Job ID = 14172233 SRX = SRX9281743 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7513602 spots for SRR12813261/SRR12813261.sra Written 7513602 spots for SRR12813261/SRR12813261.sra Read 7466449 spots for SRR12813262/SRR12813262.sra Written 7466449 spots for SRR12813262/SRR12813262.sra Read 7622747 spots for SRR12813263/SRR12813263.sra Written 7622747 spots for SRR12813263/SRR12813263.sra Read 7576437 spots for SRR12813264/SRR12813264.sra Written 7576437 spots for SRR12813264/SRR12813264.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172704 ("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: 00:04:48 30179235 reads; of these: 30179235 (100.00%) were paired; of these: 28896453 (95.75%) aligned concordantly 0 times 995480 (3.30%) aligned concordantly exactly 1 time 287302 (0.95%) aligned concordantly >1 times ---- 28896453 pairs aligned concordantly 0 times; of these: 2226 (0.01%) aligned discordantly 1 time ---- 28894227 pairs aligned 0 times concordantly or discordantly; of these: 57788454 mates make up the pairs; of these: 57594231 (99.66%) aligned 0 times 70135 (0.12%) aligned exactly 1 time 124088 (0.21%) aligned >1 times 4.58% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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] 43204 / 1284112 = 0.0336 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 14:59:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.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 14:59:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:59:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:59:49: 1000000 INFO @ Sat, 11 Dec 2021 14:59:55: 2000000 INFO @ Sat, 11 Dec 2021 14:59:58: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 14:59:58: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 14:59:58: #1 total tags in treatment: 1239637 INFO @ Sat, 11 Dec 2021 14:59:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:59:58: #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 14:59:58: #1 tags after filtering in treatment: 1204355 INFO @ Sat, 11 Dec 2021 14:59:58: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 14:59:58: #1 finished! INFO @ Sat, 11 Dec 2021 14:59:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:59:59: #2 number of paired peaks: 1826 INFO @ Sat, 11 Dec 2021 14:59:59: start model_add_line... INFO @ Sat, 11 Dec 2021 14:59:59: start X-correlation... INFO @ Sat, 11 Dec 2021 14:59:59: end of X-cor INFO @ Sat, 11 Dec 2021 14:59:59: #2 finished! INFO @ Sat, 11 Dec 2021 14:59:59: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 14:59:59: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 11 Dec 2021 14:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.05_model.r INFO @ Sat, 11 Dec 2021 14:59:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:00:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:00:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.05_summits.bed INFO @ Sat, 11 Dec 2021 15:00:03: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 1 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 15:00:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.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 15:00:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:00:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:00:19: 1000000 INFO @ Sat, 11 Dec 2021 15:00:24: 2000000 INFO @ Sat, 11 Dec 2021 15:00:28: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:00:28: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:00:28: #1 total tags in treatment: 1239637 INFO @ Sat, 11 Dec 2021 15:00:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:00:28: #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 15:00:28: #1 tags after filtering in treatment: 1204355 INFO @ Sat, 11 Dec 2021 15:00:28: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 15:00:28: #1 finished! INFO @ Sat, 11 Dec 2021 15:00:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:00:28: #2 number of paired peaks: 1826 INFO @ Sat, 11 Dec 2021 15:00:28: start model_add_line... INFO @ Sat, 11 Dec 2021 15:00:28: start X-correlation... INFO @ Sat, 11 Dec 2021 15:00:28: end of X-cor INFO @ Sat, 11 Dec 2021 15:00:28: #2 finished! INFO @ Sat, 11 Dec 2021 15:00:28: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 15:00:28: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 11 Dec 2021 15:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.10_model.r INFO @ Sat, 11 Dec 2021 15:00:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:00:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:00:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:00:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:00:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.10_summits.bed INFO @ Sat, 11 Dec 2021 15:00:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (116 records, 4 fields): 27 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 15:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.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 15:00:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:00:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:00:49: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:00:55: 2000000 INFO @ Sat, 11 Dec 2021 15:00:58: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:00:58: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:00:58: #1 total tags in treatment: 1239637 INFO @ Sat, 11 Dec 2021 15:00:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:00:58: #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 15:00:58: #1 tags after filtering in treatment: 1204355 INFO @ Sat, 11 Dec 2021 15:00:58: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 15:00:58: #1 finished! INFO @ Sat, 11 Dec 2021 15:00:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:00:58: #2 number of paired peaks: 1826 INFO @ Sat, 11 Dec 2021 15:00:58: start model_add_line... INFO @ Sat, 11 Dec 2021 15:00:58: start X-correlation... INFO @ Sat, 11 Dec 2021 15:00:58: end of X-cor INFO @ Sat, 11 Dec 2021 15:00:58: #2 finished! INFO @ Sat, 11 Dec 2021 15:00:58: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 15:00:58: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 11 Dec 2021 15:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.20_model.r INFO @ Sat, 11 Dec 2021 15:00:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:00:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:01:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281743/SRX9281743.20_summits.bed INFO @ Sat, 11 Dec 2021 15:01:02: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 1 millis CompletedMACS2peakCalling