Job ID = 14172422 SRX = SRX7628884 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18162897 spots for SRR10963246/SRR10963246.sra Written 18162897 spots for SRR10963246/SRR10963246.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172982 ("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: 00:30:12 18162897 reads; of these: 18162897 (100.00%) were paired; of these: 3369951 (18.55%) aligned concordantly 0 times 11056612 (60.87%) aligned concordantly exactly 1 time 3736334 (20.57%) aligned concordantly >1 times ---- 3369951 pairs aligned concordantly 0 times; of these: 314123 (9.32%) aligned discordantly 1 time ---- 3055828 pairs aligned 0 times concordantly or discordantly; of these: 6111656 mates make up the pairs; of these: 4659218 (76.23%) aligned 0 times 599735 (9.81%) aligned exactly 1 time 852703 (13.95%) aligned >1 times 87.17% overall alignment rate Time searching: 00:30:12 Overall time: 00:30:12 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] 937211 / 15097867 = 0.0621 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 15:59:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.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 15:59:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:59:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:59:42: 1000000 INFO @ Sat, 11 Dec 2021 15:59:46: 2000000 INFO @ Sat, 11 Dec 2021 15:59:51: 3000000 INFO @ Sat, 11 Dec 2021 15:59:55: 4000000 INFO @ Sat, 11 Dec 2021 16:00:00: 5000000 INFO @ Sat, 11 Dec 2021 16:00:05: 6000000 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 16:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.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 16:00:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:00:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:00:10: 7000000 INFO @ Sat, 11 Dec 2021 16:00:13: 1000000 INFO @ Sat, 11 Dec 2021 16:00:15: 8000000 INFO @ Sat, 11 Dec 2021 16:00:19: 2000000 INFO @ Sat, 11 Dec 2021 16:00:20: 9000000 INFO @ Sat, 11 Dec 2021 16:00:25: 3000000 INFO @ Sat, 11 Dec 2021 16:00:26: 10000000 INFO @ Sat, 11 Dec 2021 16:00:31: 11000000 INFO @ Sat, 11 Dec 2021 16:00:31: 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 @ Sat, 11 Dec 2021 16:00:36: 12000000 INFO @ Sat, 11 Dec 2021 16:00:37: 5000000 INFO @ Sat, 11 Dec 2021 16:00:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.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 16:00:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:00:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:00:42: 13000000 INFO @ Sat, 11 Dec 2021 16:00:43: 1000000 INFO @ Sat, 11 Dec 2021 16:00:43: 6000000 INFO @ Sat, 11 Dec 2021 16:00:47: 14000000 INFO @ Sat, 11 Dec 2021 16:00:48: 2000000 INFO @ Sat, 11 Dec 2021 16:00:49: 7000000 INFO @ Sat, 11 Dec 2021 16:00:53: 15000000 INFO @ Sat, 11 Dec 2021 16:00:54: 3000000 INFO @ Sat, 11 Dec 2021 16:00:56: 8000000 INFO @ Sat, 11 Dec 2021 16:00:58: 16000000 INFO @ Sat, 11 Dec 2021 16:00:59: 4000000 INFO @ Sat, 11 Dec 2021 16:01:02: 9000000 INFO @ Sat, 11 Dec 2021 16:01:04: 17000000 INFO @ Sat, 11 Dec 2021 16:01:04: 5000000 INFO @ Sat, 11 Dec 2021 16:01:08: 10000000 INFO @ Sat, 11 Dec 2021 16:01:10: 18000000 INFO @ Sat, 11 Dec 2021 16:01:10: 6000000 INFO @ Sat, 11 Dec 2021 16:01:15: 11000000 INFO @ Sat, 11 Dec 2021 16:01:15: 19000000 INFO @ Sat, 11 Dec 2021 16:01:15: 7000000 INFO @ Sat, 11 Dec 2021 16:01:21: 20000000 INFO @ Sat, 11 Dec 2021 16:01:21: 8000000 INFO @ Sat, 11 Dec 2021 16:01:21: 12000000 INFO @ Sat, 11 Dec 2021 16:01:26: 9000000 INFO @ Sat, 11 Dec 2021 16:01:26: 21000000 INFO @ Sat, 11 Dec 2021 16:01:27: 13000000 INFO @ Sat, 11 Dec 2021 16:01:31: 10000000 INFO @ Sat, 11 Dec 2021 16:01:32: 22000000 INFO @ Sat, 11 Dec 2021 16:01:34: 14000000 INFO @ Sat, 11 Dec 2021 16:01:37: 11000000 INFO @ Sat, 11 Dec 2021 16:01:37: 23000000 INFO @ Sat, 11 Dec 2021 16:01:40: 15000000 INFO @ Sat, 11 Dec 2021 16:01:42: 12000000 INFO @ Sat, 11 Dec 2021 16:01:43: 24000000 INFO @ Sat, 11 Dec 2021 16:01:46: 16000000 INFO @ Sat, 11 Dec 2021 16:01:48: 13000000 INFO @ Sat, 11 Dec 2021 16:01:48: 25000000 INFO @ Sat, 11 Dec 2021 16:01:53: 17000000 INFO @ Sat, 11 Dec 2021 16:01:53: 14000000 INFO @ Sat, 11 Dec 2021 16:01:54: 26000000 INFO @ Sat, 11 Dec 2021 16:01:59: 15000000 INFO @ Sat, 11 Dec 2021 16:01:59: 18000000 INFO @ Sat, 11 Dec 2021 16:01:59: 27000000 INFO @ Sat, 11 Dec 2021 16:02:04: 16000000 INFO @ Sat, 11 Dec 2021 16:02:05: 28000000 INFO @ Sat, 11 Dec 2021 16:02:05: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:02:10: 17000000 INFO @ Sat, 11 Dec 2021 16:02:10: 29000000 INFO @ Sat, 11 Dec 2021 16:02:12: 20000000 INFO @ Sat, 11 Dec 2021 16:02:15: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:02:15: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:02:15: #1 total tags in treatment: 13863464 INFO @ Sat, 11 Dec 2021 16:02:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:02:15: #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 16:02:15: #1 tags after filtering in treatment: 7514632 INFO @ Sat, 11 Dec 2021 16:02:15: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 11 Dec 2021 16:02:15: #1 finished! INFO @ Sat, 11 Dec 2021 