Job ID = 14170982 SRX = SRX9005700 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11539627 spots for SRR12515101/SRR12515101.sra Written 11539627 spots for SRR12515101/SRR12515101.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171586 ("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: 00:37:40 11539627 reads; of these: 11539627 (100.00%) were paired; of these: 686969 (5.95%) aligned concordantly 0 times 7576177 (65.65%) aligned concordantly exactly 1 time 3276481 (28.39%) aligned concordantly >1 times ---- 686969 pairs aligned concordantly 0 times; of these: 38682 (5.63%) aligned discordantly 1 time ---- 648287 pairs aligned 0 times concordantly or discordantly; of these: 1296574 mates make up the pairs; of these: 916668 (70.70%) aligned 0 times 225227 (17.37%) aligned exactly 1 time 154679 (11.93%) aligned >1 times 96.03% overall alignment rate Time searching: 00:37:41 Overall time: 00:37:41 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] 1303920 / 10861716 = 0.1200 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 09:55:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.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 09:55:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:55:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:55:08: 1000000 INFO @ Sat, 11 Dec 2021 09:55:14: 2000000 INFO @ Sat, 11 Dec 2021 09:55:20: 3000000 INFO @ Sat, 11 Dec 2021 09:55:25: 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 09:55:31: 5000000 INFO @ Sat, 11 Dec 2021 09:55:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.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 09:55:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:55:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:55:38: 6000000 INFO @ Sat, 11 Dec 2021 09:55:38: 1000000 INFO @ Sat, 11 Dec 2021 09:55:45: 7000000 INFO @ Sat, 11 Dec 2021 09:55:45: 2000000 INFO @ Sat, 11 Dec 2021 09:55:51: 8000000 INFO @ Sat, 11 Dec 2021 09:55:52: 3000000 INFO @ Sat, 11 Dec 2021 09:55:58: 9000000 INFO @ Sat, 11 Dec 2021 09:55:59: 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 09:56:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.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 09:56:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:56:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:56:05: 10000000 INFO @ Sat, 11 Dec 2021 09:56:06: 5000000 INFO @ Sat, 11 Dec 2021 09:56:09: 1000000 INFO @ Sat, 11 Dec 2021 09:56:12: 11000000 INFO @ Sat, 11 Dec 2021 09:56:12: 6000000 INFO @ Sat, 11 Dec 2021 09:56:16: 2000000 INFO @ Sat, 11 Dec 2021 09:56:19: 12000000 INFO @ Sat, 11 Dec 2021 09:56:19: 7000000 INFO @ Sat, 11 Dec 2021 09:56:23: 3000000 INFO @ Sat, 11 Dec 2021 09:56:26: 13000000 INFO @ Sat, 11 Dec 2021 09:56:26: 8000000 INFO @ Sat, 11 Dec 2021 09:56:29: 4000000 INFO @ Sat, 11 Dec 2021 09:56:32: 14000000 INFO @ Sat, 11 Dec 2021 09:56:33: 9000000 INFO @ Sat, 11 Dec 2021 09:56:36: 5000000 INFO @ Sat, 11 Dec 2021 09:56:39: 15000000 INFO @ Sat, 11 Dec 2021 09:56:40: 10000000 INFO @ Sat, 11 Dec 2021 09:56:43: 6000000 INFO @ Sat, 11 Dec 2021 09:56:46: 16000000 INFO @ Sat, 11 Dec 2021 09:56:47: 11000000 INFO @ Sat, 11 Dec 2021 09:56:50: 7000000 INFO @ Sat, 11 Dec 2021 09:56:53: 17000000 INFO @ Sat, 11 Dec 2021 09:56:54: 12000000 INFO @ Sat, 11 Dec 2021 09:56:57: 8000000 INFO @ Sat, 11 Dec 2021 09:57:00: 18000000 INFO @ Sat, 11 Dec 2021 09:57:00: 13000000 INFO @ Sat, 11 Dec 2021 09:57:04: 9000000 INFO @ Sat, 11 Dec 2021 09:57:07: 19000000 INFO @ Sat, 11 Dec 2021 09:57:07: 14000000 INFO @ Sat, 11 Dec 2021 09:57:10: #1 tag size is determined as 72 bps INFO @ Sat, 11 Dec 2021 09:57:10: #1 tag size = 72 INFO @ Sat, 11 Dec 2021 09:57:10: #1 total tags in treatment: 9550748 INFO @ Sat, 11 Dec 2021 09:57:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:57:10: #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 09:57:11: 10000000 INFO @ Sat, 11 Dec 2021 09:57:11: #1 tags after filtering in treatment: 8340636 INFO @ Sat, 11 Dec 2021 09:57:11: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 09:57:11: #1 finished! INFO @ Sat, 11 Dec 2021 09:57:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:57:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:57:11: #2 number of paired peaks: 2860 INFO @ Sat, 11 Dec 2021 09:57:11: start model_add_line... INFO @ Sat, 11 Dec 2021 09:57:12: start X-correlation... INFO @ Sat, 11 Dec 2021 09:57:12: end of X-cor INFO @ Sat, 11 Dec 2021 09:57:12: #2 finished! INFO @ Sat, 11 Dec 2021 09:57:12: #2 predicted fragment length is 169 bps INFO @ Sat, 11 Dec 2021 09:57:12: #2 