Job ID = 14172224 SRX = SRX9281738 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11069487 spots for SRR12813241/SRR12813241.sra Written 11069487 spots for SRR12813241/SRR12813241.sra Read 11069177 spots for SRR12813242/SRR12813242.sra Written 11069177 spots for SRR12813242/SRR12813242.sra Read 11260092 spots for SRR12813243/SRR12813243.sra Written 11260092 spots for SRR12813243/SRR12813243.sra Read 11011428 spots for SRR12813244/SRR12813244.sra Written 11011428 spots for SRR12813244/SRR12813244.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172725 ("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: 00:08:43 44410184 reads; of these: 44410184 (100.00%) were paired; of these: 42027098 (94.63%) aligned concordantly 0 times 1776336 (4.00%) aligned concordantly exactly 1 time 606750 (1.37%) aligned concordantly >1 times ---- 42027098 pairs aligned concordantly 0 times; of these: 8692 (0.02%) aligned discordantly 1 time ---- 42018406 pairs aligned 0 times concordantly or discordantly; of these: 84036812 mates make up the pairs; of these: 83352228 (99.19%) aligned 0 times 238553 (0.28%) aligned exactly 1 time 446031 (0.53%) aligned >1 times 6.16% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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] 107092 / 2388662 = 0.0448 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 15:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.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 15:03:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:03:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:03:32: 1000000 INFO @ Sat, 11 Dec 2021 15:03:37: 2000000 INFO @ Sat, 11 Dec 2021 15:03:41: 3000000 INFO @ Sat, 11 Dec 2021 15:03:46: 4000000 INFO @ Sat, 11 Dec 2021 15:03:51: 5000000 INFO @ Sat, 11 Dec 2021 15:03:52: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:03:52: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:03:52: #1 total tags in treatment: 2276171 INFO @ Sat, 11 Dec 2021 15:03:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:03:52: #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 15:03:52: #1 tags after filtering in treatment: 2180636 INFO @ Sat, 11 Dec 2021 15:03:52: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 15:03:52: #1 finished! INFO @ Sat, 11 Dec 2021 15:03:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:03:52: #2 number of paired peaks: 1033 INFO @ Sat, 11 Dec 2021 15:03:52: start model_add_line... INFO @ Sat, 11 Dec 2021 15:03:52: start X-correlation... INFO @ Sat, 11 Dec 2021 15:03:52: end of X-cor INFO @ Sat, 11 Dec 2021 15:03:52: #2 finished! INFO @ Sat, 11 Dec 2021 15:03:52: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Dec 2021 15:03:52: #2 alternative fragment length(s) may be 106,131 bps INFO @ Sat, 11 Dec 2021 15:03:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.05_model.r INFO @ Sat, 11 Dec 2021 15:03:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:03:52: #3 Pre-compute pvalue-qvalue table... 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 15:03:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.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 15:03:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:03:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:03:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:03:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:03:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:03:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.05_summits.bed INFO @ Sat, 11 Dec 2021 15:03:59: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (352 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:04:01: 1000000 INFO @ Sat, 11 Dec 2021 15:04:07: 2000000 INFO @ Sat, 11 Dec 2021 15:04:12: 3000000 INFO @ Sat, 11 Dec 2021 15:04:17: 4000000 INFO @ Sat, 11 Dec 2021 15:04:21: 5000000 INFO @ Sat, 11 Dec 2021 15:04:22: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:04:22: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:04:22: #1 total tags in treatment: 2276171 INFO @ Sat, 11 Dec 2021 15:04:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:04:22: #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 15:04:22: #1 tags after filtering in treatment: 2180636 INFO @ Sat, 11 Dec 2021 15:04:22: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 15:04:22: #1 finished! INFO @ Sat, 11 Dec 2021 15:04:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:04:23: #2 number of paired peaks: 1033 INFO @ Sat, 11 Dec 2021 15:04:23: start model_add_line... INFO @ Sat, 11 Dec 2021 15:04:23: start X-correlation... INFO @ Sat, 11 Dec 2021 15:04:23: end of X-cor INFO @ Sat, 11 Dec 2021 15:04:23: #2 finished! INFO @ Sat, 11 Dec 2021 15:04:23: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Dec 2021 15:04:23: #2 alternative fragment length(s) may be 106,131 bps INFO @ Sat, 11 Dec 2021 15:04:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.10_model.r INFO @ Sat, 11 Dec 2021 15:04:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:04:23: #3 Pre-compute pvalue-qvalue table... 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 15:04:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.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 15:04:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:04:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:04:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.10_summits.bed INFO @ Sat, 11 Dec 2021 15:04:30: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (167 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:04:31: 1000000 INFO @ Sat, 11 Dec 2021 15:04:36: 2000000 INFO @ Sat, 11 Dec 2021 15:04:41: 3000000 INFO @ Sat, 11 Dec 2021 15:04:46: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:04:51: 5000000 INFO @ Sat, 11 Dec 2021 15:04:52: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:04:52: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:04:52: #1 total tags in treatment: 2276171 INFO @ Sat, 11 Dec 2021 15:04:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:04:52: #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 15:04:52: #1 tags after filtering in treatment: 2180636 INFO @ Sat, 11 Dec 2021 15:04:52: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 15:04:52: #1 finished! INFO @ Sat, 11 Dec 2021 15:04:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:04:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:04:52: #2 number of paired peaks: 1033 INFO @ Sat, 11 Dec 2021 15:04:52: start model_add_line... INFO @ Sat, 11 Dec 2021 15:04:52: start X-correlation... INFO @ Sat, 11 Dec 2021 15:04:52: end of X-cor INFO @ Sat, 11 Dec 2021 15:04:52: #2 finished! INFO @ Sat, 11 Dec 2021 15:04:52: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Dec 2021 15:04:52: #2 alternative fragment length(s) may be 106,131 bps INFO @ Sat, 11 Dec 2021 15:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.20_model.r INFO @ Sat, 11 Dec 2021 15:04:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:04:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281738/SRX9281738.20_summits.bed INFO @ Sat, 11 Dec 2021 15:04:59: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (79 records, 4 fields): 1 millis CompletedMACS2peakCalling