Job ID = 14172490 SRX = SRX7628897 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18982638 spots for SRR10963259/SRR10963259.sra Written 18982638 spots for SRR10963259/SRR10963259.sra fastq に変換しました。 bowtie でマッピング中... Your job 14173016 ("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: 00:23:16 18982638 reads; of these: 18982638 (100.00%) were paired; of these: 8057170 (42.44%) aligned concordantly 0 times 8045896 (42.39%) aligned concordantly exactly 1 time 2879572 (15.17%) aligned concordantly >1 times ---- 8057170 pairs aligned concordantly 0 times; of these: 101675 (1.26%) aligned discordantly 1 time ---- 7955495 pairs aligned 0 times concordantly or discordantly; of these: 15910990 mates make up the pairs; of these: 15279191 (96.03%) aligned 0 times 312285 (1.96%) aligned exactly 1 time 319514 (2.01%) aligned >1 times 59.75% overall alignment rate Time searching: 00:23:16 Overall time: 00:23:16 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] 774981 / 11021973 = 0.0703 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 16:08:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.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 16:08:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:08:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:08:26: 1000000 INFO @ Sat, 11 Dec 2021 16:08:32: 2000000 INFO @ Sat, 11 Dec 2021 16:08:37: 3000000 INFO @ Sat, 11 Dec 2021 16:08:43: 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 @ Sat, 11 Dec 2021 16:08:49: 5000000 INFO @ Sat, 11 Dec 2021 16:08:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.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 16:08:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:08:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:08:56: 6000000 INFO @ Sat, 11 Dec 2021 16:08:56: 1000000 INFO @ Sat, 11 Dec 2021 16:09:02: 7000000 INFO @ Sat, 11 Dec 2021 16:09:02: 2000000 INFO @ Sat, 11 Dec 2021 16:09:08: 8000000 INFO @ Sat, 11 Dec 2021 16:09:09: 3000000 INFO @ Sat, 11 Dec 2021 16:09:15: 9000000 INFO @ Sat, 11 Dec 2021 16:09:15: 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 16:09:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.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 16:09:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:09:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:09:21: 10000000 INFO @ Sat, 11 Dec 2021 16:09:22: 5000000 INFO @ Sat, 11 Dec 2021 16:09:26: 1000000 INFO @ Sat, 11 Dec 2021 16:09:27: 11000000 INFO @ Sat, 11 Dec 2021 16:09:28: 6000000 INFO @ Sat, 11 Dec 2021 16:09:32: 2000000 INFO @ Sat, 11 Dec 2021 16:09:34: 12000000 INFO @ Sat, 11 Dec 2021 16:09:35: 7000000 INFO @ Sat, 11 Dec 2021 16:09:39: 3000000 INFO @ Sat, 11 Dec 2021 16:09:40: 13000000 INFO @ Sat, 11 Dec 2021 16:09:41: 8000000 INFO @ Sat, 11 Dec 2021 16:09:45: 4000000 INFO @ Sat, 11 Dec 2021 16:09:46: 14000000 INFO @ Sat, 11 Dec 2021 16:09:48: 9000000 INFO @ Sat, 11 Dec 2021 16:09:51: 5000000 INFO @ Sat, 11 Dec 2021 16:09:53: 15000000 INFO @ Sat, 11 Dec 2021 16:09:54: 10000000 INFO @ Sat, 11 Dec 2021 16:09:57: 6000000 INFO @ Sat, 11 Dec 2021 16:09:59: 16000000 INFO @ Sat, 11 Dec 2021 16:10:01: 11000000 INFO @ Sat, 11 Dec 2021 16:10:04: 7000000 INFO @ Sat, 11 Dec 2021 16:10:05: 17000000 INFO @ Sat, 11 Dec 2021 16:10:07: 12000000 INFO @ Sat, 11 Dec 2021 16:10:10: 8000000 INFO @ Sat, 11 Dec 2021 16:10:12: 18000000 INFO @ Sat, 11 Dec 2021 16:10:14: 13000000 INFO @ Sat, 11 Dec 2021 16:10:16: 9000000 INFO @ Sat, 11 Dec 2021 16:10:18: 19000000 INFO @ Sat, 11 Dec 2021 16:10:20: 14000000 INFO @ Sat, 11 Dec 2021 16:10:23: 10000000 INFO @ Sat, 11 Dec 2021 16:10:24: 20000000 INFO @ Sat, 11 Dec 2021 16:10:27: 15000000 INFO @ Sat, 11 Dec 2021 16:10:29: 11000000 INFO @ Sat, 11 Dec 2021 16:10:31: 21000000 INFO @ Sat, 11 Dec 2021 16:10:32: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 16:10:32: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 16:10:32: #1 total tags in treatment: 10154870 INFO @ Sat, 11 Dec 2021 16:10:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:10:32: #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 16:10:32: #1 tags after filtering in treatment: 8794441 INFO @ Sat, 11 Dec 2021 16:10:32: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 16:10:32: #1 finished! INFO @ Sat, 11 Dec 2021 16:10:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:10:33: #2 number of paired peaks: 5900 INFO @ Sat, 11 Dec 2021 16:10:33: start