alternative fragment length(s) may be 169 bps INFO @ Sat, 11 Dec 2021 09:57:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.05_model.r INFO @ Sat, 11 Dec 2021 09:57:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:57:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:57:14: 15000000 INFO @ Sat, 11 Dec 2021 09:57:17: 11000000 INFO @ Sat, 11 Dec 2021 09:57:20: 16000000 INFO @ Sat, 11 Dec 2021 09:57:24: 12000000 INFO @ Sat, 11 Dec 2021 09:57:27: 17000000 INFO @ Sat, 11 Dec 2021 09:57:30: 13000000 INFO @ Sat, 11 Dec 2021 09:57:33: 18000000 INFO @ Sat, 11 Dec 2021 09:57:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:57:37: 14000000 INFO @ Sat, 11 Dec 2021 09:57:40: 19000000 INFO @ Sat, 11 Dec 2021 09:57:43: #1 tag size is determined as 72 bps INFO @ Sat, 11 Dec 2021 09:57:43: #1 tag size = 72 INFO @ Sat, 11 Dec 2021 09:57:43: #1 total tags in treatment: 9550748 INFO @ Sat, 11 Dec 2021 09:57:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:57:43: #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 09:57:43: 15000000 INFO @ Sat, 11 Dec 2021 09:57:43: #1 tags after filtering in treatment: 8340636 INFO @ Sat, 11 Dec 2021 09:57:43: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 09:57:43: #1 finished! INFO @ Sat, 11 Dec 2021 09:57:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:57:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:57:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:57:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:57:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.05_summits.bed INFO @ Sat, 11 Dec 2021 09:57:44: Done! INFO @ Sat, 11 Dec 2021 09:57:44: #2 number of paired peaks: 2860 INFO @ Sat, 11 Dec 2021 09:57:44: start model_add_line... INFO @ Sat, 11 Dec 2021 09:57:44: start X-correlation... pass1 - making usageList (15 chroms)INFO @ Sat, 11 Dec 2021 09:57:44: end of X-cor : 2 millis INFO @ Sat, 11 Dec 2021 09:57:44: #2 finished! INFO @ Sat, 11 Dec 2021 09:57:44: #2 predicted fragment length is 169 bps INFO @ Sat, 11 Dec 2021 09:57:44: #2 alternative fragment length(s) may be 169 bps INFO @ Sat, 11 Dec 2021 09:57:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.10_model.r INFO @ Sat, 11 Dec 2021 09:57:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:57:44: #3 Pre-compute pvalue-qvalue table... pass2 - checking and writing primary data (7782 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:57:49: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:57:55: 17000000 INFO @ Sat, 11 Dec 2021 09:58:01: 18000000 INFO @ Sat, 11 Dec 2021 09:58:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:58:07: 19000000 INFO @ Sat, 11 Dec 2021 09:58:11: #1 tag size is determined as 72 bps INFO @ Sat, 11 Dec 2021 09:58:11: #1 tag size = 72 INFO @ Sat, 11 Dec 2021 09:58:11: #1 total tags in treatment: 9550748 INFO @ Sat, 11 Dec 2021 09:58:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:58:11: #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 09:58:11: #1 tags after filtering in treatment: 8340636 INFO @ Sat, 11 Dec 2021 09:58:11: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 09:58:11: #1 finished! INFO @ Sat, 11 Dec 2021 09:58:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:58:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:58:12: #2 number of paired peaks: 2860 INFO @ Sat, 11 Dec 2021 09:58:12: start model_add_line... INFO @ Sat, 11 Dec 2021 09:58:12: start X-correlation... INFO @ Sat, 11 Dec 2021 09:58:12: end of X-cor INFO @ Sat, 11 Dec 2021 09:58:12: #2 finished! INFO @ Sat, 11 Dec 2021 09:58:12: #2 predicted fragment length is 169 bps INFO @ Sat, 11 Dec 2021 09:58:12: #2 alternative fragment length(s) may be 169 bps INFO @ Sat, 11 Dec 2021 09:58:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.20_model.r INFO @ Sat, 11 Dec 2021 09:58:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:58:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:58:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:58:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.10_summits.bed INFO @ Sat, 11 Dec 2021 09:58:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5453 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:58:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:58:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:58:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:58:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005700/SRX9005700.20_summits.bed INFO @ Sat, 11 Dec 2021 09:58:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3475 records, 4 fields): 7 millis CompletedMACS2peakCalling