Job ID = 14171419 SRX = SRX9555276 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8804409 spots for SRR13110675/SRR13110675.sra Written 8804409 spots for SRR13110675/SRR13110675.sra Read 8549279 spots for SRR13110676/SRR13110676.sra Written 8549279 spots for SRR13110676/SRR13110676.sra Read 9023498 spots for SRR13110677/SRR13110677.sra Written 9023498 spots for SRR13110677/SRR13110677.sra Read 8734907 spots for SRR13110678/SRR13110678.sra Written 8734907 spots for SRR13110678/SRR13110678.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171924 ("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: 00:05:52 35112093 reads; of these: 35112093 (100.00%) were paired; of these: 34175058 (97.33%) aligned concordantly 0 times 740147 (2.11%) aligned concordantly exactly 1 time 196888 (0.56%) aligned concordantly >1 times ---- 34175058 pairs aligned concordantly 0 times; of these: 2907 (0.01%) aligned discordantly 1 time ---- 34172151 pairs aligned 0 times concordantly or discordantly; of these: 68344302 mates make up the pairs; of these: 67719305 (99.09%) aligned 0 times 127309 (0.19%) aligned exactly 1 time 497688 (0.73%) aligned >1 times 3.57% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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] 42126 / 938234 = 0.0449 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 11:45:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.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 11:45:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:45:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:45:35: 1000000 INFO @ Sat, 11 Dec 2021 11:45:39: 2000000 INFO @ Sat, 11 Dec 2021 11:45:41: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:45:41: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:45:41: #1 total tags in treatment: 895004 INFO @ Sat, 11 Dec 2021 11:45:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:45:41: #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 11:45:41: #1 tags after filtering in treatment: 873889 INFO @ Sat, 11 Dec 2021 11:45:41: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:45:41: #1 finished! INFO @ Sat, 11 Dec 2021 11:45:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:45:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:45:41: #2 number of paired peaks: 3387 INFO @ Sat, 11 Dec 2021 11:45:41: start model_add_line... INFO @ Sat, 11 Dec 2021 11:45:41: start X-correlation... INFO @ Sat, 11 Dec 2021 11:45:41: end of X-cor INFO @ Sat, 11 Dec 2021 11:45:41: #2 finished! INFO @ Sat, 11 Dec 2021 11:45:41: #2 predicted fragment length is 210 bps INFO @ Sat, 11 Dec 2021 11:45:41: #2 alternative fragment length(s) may be 210,266 bps INFO @ Sat, 11 Dec 2021 11:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.05_model.r INFO @ Sat, 11 Dec 2021 11:45:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:45:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:45:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:45:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:45:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.05_summits.bed INFO @ Sat, 11 Dec 2021 11:45:44: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (176 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 11:45:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.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 11:45:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:45:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:46:04: 1000000 INFO @ Sat, 11 Dec 2021 11:46:08: 2000000 INFO @ Sat, 11 Dec 2021 11:46:09: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:46:09: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:46:09: #1 total tags in treatment: 895004 INFO @ Sat, 11 Dec 2021 11:46:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:46:09: #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 11:46:09: #1 tags after filtering in treatment: 873889 INFO @ Sat, 11 Dec 2021 11:46:09: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:46:09: #1 finished! INFO @ Sat, 11 Dec 2021 11:46:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:46:10: #2 number of paired peaks: 3387 INFO @ Sat, 11 Dec 2021 11:46:10: start model_add_line... INFO @ Sat, 11 Dec 2021 11:46:10: start X-correlation... INFO @ Sat, 11 Dec 2021 11:46:10: end of X-cor INFO @ Sat, 11 Dec 2021 11:46:10: #2 finished! INFO @ Sat, 11 Dec 2021 11:46:10: #2 predicted fragment length is 210 bps INFO @ Sat, 11 Dec 2021 11:46:10: #2 alternative fragment length(s) may be 210,266 bps INFO @ Sat, 11 Dec 2021 11:46:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.10_model.r INFO @ Sat, 11 Dec 2021 11:46:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:46:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:46:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:46:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:46:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:46:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.10_summits.bed INFO @ Sat, 11 Dec 2021 11:46:12: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (87 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 11:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.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 11:46:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:46:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:46:34: 1000000 INFO @ Sat, 11 Dec 2021 11:46:38: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:46:39: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:46:39: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:46:39: #1 total tags in treatment: 895004 INFO @ Sat, 11 Dec 2021 11:46:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:46:39: #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 11:46:39: #1 tags after filtering in treatment: 873889 INFO @ Sat, 11 Dec 2021 11:46:39: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:46:39: #1 finished! INFO @ Sat, 11 Dec 2021 11:46:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:46:39: #2 number of paired peaks: 3387 INFO @ Sat, 11 Dec 2021 11:46:39: start model_add_line... INFO @ Sat, 11 Dec 2021 11:46:39: start X-correlation... INFO @ Sat, 11 Dec 2021 11:46:39: end of X-cor INFO @ Sat, 11 Dec 2021 11:46:39: #2 finished! INFO @ Sat, 11 Dec 2021 11:46:39: #2 predicted fragment length is 210 bps INFO @ Sat, 11 Dec 2021 11:46:39: #2 alternative fragment length(s) may be 210,266 bps INFO @ Sat, 11 Dec 2021 11:46:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.20_model.r INFO @ Sat, 11 Dec 2021 11:46:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:46:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:46:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:46:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:46:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:46:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555276/SRX9555276.20_summits.bed INFO @ Sat, 11 Dec 2021 11:46:42: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 1 millis CompletedMACS2peakCalling