Job ID = 14167234 SRX = SRX8973517 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12870205 spots for SRR12479620/SRR12479620.sra Written 12870205 spots for SRR12479620/SRR12479620.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167825 ("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: 00:08:12 12870205 reads; of these: 12870205 (100.00%) were paired; of these: 7504270 (58.31%) aligned concordantly 0 times 4925436 (38.27%) aligned concordantly exactly 1 time 440499 (3.42%) aligned concordantly >1 times ---- 7504270 pairs aligned concordantly 0 times; of these: 188844 (2.52%) aligned discordantly 1 time ---- 7315426 pairs aligned 0 times concordantly or discordantly; of these: 14630852 mates make up the pairs; of these: 14120301 (96.51%) aligned 0 times 366061 (2.50%) aligned exactly 1 time 144490 (0.99%) aligned >1 times 45.14% overall alignment rate Time searching: 00:08:12 Overall time: 00:08:12 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_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] 178229 / 5553623 = 0.0321 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 11:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.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 11:23:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:23:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:23:56: 1000000 INFO @ Fri, 10 Dec 2021 11:24:04: 2000000 INFO @ Fri, 10 Dec 2021 11:24:12: 3000000 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 11:24:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.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 11:24:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:24:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:24:20: 4000000 INFO @ Fri, 10 Dec 2021 11:24:25: 1000000 INFO @ Fri, 10 Dec 2021 11:24:28: 5000000 INFO @ Fri, 10 Dec 2021 11:24:31: 2000000 INFO @ Fri, 10 Dec 2021 11:24:36: 6000000 INFO @ Fri, 10 Dec 2021 11:24:37: 3000000 INFO @ Fri, 10 Dec 2021 11:24:44: 4000000 INFO @ Fri, 10 Dec 2021 11:24:44: 7000000 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 11:24:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.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 11:24:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:24:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:24:50: 5000000 INFO @ Fri, 10 Dec 2021 11:24:52: 8000000 INFO @ Fri, 10 Dec 2021 11:24:55: 1000000 INFO @ Fri, 10 Dec 2021 11:24:58: 6000000 INFO @ Fri, 10 Dec 2021 11:25:00: 9000000 INFO @ Fri, 10 Dec 2021 11:25:02: 2000000 INFO @ Fri, 10 Dec 2021 11:25:04: 7000000 INFO @ Fri, 10 Dec 2021 11:25:08: 10000000 INFO @ Fri, 10 Dec 2021 11:25:09: 3000000 INFO @ Fri, 10 Dec 2021 11:25:11: 8000000 INFO @ Fri, 10 Dec 2021 11:25:16: 4000000 INFO @ Fri, 10 Dec 2021 11:25:16: 11000000 INFO @ Fri, 10 Dec 2021 11:25:18: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:25:18: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:25:18: #1 total tags in treatment: 5190342 INFO @ Fri, 10 Dec 2021 11:25:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:25:18: #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 11:25:18: 9000000 INFO @ Fri, 10 Dec 2021 11:25:18: #1 tags after filtering in treatment: 4951772 INFO @ Fri, 10 Dec 2021 11:25:18: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 11:25:18: #1 finished! INFO @ Fri, 10 Dec 2021 11:25:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:25:19: #2 number of paired peaks: 8368 INFO @ Fri, 10 Dec 2021 11:25:19: start model_add_line... INFO @ Fri, 10 Dec 2021 11:25:19: start X-correlation... INFO @ Fri, 10 Dec 2021 11:25:19: end of X-cor INFO @ Fri, 10 Dec 2021 11:25:19: #2 finished! INFO @ Fri, 10 Dec 2021 11:25:19: #2 predicted fragment length is 266 bps INFO @ Fri, 10 Dec 2021 11:25:19: #2 alternative fragment length(s) may be 4,266 bps INFO @ Fri, 10 Dec 2021 11:25:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.05_model.r INFO @ Fri, 10 Dec 2021 11:25:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:25:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:25:22: 5000000 INFO @ Fri, 10 Dec 2021 11:25:25: 10000000 INFO @ Fri, 10 Dec 2021 11:25:29: 6000000 INFO @ Fri, 10 Dec 2021 11:25:31: 11000000 INFO @ Fri, 10 Dec 2021 11:25:33: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:25:33: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:25:33: #1 total tags in treatment: 5190342 INFO @ Fri, 10 Dec 2021 11:25:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:25:33: #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 11:25:33: #1 tags after filtering in treatment: 4951772 INFO @ Fri, 10 Dec 2021 11:25:33: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 11:25:33: #1 finished! INFO @ Fri, 10 Dec 2021 11:25:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:25:34: #2 number of paired peaks: 8368 INFO @ Fri, 10 Dec 2021 11:25:34: start model_add_line... INFO @ Fri, 10 Dec 2021 11:25:34: start X-correlation... INFO @ Fri, 10 Dec 2021 11:25:34: end of X-cor INFO @ Fri, 10 Dec 2021 11:25:34: #2 finished! INFO @ Fri, 10 Dec 2021 11:25:34: #2 predicted fragment length is 266 bps INFO @ Fri, 10 Dec 2021 11:25:34: #2 alternative fragment length(s) may be 4,266 bps INFO @ Fri, 10 Dec 2021 11:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.10_model.r INFO @ Fri, 10 Dec 2021 11:25:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:25:36: 7000000 INFO @ Fri, 10 Dec 2021 11:25:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:25:42: 8000000 INFO @ Fri, 10 Dec 2021 11:25:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:25:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:25:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.05_summits.bed INFO @ Fri, 10 Dec 2021 11:25:46: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5508 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:25:49: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:25:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:25:55: 10000000 INFO @ Fri, 10 Dec 2021 11:26:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:26:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:26:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.10_summits.bed INFO @ Fri, 10 Dec 2021 11:26:01: Done! INFO @ Fri, 10 Dec 2021 11:26:01: 11000000 pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2205 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:26:03: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:26:03: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:26:03: #1 total tags in treatment: 5190342 INFO @ Fri, 10 Dec 2021 11:26:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:26:03: #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 11:26:03: #1 tags after filtering in treatment: 4951772 INFO @ Fri, 10 Dec 2021 11:26:03: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 11:26:03: #1 finished! INFO @ Fri, 10 Dec 2021 11:26:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:26:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:26:04: #2 number of paired peaks: 8368 INFO @ Fri, 10 Dec 2021 11:26:04: start model_add_line... INFO @ Fri, 10 Dec 2021 11:26:04: start X-correlation... INFO @ Fri, 10 Dec 2021 11:26:04: end of X-cor INFO @ Fri, 10 Dec 2021 11:26:04: #2 finished! INFO @ Fri, 10 Dec 2021 11:26:04: #2 predicted fragment length is 266 bps INFO @ Fri, 10 Dec 2021 11:26:04: #2 alternative fragment length(s) may be 4,266 bps INFO @ Fri, 10 Dec 2021 11:26:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.20_model.r INFO @ Fri, 10 Dec 2021 11:26:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:26:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:26:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:26:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:26:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:26:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973517/SRX8973517.20_summits.bed INFO @ Fri, 10 Dec 2021 11:26:31: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (308 records, 4 fields): 3 millis CompletedMACS2peakCalling