Job ID = 14168035 SRX = ERX3978932 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30037671 spots for ERR3976002/ERR3976002.sra Written 30037671 spots for ERR3976002/ERR3976002.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168962 ("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: 01:11:28 30037671 reads; of these: 30037671 (100.00%) were paired; of these: 3397315 (11.31%) aligned concordantly 0 times 22427753 (74.67%) aligned concordantly exactly 1 time 4212603 (14.02%) aligned concordantly >1 times ---- 3397315 pairs aligned concordantly 0 times; of these: 829827 (24.43%) aligned discordantly 1 time ---- 2567488 pairs aligned 0 times concordantly or discordantly; of these: 5134976 mates make up the pairs; of these: 2898765 (56.45%) aligned 0 times 1110349 (21.62%) aligned exactly 1 time 1125862 (21.93%) aligned >1 times 95.17% overall alignment rate Time searching: 01:11:28 Overall time: 01:11:28 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 24 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] 22550591 / 27337515 = 0.8249 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 16:01:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.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 16:01:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:01:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:01:37: 1000000 INFO @ Fri, 10 Dec 2021 16:01:43: 2000000 INFO @ Fri, 10 Dec 2021 16:01:50: 3000000 INFO @ Fri, 10 Dec 2021 16:01:56: 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 @ Fri, 10 Dec 2021 16:02:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.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 16:02:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:02:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:02:02: 5000000 INFO @ Fri, 10 Dec 2021 16:02:08: 1000000 INFO @ Fri, 10 Dec 2021 16:02:09: 6000000 INFO @ Fri, 10 Dec 2021 16:02:15: 2000000 INFO @ Fri, 10 Dec 2021 16:02:16: 7000000 INFO @ Fri, 10 Dec 2021 16:02:22: 3000000 INFO @ Fri, 10 Dec 2021 16:02:23: 8000000 INFO @ Fri, 10 Dec 2021 16:02:29: 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 @ Fri, 10 Dec 2021 16:02:30: 9000000 INFO @ Fri, 10 Dec 2021 16:02:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.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 16:02:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:02:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:02:36: 5000000 INFO @ Fri, 10 Dec 2021 16:02:38: 10000000 INFO @ Fri, 10 Dec 2021 16:02:40: 1000000 INFO @ Fri, 10 Dec 2021 16:02:44: 6000000 INFO @ Fri, 10 Dec 2021 16:02:46: 11000000 INFO @ Fri, 10 Dec 2021 16:02:48: 2000000 INFO @ Fri, 10 Dec 2021 16:02:51: 7000000 INFO @ Fri, 10 Dec 2021 16:02:54: 12000000 INFO @ Fri, 10 Dec 2021 16:02:54: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:02:54: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:02:54: #1 total tags in treatment: 4748583 INFO @ Fri, 10 Dec 2021 16:02:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:02:54: #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 16:02:54: #1 tags after filtering in treatment: 4173202 INFO @ Fri, 10 Dec 2021 16:02:54: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 16:02:54: #1 finished! INFO @ Fri, 10 Dec 2021 16:02:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:02:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:02:55: #2 number of paired peaks: 6765 INFO @ Fri, 10 Dec 2021 16:02:55: start model_add_line... INFO @ Fri, 10 Dec 2021 16:02:55: start X-correlation... INFO @ Fri, 10 Dec 2021 16:02:55: end of X-cor INFO @ Fri, 10 Dec 2021 16:02:55: #2 finished! INFO @ Fri, 10 Dec 2021 16:02:55: #2 predicted fragment length is 169 bps INFO @ Fri, 10 Dec 2021 16:02:55: #2 alternative fragment length(s) may be 169 bps INFO @ Fri, 10 Dec 2021 16:02:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.05_model.r INFO @ Fri, 10 Dec 2021 16:02:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:02:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:02:57: 3000000 INFO @ Fri, 10 Dec 2021 16:02:59: 8000000 INFO @ Fri, 10 Dec 2021 16:03:05: 4000000 INFO @ Fri, 10 Dec 2021 16:03:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:03:07: 9000000 INFO @ Fri, 10 Dec 2021 16:03:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:03:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:03:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.05_summits.bed INFO @ Fri, 10 Dec 2021 16:03:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9179 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:03:13: 5000000 INFO @ Fri, 10 Dec 2021 16:03:15: 10000000 INFO @ Fri, 10 Dec 2021 16:03:22: 6000000 INFO @ Fri, 10 Dec 2021 16:03:23: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:03:30: 7000000 INFO @ Fri, 10 Dec 2021 16:03:31: 12000000 INFO @ Fri, 10 Dec 2021 16:03:31: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:03:31: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:03:31: #1 total tags in treatment: 4748583 INFO @ Fri, 10 Dec 2021 16:03:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:03:31: #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 16:03:31: #1 tags after filtering in treatment: 4173202 INFO @ Fri, 10 Dec 2021 16:03:31: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 16:03:31: #1 finished! INFO @ Fri, 10 Dec 2021 16:03:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:03:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:03:32: #2 number of paired peaks: 6765 INFO @ Fri, 10 Dec 2021 16:03:32: start model_add_line... INFO @ Fri, 10 Dec 2021 16:03:32: start X-correlation... INFO @ Fri, 10 Dec 2021 16:03:32: end of X-cor INFO @ Fri, 10 Dec 2021 16:03:32: #2 finished! INFO @ Fri, 10 Dec 2021 16:03:32: #2 predicted fragment length is 169 bps INFO @ Fri, 10 Dec 2021 16:03:32: #2 alternative fragment length(s) may be 169 bps INFO @ Fri, 10 Dec 2021 16:03:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.10_model.r INFO @ Fri, 10 Dec 2021 16:03:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:03:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:03:38: 8000000 INFO @ Fri, 10 Dec 2021 16:03:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:03:46: 9000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:03:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:03:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:03:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.10_summits.bed INFO @ Fri, 10 Dec 2021 16:03:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6582 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:03:54: 10000000 INFO @ Fri, 10 Dec 2021 16:04:02: 11000000 INFO @ Fri, 10 Dec 2021 16:04:10: 12000000 INFO @ Fri, 10 Dec 2021 16:04:10: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:04:10: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:04:10: #1 total tags in treatment: 4748583 INFO @ Fri, 10 Dec 2021 16:04:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:04:10: #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 16:04:10: #1 tags after filtering in treatment: 4173202 INFO @ Fri, 10 Dec 2021 16:04:10: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 16:04:10: #1 finished! INFO @ Fri, 10 Dec 2021 16:04:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:04:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:04:11: #2 number of paired peaks: 6765 INFO @ Fri, 10 Dec 2021 16:04:11: start model_add_line... INFO @ Fri, 10 Dec 2021 16:04:11: start X-correlation... INFO @ Fri, 10 Dec 2021 16:04:11: end of X-cor INFO @ Fri, 10 Dec 2021 16:04:11: #2 finished! INFO @ Fri, 10 Dec 2021 16:04:11: #2 predicted fragment length is 169 bps INFO @ Fri, 10 Dec 2021 16:04:11: #2 alternative fragment length(s) may be 169 bps INFO @ Fri, 10 Dec 2021 16:04:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.20_model.r INFO @ Fri, 10 Dec 2021 16:04:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:04:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:04:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:04:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:04:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978932/ERX3978932.20_summits.bed INFO @ Fri, 10 Dec 2021 16:04:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4572 records, 4 fields): 6 millis CompletedMACS2peakCalling