Job ID = 14172492 SRX = SRX7628899 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21097651 spots for SRR10963261/SRR10963261.sra Written 21097651 spots for SRR10963261/SRR10963261.sra fastq に変換しました。 bowtie でマッピング中... Your job 14173045 ("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: 00:31:08 21097651 reads; of these: 21097651 (100.00%) were paired; of these: 5429862 (25.74%) aligned concordantly 0 times 11705101 (55.48%) aligned concordantly exactly 1 time 3962688 (18.78%) aligned concordantly >1 times ---- 5429862 pairs aligned concordantly 0 times; of these: 92514 (1.70%) aligned discordantly 1 time ---- 5337348 pairs aligned 0 times concordantly or discordantly; of these: 10674696 mates make up the pairs; of these: 9644602 (90.35%) aligned 0 times 470274 (4.41%) aligned exactly 1 time 559820 (5.24%) aligned >1 times 77.14% overall alignment rate Time searching: 00:31:08 Overall time: 00:31:08 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] 1560774 / 15754011 = 0.0991 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 @ Sat, 11 Dec 2021 16:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.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, 11 Dec 2021 16:20:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:20:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:20:49: 1000000 INFO @ Sat, 11 Dec 2021 16:20:55: 2000000 INFO @ Sat, 11 Dec 2021 16:21:01: 3000000 INFO @ Sat, 11 Dec 2021 16:21:06: 4000000 INFO @ Sat, 11 Dec 2021 16:21:12: 5000000 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 @ Sat, 11 Dec 2021 16:21:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.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, 11 Dec 2021 16:21:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:21:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:21:17: 6000000 INFO @ Sat, 11 Dec 2021 16:21:20: 1000000 INFO @ Sat, 11 Dec 2021 16:21:23: 7000000 INFO @ Sat, 11 Dec 2021 16:21:26: 2000000 INFO @ Sat, 11 Dec 2021 16:21:29: 8000000 INFO @ Sat, 11 Dec 2021 16:21:32: 3000000 INFO @ Sat, 11 Dec 2021 16:21:35: 9000000 INFO @ Sat, 11 Dec 2021 16:21:38: 4000000 INFO @ Sat, 11 Dec 2021 16:21:41: 10000000 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 @ Sat, 11 Dec 2021 16:21:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.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, 11 Dec 2021 16:21:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:21:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:21:44: 5000000 INFO @ Sat, 11 Dec 2021 16:21:47: 11000000 INFO @ Sat, 11 Dec 2021 16:21:50: 1000000 INFO @ Sat, 11 Dec 2021 16:21:50: 6000000 INFO @ Sat, 11 Dec 2021 16:21:53: 12000000 INFO @ Sat, 11 Dec 2021 16:21:56: 2000000 INFO @ Sat, 11 Dec 2021 16:21:57: 7000000 INFO @ Sat, 11 Dec 2021 16:22:00: 13000000 INFO @ Sat, 11 Dec 2021 16:22:03: 3000000 INFO @ Sat, 11 Dec 2021 16:22:03: 8000000 INFO @ Sat, 11 Dec 2021 16:22:06: 14000000 INFO @ Sat, 11 Dec 2021 16:22:09: 4000000 INFO @ Sat, 11 Dec 2021 16:22:09: 9000000 INFO @ Sat, 11 Dec 2021 16:22:13: 15000000 INFO @ Sat, 11 Dec 2021 16:22:15: 10000000 INFO @ Sat, 11 Dec 2021 16:22:16: 5000000 INFO @ Sat, 11 Dec 2021 16:22:19: 16000000 INFO @ Sat, 11 Dec 2021 16:22:21: 11000000 INFO @ Sat, 11 Dec 2021 16:22:22: 6000000 INFO @ Sat, 11 Dec 2021 16:22:25: 17000000 INFO @ Sat, 11 Dec 2021 16:22:27: 12000000 INFO @ Sat, 11 Dec 2021 16:22:28: 7000000 INFO @ Sat, 11 Dec 2021 16:22:31: 18000000 INFO @ Sat, 11 Dec 2021 16:22:34: 13000000 INFO @ Sat, 11 Dec 2021 16:22:35: 8000000 INFO @ Sat, 11 Dec 2021 16:22:38: 19000000 INFO @ Sat, 11 Dec 2021 16:22:40: 14000000 INFO @ Sat, 11 Dec 2021 16:22:41: 9000000 INFO @ Sat, 11 Dec 2021 16:22:44: 20000000 INFO @ Sat, 11 Dec 2021 16:22:46: 15000000 INFO @ Sat, 11 Dec 2021 16:22:47: 10000000 INFO @ Sat, 11 Dec 2021 16:22:50: 21000000 INFO @ Sat, 11 Dec 2021 16:22:52: 16000000 INFO @ Sat, 11 Dec 2021 16:22:53: 11000000 INFO @ Sat, 11 Dec 2021 16:22:56: 22000000 INFO @ Sat, 11 Dec 2021 16:22:58: 17000000 INFO @ Sat, 11 Dec 2021 16:23:00: 12000000 INFO @ Sat, 11 Dec 2021 16:23:03: 23000000 INFO @ Sat, 11 Dec 2021 16:23:05: 18000000 INFO @ Sat, 11 Dec 2021 16:23:07: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:23:09: 24000000 INFO @ Sat, 11 Dec 2021 16:23:12: 19000000 INFO @ Sat, 11 Dec 2021 16:23:13: 14000000 INFO @ Sat, 11 Dec 2021 16:23:15: 25000000 INFO @ Sat, 11 Dec 2021 16:23:19: 20000000 INFO @ Sat, 11 Dec 2021 16:23:20: 15000000 INFO @ Sat, 11 Dec 2021 16:23:22: 26000000 INFO @ Sat, 11 Dec 2021 16:23:25: 21000000 INFO @ Sat, 11 Dec 2021 16:23:26: 16000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:23:28: 27000000 INFO @ Sat, 11 Dec 2021 16:23:32: 22000000 INFO @ Sat, 11 Dec 2021 16:23:32: 17000000 INFO @ Sat, 11 Dec 2021 16:23:35: 28000000 INFO @ Sat, 11 Dec 2021 16:23:38: 18000000 INFO @ Sat, 11 Dec 2021 16:23:39: 23000000 INFO @ Sat, 11 Dec 2021 16:23:41: 29000000 INFO @ Sat, 11 Dec 2021 16:23:44: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:23:44: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:23:44: #1 total tags in treatment: 14110708 INFO @ Sat, 11 Dec 2021 16:23:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:23:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:23:44: 19000000 