 INFO @ Fri, 10 Dec 2021 20:12:08: 24000000 INFO @ Fri, 10 Dec 2021 20:12:10: 29000000 INFO @ Fri, 10 Dec 2021 20:12:10: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:12:10: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:12:10: #1 total tags in treatment: 7482138 INFO @ Fri, 10 Dec 2021 20:12:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:12:10: #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 20:12:10: #1 tags after filtering in treatment: 4697498 INFO @ Fri, 10 Dec 2021 20:12:10: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 10 Dec 2021 20:12:10: #1 finished! INFO @ Fri, 10 Dec 2021 20:12:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:12:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:12:11: #2 number of paired peaks: 3818 INFO @ Fri, 10 Dec 2021 20:12:11: start model_add_line... INFO @ Fri, 10 Dec 2021 20:12:11: start X-correlation... INFO @ Fri, 10 Dec 2021 20:12:11: end of X-cor INFO @ Fri, 10 Dec 2021 20:12:11: #2 finished! INFO @ Fri, 10 Dec 2021 20:12:11: #2 predicted fragment length is 209 bps INFO @ Fri, 10 Dec 2021 20:12:11: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 10 Dec 2021 20:12:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.05_model.r WARNING @ Fri, 10 Dec 2021 20:12:11: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:12:11: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Fri, 10 Dec 2021 20:12:11: #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 20:12:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:12:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:12:14: 26000000 INFO @ Fri, 10 Dec 2021 20:12:14: 25000000 INFO @ Fri, 10 Dec 2021 20:12:21: 26000000 INFO @ Fri, 10 Dec 2021 20:12:22: 27000000 INFO @ Fri, 10 Dec 2021 20:12:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:12:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:12:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:12:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.05_summits.bed INFO @ Fri, 10 Dec 2021 20:12:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8848 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:12:28: 27000000 INFO @ Fri, 10 Dec 2021 20:12:30: 28000000 INFO @ Fri, 10 Dec 2021 20:12:35: 28000000 INFO @ Fri, 10 Dec 2021 20:12:37: 29000000 INFO @ Fri, 10 Dec 2021 20:12:38: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:12:38: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:12:38: #1 total tags in treatment: 7482138 INFO @ Fri, 10 Dec 2021 20:12:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:12:38: #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 20:12:38: #1 tags after filtering in treatment: 4697498 INFO @ Fri, 10 Dec 2021 20:12:38: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 10 Dec 2021 20:12:38: #1 finished! INFO @ Fri, 10 Dec 2021 20:12:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:12:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:12:38: #2 number of paired peaks: 3818 INFO @ Fri, 10 Dec 2021 20:12:38: start model_add_line... INFO @ Fri, 10 Dec 2021 20:12:38: start X-correlation... INFO @ Fri, 10 Dec 2021 20:12:38: end of X-cor INFO @ Fri, 10 Dec 2021 20:12:38: #2 finished! INFO @ Fri, 10 Dec 2021 20:12:38: #2 predicted fragment length is 209 bps INFO @ Fri, 10 Dec 2021 20:12:38: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 10 Dec 2021 20:12:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.10_model.r WARNING @ Fri, 10 Dec 2021 20:12:38: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:12:38: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Fri, 10 Dec 2021 20:12:38: #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 20:12:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:12:41: 29000000 INFO @ Fri, 10 Dec 2021 20:12:42: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:12:42: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:12:42: #1 total tags in treatment: 7482138 INFO @ Fri, 10 Dec 2021 20:12:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:12:42: #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 20:12:42: #1 tags after filtering in treatment: 4697498 INFO @ Fri, 10 Dec 2021 20:12:42: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 10 Dec 2021 20:12:42: #1 finished! INFO @ Fri, 10 Dec 2021 20:12:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:12:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:12:42: #2 number of paired peaks: 3818 INFO @ Fri, 10 Dec 2021 20:12:42: start model_add_line... INFO @ Fri, 10 Dec 2021 20:12:42: start X-correlation... INFO @ Fri, 10 Dec 2021 20:12:42: end of X-cor INFO @ Fri, 10 Dec 2021 20:12:42: #2 finished! INFO @ Fri, 10 Dec 2021 20:12:42: #2 predicted fragment length is 209 bps INFO @ Fri, 10 Dec 2021 20:12:42: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 10 Dec 2021 20:12:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.20_model.r WARNING @ Fri, 10 Dec 2021 20:12:42: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:12:42: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Fri, 10 Dec 2021 20:12:42: #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 20:12:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:12:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:12:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:12:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:12:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:12:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:12:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.10_summits.bed INFO @ Fri, 10 Dec 2021 20:12:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5243 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978751/ERX3978751.20_summits.bed INFO @ Fri, 10 Dec 2021 20:12:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1941 records, 4 fields): 18 millis CompletedMACS2peakCalling