Job ID = 12265474 SRX = SRX7192195 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29690221 spots for SRR10503240/SRR10503240.sra Written 29690221 spots for SRR10503240/SRR10503240.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265699 ("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: 00:27:53 29690221 reads; of these: 29690221 (100.00%) were paired; of these: 10763227 (36.25%) aligned concordantly 0 times 15918710 (53.62%) aligned concordantly exactly 1 time 3008284 (10.13%) aligned concordantly >1 times ---- 10763227 pairs aligned concordantly 0 times; of these: 729652 (6.78%) aligned discordantly 1 time ---- 10033575 pairs aligned 0 times concordantly or discordantly; of these: 20067150 mates make up the pairs; of these: 19429070 (96.82%) aligned 0 times 451703 (2.25%) aligned exactly 1 time 186377 (0.93%) aligned >1 times 67.28% overall alignment rate Time searching: 00:27:53 Overall time: 00:27:53 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 20 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] 8348923 / 19605208 = 0.4259 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:54:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.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, 03 Apr 2021 07:54:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:54:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:54:36: 1000000 INFO @ Sat, 03 Apr 2021 07:54:42: 2000000 INFO @ Sat, 03 Apr 2021 07:54:47: 3000000 INFO @ Sat, 03 Apr 2021 07:54:53: 4000000 INFO @ Sat, 03 Apr 2021 07:54:58: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:55:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.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, 03 Apr 2021 07:55:01: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:55:01: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:55:04: 6000000 INFO @ Sat, 03 Apr 2021 07:55:07: 1000000 INFO @ Sat, 03 Apr 2021 07:55:10: 7000000 INFO @ Sat, 03 Apr 2021 07:55:14: 2000000 INFO @ Sat, 03 Apr 2021 07:55:16: 8000000 INFO @ Sat, 03 Apr 2021 07:55:20: 3000000 INFO @ Sat, 03 Apr 2021 07:55:22: 9000000 INFO @ Sat, 03 Apr 2021 07:55:26: 4000000 INFO @ Sat, 03 Apr 2021 07:55:28: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:55:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.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, 03 Apr 2021 07:55:30: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:55:30: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:55:32: 5000000 INFO @ Sat, 03 Apr 2021 07:55:34: 11000000 INFO @ Sat, 03 Apr 2021 07:55:37: 1000000 INFO @ Sat, 03 Apr 2021 07:55:39: 6000000 INFO @ Sat, 03 Apr 2021 07:55:40: 12000000 INFO @ Sat, 03 Apr 2021 07:55:44: 2000000 INFO @ Sat, 03 Apr 2021 07:55:45: 7000000 INFO @ Sat, 03 Apr 2021 07:55:46: 13000000 INFO @ Sat, 03 Apr 2021 07:55:51: 3000000 INFO @ Sat, 03 Apr 2021 07:55:52: 8000000 INFO @ Sat, 03 Apr 2021 07:55:52: 14000000 INFO @ Sat, 03 Apr 2021 07:55:57: 4000000 INFO @ Sat, 03 Apr 2021 07:55:58: 9000000 INFO @ Sat, 03 Apr 2021 07:55:59: 15000000 INFO @ Sat, 03 Apr 2021 07:56:04: 5000000 INFO @ Sat, 03 Apr 2021 07:56:04: 10000000 INFO @ Sat, 03 Apr 2021 07:56:05: 16000000 INFO @ Sat, 03 Apr 2021 07:56:10: 6000000 INFO @ Sat, 03 Apr 2021 07:56:11: 17000000 INFO @ Sat, 03 Apr 2021 07:56:11: 11000000 INFO @ Sat, 03 Apr 2021 07:56:16: 18000000 INFO @ Sat, 03 Apr 2021 07:56:17: 7000000 INFO @ Sat, 03 Apr 2021 07:56:17: 12000000 INFO @ Sat, 03 Apr 2021 07:56:23: 19000000 INFO @ Sat, 03 Apr 2021 07:56:23: 8000000 INFO @ Sat, 03 Apr 2021 07:56:24: 13000000 INFO @ Sat, 03 Apr 2021 07:56:29: 20000000 INFO @ Sat, 03 Apr 2021 07:56:30: 14000000 INFO @ Sat, 03 Apr 2021 07:56:30: 9000000 INFO @ Sat, 03 Apr 2021 07:56:35: 21000000 INFO @ Sat, 03 Apr 2021 07:56:36: 15000000 INFO @ Sat, 03 Apr 2021 07:56:37: 10000000 INFO @ Sat, 03 Apr 2021 07:56:41: 22000000 INFO @ Sat, 03 Apr 2021 07:56:42: 16000000 INFO @ Sat, 03 Apr 2021 07:56:43: 11000000 INFO @ Sat, 03 Apr 2021 07:56:47: 23000000 INFO @ Sat, 03 Apr 2021 07:56:49: 17000000 INFO @ Sat, 03 Apr 2021 07:56:49: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 07:56:49: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 07:56:49: #1 total tags in treatment: 10703833 INFO @ Sat, 03 Apr 2021 07:56:49: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:56:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:56:49: #1 tags after filtering in treatment: 7089252 INFO @ Sat, 03 Apr 2021 07:56:49: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 03 Apr 2021 07:56:49: #1 finished! INFO @ Sat, 03 Apr 2021 07:56:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:56:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:56:50: 12000000 INFO @ Sat, 03 Apr 2021 07:56:50: #2 number of paired peaks: 5363 INFO @ Sat, 03 Apr 2021 07:56:50: start model_add_line... INFO @ Sat, 03 Apr 2021 07:56:50: start X-correlation... INFO @ Sat, 03 Apr 2021 07:56:50: