Job ID = 14171393 SRX = SRX9555266 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1787374 spots for SRR13110635/SRR13110635.sra Written 1787374 spots for SRR13110635/SRR13110635.sra Read 1793209 spots for SRR13110636/SRR13110636.sra Written 1793209 spots for SRR13110636/SRR13110636.sra Read 1823122 spots for SRR13110637/SRR13110637.sra Written 1823122 spots for SRR13110637/SRR13110637.sra Read 1815566 spots for SRR13110638/SRR13110638.sra Written 1815566 spots for SRR13110638/SRR13110638.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171849 ("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: 00:01:10 7219271 reads; of these: 7219271 (100.00%) were paired; of these: 6934722 (96.06%) aligned concordantly 0 times 204598 (2.83%) aligned concordantly exactly 1 time 79951 (1.11%) aligned concordantly >1 times ---- 6934722 pairs aligned concordantly 0 times; of these: 1448 (0.02%) aligned discordantly 1 time ---- 6933274 pairs aligned 0 times concordantly or discordantly; of these: 13866548 mates make up the pairs; of these: 13818609 (99.65%) aligned 0 times 17797 (0.13%) aligned exactly 1 time 30142 (0.22%) aligned >1 times 4.29% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 6025 / 285743 = 0.0211 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 11:33:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.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 11:33:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:33:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:33:58: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:33:58: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:33:58: #1 total tags in treatment: 278539 INFO @ Sat, 11 Dec 2021 11:33:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:33:58: #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 11:33:58: #1 tags after filtering in treatment: 275130 INFO @ Sat, 11 Dec 2021 11:33:58: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:33:58: #1 finished! INFO @ Sat, 11 Dec 2021 11:33:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:33:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:33:58: #2 number of paired peaks: 1403 INFO @ Sat, 11 Dec 2021 11:33:58: start model_add_line... INFO @ Sat, 11 Dec 2021 11:33:58: start X-correlation... INFO @ Sat, 11 Dec 2021 11:33:58: end of X-cor INFO @ Sat, 11 Dec 2021 11:33:58: #2 finished! INFO @ Sat, 11 Dec 2021 11:33:58: #2 predicted fragment length is 162 bps INFO @ Sat, 11 Dec 2021 11:33:58: #2 alternative fragment length(s) may be 94,162,200,232,250 bps INFO @ Sat, 11 Dec 2021 11:33:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.05_model.r INFO @ Sat, 11 Dec 2021 11:33:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:33:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:33:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:33:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:33:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:33:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.05_summits.bed INFO @ Sat, 11 Dec 2021 11:33:59: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (66 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 11:34:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.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 11:34:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:34:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:34:28: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:34:28: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:34:28: #1 total tags in treatment: 278539 INFO @ Sat, 11 Dec 2021 11:34:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:34:28: #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 11:34:28: #1 tags after filtering in treatment: 275130 INFO @ Sat, 11 Dec 2021 11:34:28: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:34:28: #1 finished! INFO @ Sat, 11 Dec 2021 11:34:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:34:28: #2 number of paired peaks: 1403 INFO @ Sat, 11 Dec 2021 11:34:28: start model_add_line... INFO @ Sat, 11 Dec 2021 11:34:28: start X-correlation... INFO @ Sat, 11 Dec 2021 11:34:28: end of X-cor INFO @ Sat, 11 Dec 2021 11:34:28: #2 finished! INFO @ Sat, 11 Dec 2021 11:34:28: #2 predicted fragment length is 162 bps INFO @ Sat, 11 Dec 2021 11:34:28: #2 alternative fragment length(s) may be 94,162,200,232,250 bps INFO @ Sat, 11 Dec 2021 11:34:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.10_model.r INFO @ Sat, 11 Dec 2021 11:34:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:34:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:34:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:34:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:34:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:34:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.10_summits.bed INFO @ Sat, 11 Dec 2021 11:34:29: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (40 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 11:34:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.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 11:34:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:34:55: #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 11:34:58: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:34:58: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:34:58: #1 total tags in treatment: 278539 INFO @ Sat, 11 Dec 2021 11:34:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:34:58: #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 11:34:58: #1 tags after filtering in treatment: 275130 INFO @ Sat, 11 Dec 2021 11:34:58: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:34:58: #1 finished! INFO @ Sat, 11 Dec 2021 11:34:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:34:58: #2 number of paired peaks: 1403 INFO @ Sat, 11 Dec 2021 11:34:58: start model_add_line... INFO @ Sat, 11 Dec 2021 11:34:58: start X-correlation... INFO @ Sat, 11 Dec 2021 11:34:58: end of X-cor INFO @ Sat, 11 Dec 2021 11:34:58: #2 finished! INFO @ Sat, 11 Dec 2021 11:34:58: #2 predicted fragment length is 162 bps INFO @ Sat, 11 Dec 2021 11:34:58: #2 alternative fragment length(s) may be 94,162,200,232,250 bps INFO @ Sat, 11 Dec 2021 11:34:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.20_model.r INFO @ Sat, 11 Dec 2021 11:34:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:34:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:34:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:34:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:34:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:34:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555266/SRX9555266.20_summits.bed INFO @ Sat, 11 Dec 2021 11:34:59: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 1 millis CompletedMACS2peakCalling