Job ID = 14171448 SRX = SRX9555294 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7466649 spots for SRR13110747/SRR13110747.sra Written 7466649 spots for SRR13110747/SRR13110747.sra Read 7417965 spots for SRR13110748/SRR13110748.sra Written 7417965 spots for SRR13110748/SRR13110748.sra Read 7485383 spots for SRR13110749/SRR13110749.sra Written 7485383 spots for SRR13110749/SRR13110749.sra Read 7437089 spots for SRR13110750/SRR13110750.sra Written 7437089 spots for SRR13110750/SRR13110750.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171942 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:42 29807086 reads; of these: 29807086 (100.00%) were paired; of these: 28669180 (96.18%) aligned concordantly 0 times 863253 (2.90%) aligned concordantly exactly 1 time 274653 (0.92%) aligned concordantly >1 times ---- 28669180 pairs aligned concordantly 0 times; of these: 4441 (0.02%) aligned discordantly 1 time ---- 28664739 pairs aligned 0 times concordantly or discordantly; of these: 57329478 mates make up the pairs; of these: 57144207 (99.68%) aligned 0 times 68169 (0.12%) aligned exactly 1 time 117102 (0.20%) aligned >1 times 4.14% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 44985 / 1141724 = 0.0394 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 11:48:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.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 11:48:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:48:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:49:04: 1000000 INFO @ Sat, 11 Dec 2021 11:49:09: 2000000 INFO @ Sat, 11 Dec 2021 11:49:11: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:49:11: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:49:11: #1 total tags in treatment: 1092988 INFO @ Sat, 11 Dec 2021 11:49:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:49:11: #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 11:49:11: #1 tags after filtering in treatment: 983546 INFO @ Sat, 11 Dec 2021 11:49:11: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 11:49:11: #1 finished! INFO @ Sat, 11 Dec 2021 11:49:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:49:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:49:11: #2 number of paired peaks: 7877 INFO @ Sat, 11 Dec 2021 11:49:11: start model_add_line... INFO @ Sat, 11 Dec 2021 11:49:11: start X-correlation... INFO @ Sat, 11 Dec 2021 11:49:11: end of X-cor INFO @ Sat, 11 Dec 2021 11:49:11: #2 finished! INFO @ Sat, 11 Dec 2021 11:49:11: #2 predicted fragment length is 166 bps INFO @ Sat, 11 Dec 2021 11:49:11: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 11 Dec 2021 11:49:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.05_model.r INFO @ Sat, 11 Dec 2021 11:49:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:49:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:49:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:49:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:49:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:49:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.05_summits.bed INFO @ Sat, 11 Dec 2021 11:49:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2571 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 11:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.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 11:49:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:49:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:49:34: 1000000 INFO @ Sat, 11 Dec 2021 11:49:38: 2000000 INFO @ Sat, 11 Dec 2021 11:49:40: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:49:40: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:49:40: #1 total tags in treatment: 1092988 INFO @ Sat, 11 Dec 2021 11:49:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:49:40: #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 11:49:40: #1 tags after filtering in treatment: 983546 INFO @ Sat, 11 Dec 2021 11:49:40: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 11:49:40: #1 finished! INFO @ Sat, 11 Dec 2021 11:49:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:49:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:49:40: #2 number of paired peaks: 7877 INFO @ Sat, 11 Dec 2021 11:49:40: start model_add_line... INFO @ Sat, 11 Dec 2021 11:49:40: start X-correlation... INFO @ Sat, 11 Dec 2021 11:49:40: end of X-cor INFO @ Sat, 11 Dec 2021 11:49:40: #2 finished! INFO @ Sat, 11 Dec 2021 11:49:40: #2 predicted fragment length is 166 bps INFO @ Sat, 11 Dec 2021 11:49:40: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 11 Dec 2021 11:49:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.10_model.r INFO @ Sat, 11 Dec 2021 11:49:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:49:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:49:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:49:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:49:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:49:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.10_summits.bed INFO @ Sat, 11 Dec 2021 11:49:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (879 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 11:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.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 11:50:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:50:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:50:04: 1000000 INFO @ Sat, 11 Dec 2021 11:50:08: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:50:09: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:50:09: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:50:09: #1 total tags in treatment: 1092988 INFO @ Sat, 11 Dec 2021 11:50:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:50:09: #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 11:50:09: #1 tags after filtering in treatment: 983546 INFO @ Sat, 11 Dec 2021 11:50:09: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 11:50:09: #1 finished! INFO @ Sat, 11 Dec 2021 11:50:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:50:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:50:09: #2 number of paired peaks: 7877 INFO @ Sat, 11 Dec 2021 11:50:09: start model_add_line... INFO @ Sat, 11 Dec 2021 11:50:09: start X-correlation... INFO @ Sat, 11 Dec 2021 11:50:09: end of X-cor INFO @ Sat, 11 Dec 2021 11:50:09: #2 finished! INFO @ Sat, 11 Dec 2021 11:50:09: #2 predicted fragment length is 166 bps INFO @ Sat, 11 Dec 2021 11:50:09: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 11 Dec 2021 11:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.20_model.r INFO @ Sat, 11 Dec 2021 11:50:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:50:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:50:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:50:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:50:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:50:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555294/SRX9555294.20_summits.bed INFO @ Sat, 11 Dec 2021 11:50:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 1 millis CompletedMACS2peakCalling