Job ID = 14167227 SRX = SRX8973510 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6194867 spots for SRR12479625/SRR12479625.sra Written 6194867 spots for SRR12479625/SRR12479625.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167769 ("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: 00:02:40 6194867 reads; of these: 6194867 (100.00%) were paired; of these: 4365547 (70.47%) aligned concordantly 0 times 1629309 (26.30%) aligned concordantly exactly 1 time 200011 (3.23%) aligned concordantly >1 times ---- 4365547 pairs aligned concordantly 0 times; of these: 60545 (1.39%) aligned discordantly 1 time ---- 4305002 pairs aligned 0 times concordantly or discordantly; of these: 8610004 mates make up the pairs; of these: 8238697 (95.69%) aligned 0 times 329280 (3.82%) aligned exactly 1 time 42027 (0.49%) aligned >1 times 33.50% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 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] 71123 / 1889202 = 0.0376 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 11:11:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.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 11:11:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:11:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:11:36: 1000000 INFO @ Fri, 10 Dec 2021 11:11:41: 2000000 INFO @ Fri, 10 Dec 2021 11:11:46: 3000000 INFO @ Fri, 10 Dec 2021 11:11:51: 4000000 INFO @ Fri, 10 Dec 2021 11:11:51: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:11:51: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:11:51: #1 total tags in treatment: 1759264 INFO @ Fri, 10 Dec 2021 11:11:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:11:51: #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 11:11:51: #1 tags after filtering in treatment: 1715819 INFO @ Fri, 10 Dec 2021 11:11:51: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:11:51: #1 finished! INFO @ Fri, 10 Dec 2021 11:11:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:11:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:11:51: #2 number of paired peaks: 8245 INFO @ Fri, 10 Dec 2021 11:11:51: start model_add_line... INFO @ Fri, 10 Dec 2021 11:11:51: start X-correlation... INFO @ Fri, 10 Dec 2021 11:11:51: end of X-cor INFO @ Fri, 10 Dec 2021 11:11:51: #2 finished! INFO @ Fri, 10 Dec 2021 11:11:51: #2 predicted fragment length is 278 bps INFO @ Fri, 10 Dec 2021 11:11:51: #2 alternative fragment length(s) may be 4,278 bps INFO @ Fri, 10 Dec 2021 11:11:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.05_model.r INFO @ Fri, 10 Dec 2021 11:11:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:11:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:11:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:11:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:11:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.05_summits.bed INFO @ Fri, 10 Dec 2021 11:11:57: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (514 records, 4 fields): 15 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 @ Fri, 10 Dec 2021 11:12:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.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 11:12:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:12:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:12:06: 1000000 INFO @ Fri, 10 Dec 2021 11:12:11: 2000000 INFO @ Fri, 10 Dec 2021 11:12:16: 3000000 INFO @ Fri, 10 Dec 2021 11:12:21: 4000000 INFO @ Fri, 10 Dec 2021 11:12:21: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:12:21: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:12:21: #1 total tags in treatment: 1759264 INFO @ Fri, 10 Dec 2021 11:12:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:12:21: #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 11:12:21: #1 tags after filtering in treatment: 1715819 INFO @ Fri, 10 Dec 2021 11:12:21: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:12:21: #1 finished! INFO @ Fri, 10 Dec 2021 11:12:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:12:21: #2 number of paired peaks: 8245 INFO @ Fri, 10 Dec 2021 11:12:21: start model_add_line... INFO @ Fri, 10 Dec 2021 11:12:21: start X-correlation... INFO @ Fri, 10 Dec 2021 11:12:21: end of X-cor INFO @ Fri, 10 Dec 2021 11:12:21: #2 finished! INFO @ Fri, 10 Dec 2021 11:12:21: #2 predicted fragment length is 278 bps INFO @ Fri, 10 Dec 2021 11:12:21: #2 alternative fragment length(s) may be 4,278 bps INFO @ Fri, 10 Dec 2021 11:12:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.10_model.r INFO @ Fri, 10 Dec 2021 11:12:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:12:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:12:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:12:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:12:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.10_summits.bed INFO @ Fri, 10 Dec 2021 11:12:27: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (299 records, 4 fields): 30 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 @ Fri, 10 Dec 2021 11:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.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 11:12:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:12:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:12:35: 1000000 INFO @ Fri, 10 Dec 2021 11:12:39: 2000000 INFO @ Fri, 10 Dec 2021 11:12:43: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:12:47: 4000000 INFO @ Fri, 10 Dec 2021 11:12:47: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:12:47: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:12:47: #1 total tags in treatment: 1759264 INFO @ Fri, 10 Dec 2021 11:12:47: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:12:47: #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 11:12:47: #1 tags after filtering in treatment: 1715819 INFO @ Fri, 10 Dec 2021 11:12:47: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:12:47: #1 finished! INFO @ Fri, 10 Dec 2021 11:12:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:12:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:12:48: #2 number of paired peaks: 8245 INFO @ Fri, 10 Dec 2021 11:12:48: start model_add_line... INFO @ Fri, 10 Dec 2021 11:12:48: start X-correlation... INFO @ Fri, 10 Dec 2021 11:12:48: end of X-cor INFO @ Fri, 10 Dec 2021 11:12:48: #2 finished! INFO @ Fri, 10 Dec 2021 11:12:48: #2 predicted fragment length is 278 bps INFO @ Fri, 10 Dec 2021 11:12:48: #2 alternative fragment length(s) may be 4,278 bps INFO @ Fri, 10 Dec 2021 11:12:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.20_model.r INFO @ Fri, 10 Dec 2021 11:12:48: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:12:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:12:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:12:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:12:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:12:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973510/SRX8973510.20_summits.bed INFO @ Fri, 10 Dec 2021 11:12:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (145 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。