end of X-cor INFO @ Sat, 03 Apr 2021 07:56:50: #2 finished! INFO @ Sat, 03 Apr 2021 07:56:50: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Apr 2021 07:56:50: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 03 Apr 2021 07:56:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.05_model.r INFO @ Sat, 03 Apr 2021 07:56:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:56:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:56:54: 18000000 INFO @ Sat, 03 Apr 2021 07:56:56: 13000000 INFO @ Sat, 03 Apr 2021 07:56:59: 19000000 INFO @ Sat, 03 Apr 2021 07:57:03: 14000000 INFO @ Sat, 03 Apr 2021 07:57:05: 20000000 INFO @ Sat, 03 Apr 2021 07:57:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:57:10: 15000000 INFO @ Sat, 03 Apr 2021 07:57:11: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:57:16: 16000000 INFO @ Sat, 03 Apr 2021 07:57:16: 22000000 INFO @ Sat, 03 Apr 2021 07:57:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:57:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:57:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.05_summits.bed INFO @ Sat, 03 Apr 2021 07:57:17: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (14493 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:57:22: 23000000 INFO @ Sat, 03 Apr 2021 07:57:23: 17000000 INFO @ Sat, 03 Apr 2021 07:57:23: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 07:57:23: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 07:57:23: #1 total tags in treatment: 10703833 INFO @ Sat, 03 Apr 2021 07:57:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:57:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:57:23: #1 tags after filtering in treatment: 7089252 INFO @ Sat, 03 Apr 2021 07:57:23: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 03 Apr 2021 07:57:23: #1 finished! INFO @ Sat, 03 Apr 2021 07:57:23: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:57:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:57:24: #2 number of paired peaks: 5363 INFO @ Sat, 03 Apr 2021 07:57:24: start model_add_line... INFO @ Sat, 03 Apr 2021 07:57:24: start X-correlation... INFO @ Sat, 03 Apr 2021 07:57:24: end of X-cor INFO @ Sat, 03 Apr 2021 07:57:24: #2 finished! INFO @ Sat, 03 Apr 2021 07:57:24: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Apr 2021 07:57:24: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 03 Apr 2021 07:57:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.10_model.r INFO @ Sat, 03 Apr 2021 07:57:24: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:57:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:57:29: 18000000 INFO @ Sat, 03 Apr 2021 07:57:35: 19000000 INFO @ Sat, 03 Apr 2021 07:57:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:57:42: 20000000 INFO @ Sat, 03 Apr 2021 07:57:48: 21000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:57:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:57:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:57:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.10_summits.bed INFO @ Sat, 03 Apr 2021 07:57:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9751 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:57:55: 22000000 INFO @ Sat, 03 Apr 2021 07:58:01: 23000000 INFO @ Sat, 03 Apr 2021 07:58:03: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 07:58:03: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 07:58:03: #1 total tags in treatment: 10703833 INFO @ Sat, 03 Apr 2021 07:58:03: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:58:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:58:03: #1 tags after filtering in treatment: 7089252 INFO @ Sat, 03 Apr 2021 07:58:03: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 03 Apr 2021 07:58:03: #1 finished! INFO @ Sat, 03 Apr 2021 07:58:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:58:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:58:04: #2 number of paired peaks: 5363 INFO @ Sat, 03 Apr 2021 07:58:04: start model_add_line... INFO @ Sat, 03 Apr 2021 07:58:04: start X-correlation... INFO @ Sat, 03 Apr 2021 07:58:04: end of X-cor INFO @ Sat, 03 Apr 2021 07:58:04: #2 finished! INFO @ Sat, 03 Apr 2021 07:58:04: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Apr 2021 07:58:04: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 03 Apr 2021 07:58:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.20_model.r INFO @ Sat, 03 Apr 2021 07:58:04: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:58:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:58:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:58:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:58:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:58:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192195/SRX7192195.20_summits.bed INFO @ Sat, 03 Apr 2021 07:58:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4771 records, 4 fields): 8 millis CompletedMACS2peakCalling