Job ID = 14167978 SRX = ERX3978928 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25878538 spots for ERR3975998/ERR3975998.sra Written 25878538 spots for ERR3975998/ERR3975998.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168991 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:49:18 25878538 reads; of these: 25878538 (100.00%) were paired; of these: 3858482 (14.91%) aligned concordantly 0 times 17226973 (66.57%) aligned concordantly exactly 1 time 4793083 (18.52%) aligned concordantly >1 times ---- 3858482 pairs aligned concordantly 0 times; of these: 614587 (15.93%) aligned discordantly 1 time ---- 3243895 pairs aligned 0 times concordantly or discordantly; of these: 6487790 mates make up the pairs; of these: 2990561 (46.10%) aligned 0 times 1669415 (25.73%) aligned exactly 1 time 1827814 (28.17%) aligned >1 times 94.22% overall alignment rate Time searching: 01:49:19 Overall time: 01:49:19 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] 15334414 / 22446746 = 0.6831 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 16:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.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 16:15:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:15:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:15:19: 1000000 INFO @ Fri, 10 Dec 2021 16:15:28: 2000000 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 16:15:37: 3000000 INFO @ Fri, 10 Dec 2021 16:15:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.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 16:15:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:15:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:15:47: 4000000 INFO @ Fri, 10 Dec 2021 16:15:49: 1000000 INFO @ Fri, 10 Dec 2021 16:15:59: 5000000 INFO @ Fri, 10 Dec 2021 16:16:00: 2000000 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 16:16:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.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 16:16:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:16:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:16:10: 3000000 INFO @ Fri, 10 Dec 2021 16:16:11: 6000000 INFO @ Fri, 10 Dec 2021 16:16:20: 4000000 INFO @ Fri, 10 Dec 2021 16:16:23: 7000000 INFO @ Fri, 10 Dec 2021 16:16:24: 1000000 INFO @ Fri, 10 Dec 2021 16:16:30: 5000000 INFO @ Fri, 10 Dec 2021 16:16:34: 8000000 INFO @ Fri, 10 Dec 2021 16:16:38: 2000000 INFO @ Fri, 10 Dec 2021 16:16:42: 6000000 INFO @ Fri, 10 Dec 2021 16:16:45: 9000000 INFO @ Fri, 10 Dec 2021 16:16:50: 3000000 INFO @ Fri, 10 Dec 2021 16:16:53: 7000000 INFO @ Fri, 10 Dec 2021 16:16:56: 10000000 INFO @ Fri, 10 Dec 2021 16:17:02: 4000000 INFO @ Fri, 10 Dec 2021 16:17:04: 8000000 INFO @ Fri, 10 Dec 2021 16:17:08: 11000000 INFO @ Fri, 10 Dec 2021 16:17:14: 5000000 INFO @ Fri, 10 Dec 2021 16:17:15: 9000000 INFO @ Fri, 10 Dec 2021 16:17:19: 12000000 INFO @ Fri, 10 Dec 2021 16:17:27: 10000000 INFO @ Fri, 10 Dec 2021 16:17:29: 6000000 INFO @ Fri, 10 Dec 2021 16:17:30: 13000000 INFO @ Fri, 10 Dec 2021 16:17:38: 11000000 INFO @ Fri, 10 Dec 2021 16:17:41: 14000000 INFO @ Fri, 10 Dec 2021 16:17:41: 7000000 INFO @ Fri, 10 Dec 2021 16:17:49: 12000000 INFO @ Fri, 10 Dec 2021 16:17:52: 15000000 INFO @ Fri, 10 Dec 2021 16:17:55: 8000000 INFO @ Fri, 10 Dec 2021 16:18:00: 13000000 INFO @ Fri, 10 Dec 2021 16:18:03: 16000000 INFO @ Fri, 10 Dec 2021 16:18:09: 9000000 INFO @ Fri, 10 Dec 2021 16:18:11: 14000000 INFO @ Fri, 10 Dec 2021 16:18:16: 17000000 INFO @ Fri, 10 Dec 2021 16:18:22: 15000000 INFO @ Fri, 10 Dec 2021 16:18:23: 10000000 INFO @ Fri, 10 Dec 2021 16:18:26: 18000000 INFO @ Fri, 10 Dec 2021 16:18:27: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:18:27: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:18:27: #1 total tags in treatment: 7026984 INFO @ Fri, 10 Dec 2021 16:18:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:18:27: #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 16:18:27: #1 tags after filtering in treatment: 6445176 INFO @ Fri, 10 Dec 2021 16:18:27: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 16:18:27: #1 finished! INFO @ Fri, 10 Dec 2021 16:18:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:18:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:18:28: #2 number of paired peaks: 3065 INFO @ Fri, 10 Dec 2021 16:18:28: start model_add_line... INFO @ Fri, 10 Dec 2021 16:18:28: start