Job ID = 12265188 SRX = SRX3426790 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4135174 spots for SRR6327141/SRR6327141.sra Written 4135174 spots for SRR6327141/SRR6327141.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265345 ("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: 00:04:06 4135174 reads; of these: 4135174 (100.00%) were paired; of these: 2117074 (51.20%) aligned concordantly 0 times 1699436 (41.10%) aligned concordantly exactly 1 time 318664 (7.71%) aligned concordantly >1 times ---- 2117074 pairs aligned concordantly 0 times; of these: 258061 (12.19%) aligned discordantly 1 time ---- 1859013 pairs aligned 0 times concordantly or discordantly; of these: 3718026 mates make up the pairs; of these: 2027522 (54.53%) aligned 0 times 1257699 (33.83%) aligned exactly 1 time 432805 (11.64%) aligned >1 times 75.48% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 116615 / 2262505 = 0.0515 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.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, 03 Apr 2021 06:18:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:18:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:18:41: 1000000 INFO @ Sat, 03 Apr 2021 06:18:46: 2000000 INFO @ Sat, 03 Apr 2021 06:18:50: 3000000 INFO @ Sat, 03 Apr 2021 06:18:54: 4000000 INFO @ Sat, 03 Apr 2021 06:18:58: 5000000 INFO @ Sat, 03 Apr 2021 06:19:03: 6000000 INFO @ Sat, 03 Apr 2021 06:19:03: #1 tag size is determined as 34 bps INFO @ Sat, 03 Apr 2021 06:19:03: #1 tag size = 34 INFO @ Sat, 03 Apr 2021 06:19:03: #1 total tags in treatment: 1914907 INFO @ Sat, 03 Apr 2021 06:19:03: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:19:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:19:03: #1 tags after filtering in treatment: 1649151 INFO @ Sat, 03 Apr 2021 06:19:03: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 06:19:03: #1 finished! INFO @ Sat, 03 Apr 2021 06:19:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:19:03: #2 number of paired peaks: 5004 INFO @ Sat, 03 Apr 2021 06:19:03: start model_add_line... INFO @ Sat, 03 Apr 2021 06:19:03: start X-correlation... INFO @ Sat, 03 Apr 2021 06:19:03: end of X-cor INFO @ Sat, 03 Apr 2021 06:19:03: #2 finished! INFO @ Sat, 03 Apr 2021 06:19:03: #2 predicted fragment length is 116 bps INFO @ Sat, 03 Apr 2021 06:19:03: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 03 Apr 2021 06:19:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.05_model.r INFO @ Sat, 03 Apr 2021 06:19:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:19:03: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:19:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:19:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.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, 03 Apr 2021 06:19:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:19:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:19:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.05_summits.bed INFO @ Sat, 03 Apr 2021 06:19:09: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6451 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:19:11: 1000000 INFO @ Sat, 03 Apr 2021 06:19:15: 2000000 INFO @ Sat, 03 Apr 2021 06:19:20: 3000000 INFO @ Sat, 03 Apr 2021 06:19:24: 4000000 INFO @ Sat, 03 Apr 2021 06:19:28: 5000000 INFO @ Sat, 03 Apr 2021 06:19:33: 6000000 INFO @ Sat, 03 Apr 2021 06:19:33: #1 tag size is determined as 34 bps INFO @ Sat, 03 Apr 2021 06:19:33: #1 tag size = 34 INFO @ Sat, 03 Apr 2021 06:19:33: #1 total tags in treatment: 1914907 INFO @ Sat, 03 Apr 2021 06:19:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:19:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:19:33: #1 tags after filtering in treatment: 1649151 INFO @ Sat, 03 Apr 2021 06:19:33: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 06:19:33: #1 finished! INFO @ Sat, 03 Apr 2021 06:19:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:19:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:19:33: #2 number of paired peaks: 5004 INFO @ Sat, 03 Apr 2021 06:19:33: start model_add_line... INFO @ Sat, 03 Apr 2021 06:19:33: start X-correlation... INFO @ Sat, 03 Apr 2021 06:19:33: end of X-cor INFO @ Sat, 03 Apr 2021 06:19:33: #2 finished! INFO @ Sat, 03 Apr 2021 06:19:33: #2 predicted fragment length is 116 bps INFO @ Sat, 03 Apr 2021 06:19:33: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 03 Apr 2021 06:19:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.10_model.r INFO @ Sat, 03 Apr 2021 06:19:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:19:33: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:19:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:19:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.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, 03 Apr 2021 06:19:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:19:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:19:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:19:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:19:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.10_summits.bed INFO @ Sat, 03 Apr 2021 06:19:38: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3292 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:19:41: 1000000 INFO @ Sat, 03 Apr 2021 06:19:46: 2000000 INFO @ Sat, 03 Apr 2021 06:19:50: 3000000 INFO @ Sat, 03 Apr 2021 06:19:55: 4000000 INFO @ Sat, 03 Apr 2021 06:19:59: 5000000 INFO @ Sat, 03 Apr 2021 06:20:04: 6000000 INFO @ Sat, 03 Apr 2021 06:20:05: #1 tag size is determined as 34 bps INFO @ Sat, 03 Apr 2021 06:20:05: #1 tag size = 34 INFO @ Sat, 03 Apr 2021 06:20:05: #1 total tags in treatment: 1914907 INFO @ Sat, 03 Apr 2021 06:20:05: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:20:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:20:05: #1 tags after filtering in treatment: 1649151 INFO @ Sat, 03 Apr 2021 06:20:05: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 06:20:05: #1 finished! INFO @ Sat, 03 Apr 2021 06:20:05: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:20:05: #2 number of paired peaks: 5004 INFO @ Sat, 03 Apr 2021 06:20:05: start model_add_line... INFO @ Sat, 03 Apr 2021 06:20:05: start X-correlation... INFO @ Sat, 03 Apr 2021 06:20:05: end of X-cor INFO @ Sat, 03 Apr 2021 06:20:05: #2 finished! INFO @ Sat, 03 Apr 2021 06:20:05: #2 predicted fragment length is 116 bps INFO @ Sat, 03 Apr 2021 06:20:05: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 03 Apr 2021 06:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.20_model.r INFO @ Sat, 03 Apr 2021 06:20:05: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:20:05: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:20:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:20:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:20:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:20:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3426790/SRX3426790.20_summits.bed INFO @ Sat, 03 Apr 2021 06:20:10: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1024 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。