model_add_line... INFO @ Sat, 11 Dec 2021 16:10:33: start X-correlation... INFO @ Sat, 11 Dec 2021 16:10:33: end of X-cor INFO @ Sat, 11 Dec 2021 16:10:33: #2 finished! INFO @ Sat, 11 Dec 2021 16:10:33: #2 predicted fragment length is 181 bps INFO @ Sat, 11 Dec 2021 16:10:33: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 11 Dec 2021 16:10:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.05_model.r INFO @ Sat, 11 Dec 2021 16:10:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:10:33: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:10:35: 12000000 INFO @ Sat, 11 Dec 2021 16:10:40: 17000000 INFO @ Sat, 11 Dec 2021 16:10:41: 13000000 INFO @ Sat, 11 Dec 2021 16:10:46: 18000000 INFO @ Sat, 11 Dec 2021 16:10:48: 14000000 INFO @ Sat, 11 Dec 2021 16:10:53: 19000000 INFO @ Sat, 11 Dec 2021 16:10:54: 15000000 INFO @ Sat, 11 Dec 2021 16:10:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:10:59: 20000000 INFO @ Sat, 11 Dec 2021 16:11:00: 16000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:11:05: 21000000 INFO @ Sat, 11 Dec 2021 16:11:06: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 16:11:06: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 16:11:06: #1 total tags in treatment: 10154870 INFO @ Sat, 11 Dec 2021 16:11:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:11:06: #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 16:11:06: #1 tags after filtering in treatment: 8794441 INFO @ Sat, 11 Dec 2021 16:11:06: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 16:11:06: #1 finished! INFO @ Sat, 11 Dec 2021 16:11:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:11:07: 17000000 INFO @ Sat, 11 Dec 2021 16:11:07: #2 number of paired peaks: 5900 INFO @ Sat, 11 Dec 2021 16:11:07: start model_add_line... INFO @ Sat, 11 Dec 2021 16:11:07: start X-correlation... INFO @ Sat, 11 Dec 2021 16:11:08: end of X-cor INFO @ Sat, 11 Dec 2021 16:11:08: #2 finished! INFO @ Sat, 11 Dec 2021 16:11:08: #2 predicted fragment length is 181 bps INFO @ Sat, 11 Dec 2021 16:11:08: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 11 Dec 2021 16:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.10_model.r INFO @ Sat, 11 Dec 2021 16:11:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:11:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:11:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:11:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.05_summits.bed INFO @ Sat, 11 Dec 2021 16:11:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9139 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:11:13: 18000000 INFO @ Sat, 11 Dec 2021 16:11:18: 19000000 INFO @ Sat, 11 Dec 2021 16:11:24: 20000000 INFO @ Sat, 11 Dec 2021 16:11:30: 21000000 INFO @ Sat, 11 Dec 2021 16:11:31: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 16:11:31: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 16:11:31: #1 total tags in treatment: 10154870 INFO @ Sat, 11 Dec 2021 16:11:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:11:31: #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 16:11:31: #1 tags after filtering in treatment: 8794441 INFO @ Sat, 11 Dec 2021 16:11:31: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 16:11:31: #1 finished! INFO @ Sat, 11 Dec 2021 16:11:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:11:32: #2 number of paired peaks: 5900 INFO @ Sat, 11 Dec 2021 16:11:32: start model_add_line... INFO @ Sat, 11 Dec 2021 16:11:32: start X-correlation... INFO @ Sat, 11 Dec 2021 16:11:32: end of X-cor INFO @ Sat, 11 Dec 2021 16:11:32: #2 finished! INFO @ Sat, 11 Dec 2021 16:11:32: #2 predicted fragment length is 181 bps INFO @ Sat, 11 Dec 2021 16:11:32: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 11 Dec 2021 16:11:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.20_model.r INFO @ Sat, 11 Dec 2021 16:11:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:11:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:11:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:11:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.10_summits.bed INFO @ Sat, 11 Dec 2021 16:11:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6169 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:11:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628897/SRX7628897.20_summits.bed INFO @ Sat, 11 Dec 2021 16:12:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3511 records, 4 fields): 5 millis CompletedMACS2peakCalling