X-correlation... INFO @ Fri, 10 Dec 2021 16:18:28: end of X-cor INFO @ Fri, 10 Dec 2021 16:18:28: #2 finished! INFO @ Fri, 10 Dec 2021 16:18:28: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 16:18:28: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 16:18:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.05_model.r INFO @ Fri, 10 Dec 2021 16:18:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:18:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:18:32: 16000000 INFO @ Fri, 10 Dec 2021 16:18:36: 11000000 INFO @ Fri, 10 Dec 2021 16:18:42: 17000000 INFO @ Fri, 10 Dec 2021 16:18:49: 12000000 INFO @ Fri, 10 Dec 2021 16:18:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:18:51: 18000000 INFO @ Fri, 10 Dec 2021 16:18:52: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:18:52: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:18:52: #1 total tags in treatment: 7026984 INFO @ Fri, 10 Dec 2021 16:18:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:18:52: #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 16:18:52: #1 tags after filtering in treatment: 6445176 INFO @ Fri, 10 Dec 2021 16:18:52: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 16:18:52: #1 finished! INFO @ Fri, 10 Dec 2021 16:18:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:18:53: #2 number of paired peaks: 3065 INFO @ Fri, 10 Dec 2021 16:18:53: start model_add_line... INFO @ Fri, 10 Dec 2021 16:18:53: start X-correlation... INFO @ Fri, 10 Dec 2021 16:18:53: end of X-cor INFO @ Fri, 10 Dec 2021 16:18:53: #2 finished! INFO @ Fri, 10 Dec 2021 16:18:53: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 16:18:53: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 16:18:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.10_model.r INFO @ Fri, 10 Dec 2021 16:18:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:18:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:19:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:19:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:19:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.05_summits.bed INFO @ Fri, 10 Dec 2021 16:19:02: 13000000 INFO @ Fri, 10 Dec 2021 16:19:02: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10065 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:19:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:19:15: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:19:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:19:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:19:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.10_summits.bed INFO @ Fri, 10 Dec 2021 16:19:24: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6512 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:19:27: 15000000 INFO @ Fri, 10 Dec 2021 16:19:39: 16000000 INFO @ Fri, 10 Dec 2021 16:19:50: 17000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:20:00: 18000000 INFO @ Fri, 10 Dec 2021 16:20:01: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:20:01: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:20:01: #1 total tags in treatment: 7026984 INFO @ Fri, 10 Dec 2021 16:20:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:20:01: #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 16:20:01: #1 tags after filtering in treatment: 6445176 INFO @ Fri, 10 Dec 2021 16:20:01: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 16:20:01: #1 finished! INFO @ Fri, 10 Dec 2021 16:20:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:20:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:20:02: #2 number of paired peaks: 3065 INFO @ Fri, 10 Dec 2021 16:20:02: start model_add_line... INFO @ Fri, 10 Dec 2021 16:20:02: start X-correlation... INFO @ Fri, 10 Dec 2021 16:20:02: end of X-cor INFO @ Fri, 10 Dec 2021 16:20:02: #2 finished! INFO @ Fri, 10 Dec 2021 16:20:02: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 16:20:02: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 16:20:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.20_model.r INFO @ Fri, 10 Dec 2021 16:20:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:20:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:20:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978928/ERX3978928.20_summits.bed INFO @ Fri, 10 Dec 2021 16:20:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3762 records, 4 fields): 7 millis CompletedMACS2peakCalling