Job ID = 14167260 SRX = SRX8076963 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16723298 spots for SRR11504835/SRR11504835.sra Written 16723298 spots for SRR11504835/SRR11504835.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167898 ("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: 00:13:09 16723298 reads; of these: 16723298 (100.00%) were paired; of these: 6190820 (37.02%) aligned concordantly 0 times 9462704 (56.58%) aligned concordantly exactly 1 time 1069774 (6.40%) aligned concordantly >1 times ---- 6190820 pairs aligned concordantly 0 times; of these: 1533896 (24.78%) aligned discordantly 1 time ---- 4656924 pairs aligned 0 times concordantly or discordantly; of these: 9313848 mates make up the pairs; of these: 8221436 (88.27%) aligned 0 times 704227 (7.56%) aligned exactly 1 time 388185 (4.17%) aligned >1 times 75.42% overall alignment rate Time searching: 00:13:10 Overall time: 00:13:10 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] 1574850 / 12063680 = 0.1305 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 11:40:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.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 11:40:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:40:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:40:52: 1000000 INFO @ Fri, 10 Dec 2021 11:40:56: 2000000 INFO @ Fri, 10 Dec 2021 11:41:00: 3000000 INFO @ Fri, 10 Dec 2021 11:41:04: 4000000 INFO @ Fri, 10 Dec 2021 11:41:08: 5000000 INFO @ Fri, 10 Dec 2021 11:41:12: 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 @ Fri, 10 Dec 2021 11:41:16: 7000000 INFO @ Fri, 10 Dec 2021 11:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.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 11:41:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:41:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:41:20: 8000000 INFO @ Fri, 10 Dec 2021 11:41:21: 1000000 INFO @ Fri, 10 Dec 2021 11:41:24: 9000000 INFO @ Fri, 10 Dec 2021 11:41:25: 2000000 INFO @ Fri, 10 Dec 2021 11:41:28: 10000000 INFO @ Fri, 10 Dec 2021 11:41:30: 3000000 INFO @ Fri, 10 Dec 2021 11:41:32: 11000000 INFO @ Fri, 10 Dec 2021 11:41:34: 4000000 INFO @ Fri, 10 Dec 2021 11:41:36: 12000000 INFO @ Fri, 10 Dec 2021 11:41:38: 5000000 INFO @ Fri, 10 Dec 2021 11:41:40: 13000000 INFO @ Fri, 10 Dec 2021 11:41:42: 6000000 INFO @ Fri, 10 Dec 2021 11:41:45: 14000000 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 11:41:46: 7000000 INFO @ Fri, 10 Dec 2021 11:41:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.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 11:41:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:41:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:41:49: 15000000 INFO @ Fri, 10 Dec 2021 11:41:50: 8000000 INFO @ Fri, 10 Dec 2021 11:41:51: 1000000 INFO @ Fri, 10 Dec 2021 11:41:53: 16000000 INFO @ Fri, 10 Dec 2021 11:41:54: 9000000 INFO @ Fri, 10 Dec 2021 11:41:56: 2000000 INFO @ Fri, 10 Dec 2021 11:41:57: 17000000 INFO @ Fri, 10 Dec 2021 11:41:58: 10000000 INFO @ Fri, 10 Dec 2021 11:42:00: 3000000 INFO @ Fri, 10 Dec 2021 11:42:01: 18000000 INFO @ Fri, 10 Dec 2021 11:42:03: 11000000 INFO @ Fri, 10 Dec 2021 11:42:04: 4000000 INFO @ Fri, 10 Dec 2021 11:42:05: 19000000 INFO @ Fri, 10 Dec 2021 11:42:07: 12000000 INFO @ Fri, 10 Dec 2021 11:42:08: 5000000 INFO @ Fri, 10 Dec 2021 11:42:10: 20000000 INFO @ Fri, 10 Dec 2021 11:42:11: 13000000 INFO @ Fri, 10 Dec 2021 11:42:12: 6000000 INFO @ Fri, 10 Dec 2021 11:42:14: 21000000 INFO @ Fri, 10 Dec 2021 11:42:15: 14000000 INFO @ Fri, 10 Dec 2021 11:42:16: 7000000 INFO @ Fri, 10 Dec 2021 11:42:18: 22000000 INFO @ Fri, 10 Dec 2021 11:42:18: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:42:18: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:42:18: #1 total tags in treatment: 9104447 INFO @ Fri, 10 Dec 2021 11:42:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:42:18: #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 11:42:19: #1 tags after filtering in treatment: 8363089 INFO @ Fri, 10 Dec 2021 11:42:19: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 11:42:19: #1 finished! INFO @ Fri, 10 Dec 2021 11:42:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:42:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:42:19: 15000000 INFO @ Fri, 10 Dec 2021 11:42:20: #2 number of paired peaks: 8350 INFO @ Fri, 10 Dec 2021 11:42:20: start model_add_line... INFO @ Fri, 10 Dec 2021 11:42:20: start X-correlation... INFO @ Fri, 10 Dec 2021 11:42:20: end of X-cor INFO @ Fri, 10 Dec 2021 11:42:20: #2 finished! INFO @ Fri, 10 Dec 2021 11:42:20: #2 predicted fragment length is 254 bps INFO @ Fri, 10 Dec 2021 11:42:20: #2 alternative fragment length(s) may be 4,254 bps INFO @ Fri, 10 Dec 2021 11:42:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.05_model.r