Job ID = 14171145 SRX = SRX9555317 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 954841 spots for SRR13110455/SRR13110455.sra Written 954841 spots for SRR13110455/SRR13110455.sra Read 944386 spots for SRR13110456/SRR13110456.sra Written 944386 spots for SRR13110456/SRR13110456.sra Read 968881 spots for SRR13110457/SRR13110457.sra Written 968881 spots for SRR13110457/SRR13110457.sra Read 953287 spots for SRR13110458/SRR13110458.sra Written 953287 spots for SRR13110458/SRR13110458.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171610 ("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: 00:01:07 3821395 reads; of these: 3821395 (100.00%) were paired; of these: 3648045 (95.46%) aligned concordantly 0 times 123516 (3.23%) aligned concordantly exactly 1 time 49834 (1.30%) aligned concordantly >1 times ---- 3648045 pairs aligned concordantly 0 times; of these: 540 (0.01%) aligned discordantly 1 time ---- 3647505 pairs aligned 0 times concordantly or discordantly; of these: 7295010 mates make up the pairs; of these: 7272704 (99.69%) aligned 0 times 8681 (0.12%) aligned exactly 1 time 13625 (0.19%) aligned >1 times 4.84% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 3710 / 173761 = 0.0214 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 10:09:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.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 10:09:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:09:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:09:04: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 10:09:04: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 10:09:04: #1 total tags in treatment: 169650 INFO @ Sat, 11 Dec 2021 10:09:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:09:04: #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 10:09:04: #1 tags after filtering in treatment: 167998 INFO @ Sat, 11 Dec 2021 10:09:04: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 10:09:04: #1 finished! INFO @ Sat, 11 Dec 2021 10:09:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:09:04: #2 number of paired peaks: 1916 INFO @ Sat, 11 Dec 2021 10:09:04: start model_add_line... INFO @ Sat, 11 Dec 2021 10:09:04: start X-correlation... INFO @ Sat, 11 Dec 2021 10:09:04: end of X-cor INFO @ Sat, 11 Dec 2021 10:09:04: #2 finished! INFO @ Sat, 11 Dec 2021 10:09:04: #2 predicted fragment length is 291 bps INFO @ Sat, 11 Dec 2021 10:09:04: #2 alternative fragment length(s) may be 200,291 bps INFO @ Sat, 11 Dec 2021 10:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.05_model.r INFO @ Sat, 11 Dec 2021 10:09:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:09:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:09:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:09:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:09:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.05_summits.bed INFO @ Sat, 11 Dec 2021 10:09:05: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 2 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 10:09:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.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 10:09:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:09:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:09:34: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 10:09:34: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 10:09:34: #1 total tags in treatment: 169650 INFO @ Sat, 11 Dec 2021 10:09:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:09:34: #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 10:09:34: #1 tags after filtering in treatment: 167998 INFO @ Sat, 11 Dec 2021 10:09:34: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 10:09:34: #1 finished! INFO @ Sat, 11 Dec 2021 10:09:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:09:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:09:34: #2 number of paired peaks: 1916 INFO @ Sat, 11 Dec 2021 10:09:34: start model_add_line... INFO @ Sat, 11 Dec 2021 10:09:34: start X-correlation... INFO @ Sat, 11 Dec 2021 10:09:34: end of X-cor INFO @ Sat, 11 Dec 2021 10:09:34: #2 finished! INFO @ Sat, 11 Dec 2021 10:09:34: #2 predicted fragment length is 291 bps INFO @ Sat, 11 Dec 2021 10:09:34: #2 alternative fragment length(s) may be 200,291 bps INFO @ Sat, 11 Dec 2021 10:09:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.10_model.r INFO @ Sat, 11 Dec 2021 10:09:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:09:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:09:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:09:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:09:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.10_summits.bed INFO @ Sat, 11 Dec 2021 10:09:35: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (28 records, 4 fields): 1 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 10:10:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.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 10:10:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:10:01: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 10:10:04: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 10:10:04: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 10:10:04: #1 total tags in treatment: 169650 INFO @ Sat, 11 Dec 2021 10:10:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:10:04: #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 10:10:04: #1 tags after filtering in treatment: 167998 INFO @ Sat, 11 Dec 2021 10:10:04: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 10:10:04: #1 finished! INFO @ Sat, 11 Dec 2021 10:10:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:10:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:10:04: #2 number of paired peaks: 1916 INFO @ Sat, 11 Dec 2021 10:10:04: start model_add_line... INFO @ Sat, 11 Dec 2021 10:10:04: start X-correlation... INFO @ Sat, 11 Dec 2021 10:10:04: end of X-cor INFO @ Sat, 11 Dec 2021 10:10:04: #2 finished! INFO @ Sat, 11 Dec 2021 10:10:04: #2 predicted fragment length is 291 bps INFO @ Sat, 11 Dec 2021 10:10:04: #2 alternative fragment length(s) may be 200,291 bps INFO @ Sat, 11 Dec 2021 10:10:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.20_model.r INFO @ Sat, 11 Dec 2021 10:10:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:10:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:10:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:10:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:10:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555317/SRX9555317.20_summits.bed INFO @ Sat, 11 Dec 2021 10:10:05: Done! pass1 - making usageList (3 chroms): 2 millis pass2 - checking and writing primary data (12 records, 4 fields): 6 millis CompletedMACS2peakCalling