16:02:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:02:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:02:15: 18000000 INFO @ Sat, 11 Dec 2021 16:02:16: #2 number of paired peaks: 10486 INFO @ Sat, 11 Dec 2021 16:02:16: start model_add_line... INFO @ Sat, 11 Dec 2021 16:02:17: start X-correlation... INFO @ Sat, 11 Dec 2021 16:02:17: end of X-cor INFO @ Sat, 11 Dec 2021 16:02:17: #2 finished! INFO @ Sat, 11 Dec 2021 16:02:17: #2 predicted fragment length is 217 bps INFO @ Sat, 11 Dec 2021 16:02:17: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 11 Dec 2021 16:02:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.05_model.r INFO @ Sat, 11 Dec 2021 16:02:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:02:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:02:19: 21000000 INFO @ Sat, 11 Dec 2021 16:02:21: 19000000 INFO @ Sat, 11 Dec 2021 16:02:26: 22000000 INFO @ Sat, 11 Dec 2021 16:02:27: 20000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:02:33: 21000000 INFO @ Sat, 11 Dec 2021 16:02:34: 23000000 INFO @ Sat, 11 Dec 2021 16:02:39: 22000000 INFO @ Sat, 11 Dec 2021 16:02:42: 24000000 INFO @ Sat, 11 Dec 2021 16:02:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:02:45: 23000000 INFO @ Sat, 11 Dec 2021 16:02:49: 25000000 INFO @ Sat, 11 Dec 2021 16:02:51: 24000000 INFO @ Sat, 11 Dec 2021 16:02:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:02:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:02:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.05_summits.bed INFO @ Sat, 11 Dec 2021 16:02:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8850 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:02:57: 26000000 INFO @ Sat, 11 Dec 2021 16:02:57: 25000000 INFO @ Sat, 11 Dec 2021 16:03:03: 26000000 INFO @ Sat, 11 Dec 2021 16:03:04: 27000000 INFO @ Sat, 11 Dec 2021 16:03:10: 27000000 INFO @ Sat, 11 Dec 2021 16:03:12: 28000000 INFO @ Sat, 11 Dec 2021 16:03:16: 28000000 INFO @ Sat, 11 Dec 2021 16:03:19: 29000000 INFO @ Sat, 11 Dec 2021 16:03:22: 29000000 INFO @ Sat, 11 Dec 2021 16:03:25: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:03:25: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:03:25: #1 total tags in treatment: 13863464 INFO @ Sat, 11 Dec 2021 16:03:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:03:25: #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 16:03:25: #1 tags after filtering in treatment: 7514632 INFO @ Sat, 11 Dec 2021 16:03:25: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 11 Dec 2021 16:03:25: #1 finished! INFO @ Sat, 11 Dec 2021 16:03:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:03:26: #2 number of paired peaks: 10486 INFO @ Sat, 11 Dec 2021 16:03:26: start model_add_line... INFO @ Sat, 11 Dec 2021 16:03:26: start X-correlation... INFO @ Sat, 11 Dec 2021 16:03:26: end of X-cor INFO @ Sat, 11 Dec 2021 16:03:26: #2 finished! INFO @ Sat, 11 Dec 2021 16:03:26: #2 predicted fragment length is 217 bps INFO @ Sat, 11 Dec 2021 16:03:26: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 11 Dec 2021 16:03:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.10_model.r INFO @ Sat, 11 Dec 2021 16:03:27: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:03:27: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:03:27: #1 total tags in treatment: 13863464 INFO @ Sat, 11 Dec 2021 16:03:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:03:27: #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 16:03:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:03:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:03:27: #1 tags after filtering in treatment: 7514632 INFO @ Sat, 11 Dec 2021 16:03:27: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 11 Dec 2021 16:03:27: #1 finished! INFO @ Sat, 11 Dec 2021 16:03:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:03:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:03:28: #2 number of paired peaks: 10486 INFO @ Sat, 11 Dec 2021 16:03:28: start model_add_line... INFO @ Sat, 11 Dec 2021 16:03:28: start X-correlation... INFO @ Sat, 11 Dec 2021 16:03:28: end of X-cor INFO @ Sat, 11 Dec 2021 16:03:28: #2 finished! INFO @ Sat, 11 Dec 2021 16:03:28: #2 predicted fragment length is 217 bps INFO @ Sat, 11 Dec 2021 16:03:28: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 11 Dec 2021 16:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.20_model.r INFO @ Sat, 11 Dec 2021 16:03:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:03:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:03:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:04:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:04:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:04:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.10_summits.bed INFO @ Sat, 11 Dec 2021 16:04:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8109 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:04:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:04:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:04:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628884/SRX7628884.20_summits.bed INFO @ Sat, 11 Dec 2021 16:04:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7102 records, 4 fields): 8 millis CompletedMACS2peakCalling