INFO @ Fri, 10 Dec 2021 11:42:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:42:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:42:20: 8000000 INFO @ Fri, 10 Dec 2021 11:42:23: 16000000 INFO @ Fri, 10 Dec 2021 11:42:24: 9000000 INFO @ Fri, 10 Dec 2021 11:42:27: 17000000 INFO @ Fri, 10 Dec 2021 11:42:29: 10000000 INFO @ Fri, 10 Dec 2021 11:42:32: 18000000 INFO @ Fri, 10 Dec 2021 11:42:33: 11000000 INFO @ Fri, 10 Dec 2021 11:42:36: 19000000 INFO @ Fri, 10 Dec 2021 11:42:37: 12000000 INFO @ Fri, 10 Dec 2021 11:42:40: 20000000 INFO @ Fri, 10 Dec 2021 11:42:41: 13000000 INFO @ Fri, 10 Dec 2021 11:42:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:42:44: 21000000 INFO @ Fri, 10 Dec 2021 11:42:45: 14000000 INFO @ Fri, 10 Dec 2021 11:42:48: 22000000 INFO @ Fri, 10 Dec 2021 11:42:48: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:42:48: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:42:48: #1 total tags in treatment: 9104447 INFO @ Fri, 10 Dec 2021 11:42:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:42:48: #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 11:42:48: #1 tags after filtering in treatment: 8363089 INFO @ Fri, 10 Dec 2021 11:42:48: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 11:42:48: #1 finished! INFO @ Fri, 10 Dec 2021 11:42:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:42:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:42:49: 15000000 INFO @ Fri, 10 Dec 2021 11:42:49: #2 number of paired peaks: 8350 INFO @ Fri, 10 Dec 2021 11:42:49: start model_add_line... INFO @ Fri, 10 Dec 2021 11:42:50: start X-correlation... INFO @ Fri, 10 Dec 2021 11:42:50: end of X-cor INFO @ Fri, 10 Dec 2021 11:42:50: #2 finished! INFO @ Fri, 10 Dec 2021 11:42:50: #2 predicted fragment length is 254 bps INFO @ Fri, 10 Dec 2021 11:42:50: #2 alternative fragment length(s) may be 4,254 bps INFO @ Fri, 10 Dec 2021 11:42:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.10_model.r INFO @ Fri, 10 Dec 2021 11:42:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:42:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:42:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:42:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:42:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.05_summits.bed INFO @ Fri, 10 Dec 2021 11:42:51: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1101 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:42:53: 16000000 INFO @ Fri, 10 Dec 2021 11:42:57: 17000000 INFO @ Fri, 10 Dec 2021 11:43:01: 18000000 INFO @ Fri, 10 Dec 2021 11:43:05: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:43:09: 20000000 INFO @ Fri, 10 Dec 2021 11:43:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:43:13: 21000000 INFO @ Fri, 10 Dec 2021 11:43:17: 22000000 INFO @ Fri, 10 Dec 2021 11:43:17: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:43:17: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:43:17: #1 total tags in treatment: 9104447 INFO @ Fri, 10 Dec 2021 11:43:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:43:17: #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 11:43:18: #1 tags after filtering in treatment: 8363089 INFO @ Fri, 10 Dec 2021 11:43:18: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 11:43:18: #1 finished! INFO @ Fri, 10 Dec 2021 11:43:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:43:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:43:19: #2 number of paired peaks: 8350 INFO @ Fri, 10 Dec 2021 11:43:19: start model_add_line... INFO @ Fri, 10 Dec 2021 11:43:19: start X-correlation... INFO @ Fri, 10 Dec 2021 11:43:19: end of X-cor INFO @ Fri, 10 Dec 2021 11:43:19: #2 finished! INFO @ Fri, 10 Dec 2021 11:43:19: #2 predicted fragment length is 254 bps INFO @ Fri, 10 Dec 2021 11:43:19: #2 alternative fragment length(s) may be 4,254 bps INFO @ Fri, 10 Dec 2021 11:43:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.20_model.r INFO @ Fri, 10 Dec 2021 11:43:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:43:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:43:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:43:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:43:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.10_summits.bed INFO @ Fri, 10 Dec 2021 11:43:21: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (398 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:43:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:43:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:43:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:43:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076963/SRX8076963.20_summits.bed INFO @ Fri, 10 Dec 2021 11:43:51: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (134 records, 4 fields): 1 millis CompletedMACS2peakCalling