Job ID = 14171129 SRX = SRX9555311 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8472727 spots for SRR13110431/SRR13110431.sra Written 8472727 spots for SRR13110431/SRR13110431.sra Read 8412117 spots for SRR13110432/SRR13110432.sra Written 8412117 spots for SRR13110432/SRR13110432.sra Read 8644436 spots for SRR13110433/SRR13110433.sra Written 8644436 spots for SRR13110433/SRR13110433.sra Read 8511129 spots for SRR13110434/SRR13110434.sra Written 8511129 spots for SRR13110434/SRR13110434.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171592 ("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: 00:04:37 34040409 reads; of these: 34040409 (100.00%) were paired; of these: 33062061 (97.13%) aligned concordantly 0 times 803908 (2.36%) aligned concordantly exactly 1 time 174440 (0.51%) aligned concordantly >1 times ---- 33062061 pairs aligned concordantly 0 times; of these: 7617 (0.02%) aligned discordantly 1 time ---- 33054444 pairs aligned 0 times concordantly or discordantly; of these: 66108888 mates make up the pairs; of these: 65877606 (99.65%) aligned 0 times 81668 (0.12%) aligned exactly 1 time 149614 (0.23%) aligned >1 times 3.24% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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] 27752 / 985506 = 0.0282 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 09:49:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.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 09:49:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:49:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:49:27: 1000000 INFO @ Sat, 11 Dec 2021 09:49:32: 2000000 INFO @ Sat, 11 Dec 2021 09:49:33: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:49:33: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:49:33: #1 total tags in treatment: 950691 INFO @ Sat, 11 Dec 2021 09:49:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:49:33: #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 09:49:33: #1 tags after filtering in treatment: 899197 INFO @ Sat, 11 Dec 2021 09:49:33: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 09:49:33: #1 finished! INFO @ Sat, 11 Dec 2021 09:49:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:49:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:49:33: #2 number of paired peaks: 8153 INFO @ Sat, 11 Dec 2021 09:49:33: start model_add_line... INFO @ Sat, 11 Dec 2021 09:49:33: start X-correlation... INFO @ Sat, 11 Dec 2021 09:49:33: end of X-cor INFO @ Sat, 11 Dec 2021 09:49:33: #2 finished! INFO @ Sat, 11 Dec 2021 09:49:33: #2 predicted fragment length is 224 bps INFO @ Sat, 11 Dec 2021 09:49:33: #2 alternative fragment length(s) may be 224 bps INFO @ Sat, 11 Dec 2021 09:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.05_model.r INFO @ Sat, 11 Dec 2021 09:49:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:49:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:49:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:49:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:49:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.05_summits.bed INFO @ Sat, 11 Dec 2021 09:49:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (825 records, 4 fields): 6 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 09:49:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.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 09:49:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:49:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:49:57: 1000000 INFO @ Sat, 11 Dec 2021 09:50:02: 2000000 INFO @ Sat, 11 Dec 2021 09:50:03: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:50:03: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:50:03: #1 total tags in treatment: 950691 INFO @ Sat, 11 Dec 2021 09:50:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:50:03: #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 09:50:03: #1 tags after filtering in treatment: 899197 INFO @ Sat, 11 Dec 2021 09:50:03: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 09:50:03: #1 finished! INFO @ Sat, 11 Dec 2021 09:50:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:50:03: #2 number of paired peaks: 8153 INFO @ Sat, 11 Dec 2021 09:50:03: start model_add_line... INFO @ Sat, 11 Dec 2021 09:50:03: start X-correlation... INFO @ Sat, 11 Dec 2021 09:50:03: end of X-cor INFO @ Sat, 11 Dec 2021 09:50:03: #2 finished! INFO @ Sat, 11 Dec 2021 09:50:03: #2 predicted fragment length is 224 bps INFO @ Sat, 11 Dec 2021 09:50:03: #2 alternative fragment length(s) may be 224 bps INFO @ Sat, 11 Dec 2021 09:50:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.10_model.r INFO @ Sat, 11 Dec 2021 09:50:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:50:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:50:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.10_summits.bed INFO @ Sat, 11 Dec 2021 09:50:06: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (277 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 09:50:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.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 09:50:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:50:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:50:27: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:50:32: 2000000 INFO @ Sat, 11 Dec 2021 09:50:33: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:50:33: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:50:33: #1 total tags in treatment: 950691 INFO @ Sat, 11 Dec 2021 09:50:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:50:33: #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 09:50:33: #1 tags after filtering in treatment: 899197 INFO @ Sat, 11 Dec 2021 09:50:33: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 09:50:33: #1 finished! INFO @ Sat, 11 Dec 2021 09:50:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:50:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:50:33: #2 number of paired peaks: 8153 INFO @ Sat, 11 Dec 2021 09:50:33: start model_add_line... INFO @ Sat, 11 Dec 2021 09:50:33: start X-correlation... INFO @ Sat, 11 Dec 2021 09:50:33: end of X-cor INFO @ Sat, 11 Dec 2021 09:50:33: #2 finished! INFO @ Sat, 11 Dec 2021 09:50:33: #2 predicted fragment length is 224 bps INFO @ Sat, 11 Dec 2021 09:50:33: #2 alternative fragment length(s) may be 224 bps INFO @ Sat, 11 Dec 2021 09:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.20_model.r INFO @ Sat, 11 Dec 2021 09:50:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:50:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:50:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:50:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:50:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:50:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555311/SRX9555311.20_summits.bed INFO @ Sat, 11 Dec 2021 09:50:36: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (108 records, 4 fields): 2 millis CompletedMACS2peakCalling