INFO @ Sat, 11 Dec 2021 16:23:45: #1 tags after filtering in treatment: 7240520 INFO @ Sat, 11 Dec 2021 16:23:45: #1 Redundant rate of treatment: 0.49 INFO @ Sat, 11 Dec 2021 16:23:45: #1 finished! INFO @ Sat, 11 Dec 2021 16:23:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:23:45: 24000000 INFO @ Sat, 11 Dec 2021 16:23:46: #2 number of paired peaks: 10080 INFO @ Sat, 11 Dec 2021 16:23:46: start model_add_line... INFO @ Sat, 11 Dec 2021 16:23:46: start X-correlation... INFO @ Sat, 11 Dec 2021 16:23:46: end of X-cor INFO @ Sat, 11 Dec 2021 16:23:46: #2 finished! INFO @ Sat, 11 Dec 2021 16:23:46: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 16:23:46: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Dec 2021 16:23:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.05_model.r INFO @ Sat, 11 Dec 2021 16:23:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:23:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:23:51: 20000000 INFO @ Sat, 11 Dec 2021 16:23:52: 25000000 INFO @ Sat, 11 Dec 2021 16:23:57: 21000000 INFO @ Sat, 11 Dec 2021 16:23:58: 26000000 INFO @ Sat, 11 Dec 2021 16:24:03: 22000000 INFO @ Sat, 11 Dec 2021 16:24:04: 27000000 INFO @ Sat, 11 Dec 2021 16:24:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:24:08: 23000000 INFO @ Sat, 11 Dec 2021 16:24:11: 28000000 INFO @ Sat, 11 Dec 2021 16:24:14: 24000000 INFO @ Sat, 11 Dec 2021 16:24:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:24:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:24:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.05_summits.bed INFO @ Sat, 11 Dec 2021 16:24:16: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9856 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:24:18: 29000000 INFO @ Sat, 11 Dec 2021 16:24:20: 25000000 INFO @ Sat, 11 Dec 2021 16:24:21: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:24:21: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:24:21: #1 total tags in treatment: 14110708 INFO @ Sat, 11 Dec 2021 16:24:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:24:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:24:21: #1 tags after filtering in treatment: 7240520 INFO @ Sat, 11 Dec 2021 16:24:21: #1 Redundant rate of treatment: 0.49 INFO @ Sat, 11 Dec 2021 16:24:21: #1 finished! INFO @ Sat, 11 Dec 2021 16:24:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:24:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:24:22: #2 number of paired peaks: 10080 INFO @ Sat, 11 Dec 2021 16:24:22: start model_add_line... INFO @ Sat, 11 Dec 2021 16:24:22: start X-correlation... INFO @ Sat, 11 Dec 2021 16:24:22: end of X-cor INFO @ Sat, 11 Dec 2021 16:24:22: #2 finished! INFO @ Sat, 11 Dec 2021 16:24:22: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 16:24:22: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Dec 2021 16:24:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.10_model.r INFO @ Sat, 11 Dec 2021 16:24:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:24:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:24:26: 26000000 INFO @ Sat, 11 Dec 2021 16:24:32: 27000000 INFO @ Sat, 11 Dec 2021 16:24:38: 28000000 INFO @ Sat, 11 Dec 2021 16:24:44: 29000000 INFO @ Sat, 11 Dec 2021 16:24:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:24:46: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:24:46: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:24:46: #1 total tags in treatment: 14110708 INFO @ Sat, 11 Dec 2021 16:24:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:24:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:24:47: #1 tags after filtering in treatment: 7240520 INFO @ Sat, 11 Dec 2021 16:24:47: #1 Redundant rate of treatment: 0.49 INFO @ Sat, 11 Dec 2021 16:24:47: #1 finished! INFO @ Sat, 11 Dec 2021 16:24:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:24:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:24:48: #2 number of paired peaks: 10080 INFO @ Sat, 11 Dec 2021 16:24:48: start model_add_line... INFO @ Sat, 11 Dec 2021 16:24:48: start X-correlation... INFO @ Sat, 11 Dec 2021 16:24:48: end of X-cor INFO @ Sat, 11 Dec 2021 16:24:48: #2 finished! INFO @ Sat, 11 Dec 2021 16:24:48: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 16:24:48: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Dec 2021 16:24:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.20_model.r INFO @ Sat, 11 Dec 2021 16:24:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:24:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:24:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:24:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:24:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.10_summits.bed INFO @ Sat, 11 Dec 2021 16:24:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8914 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:25:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:25:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:25:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:25:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628899/SRX7628899.20_summits.bed INFO @ Sat, 11 Dec 2021 16:25:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7796 records, 4 fields): 9 millis CompletedMACS2peakCalling