Job ID = 14172340 SRX = SRX5681711 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3638518 spots for SRR8895583/SRR8895583.sra Written 3638518 spots for SRR8895583/SRR8895583.sra Read 3860949 spots for SRR8895584/SRR8895584.sra Written 3860949 spots for SRR8895584/SRR8895584.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172841 ("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: 00:11:20 7499467 reads; of these: 7499467 (100.00%) were paired; of these: 1936787 (25.83%) aligned concordantly 0 times 4981271 (66.42%) aligned concordantly exactly 1 time 581409 (7.75%) aligned concordantly >1 times ---- 1936787 pairs aligned concordantly 0 times; of these: 444351 (22.94%) aligned discordantly 1 time ---- 1492436 pairs aligned 0 times concordantly or discordantly; of these: 2984872 mates make up the pairs; of these: 2434294 (81.55%) aligned 0 times 395467 (13.25%) aligned exactly 1 time 155111 (5.20%) aligned >1 times 83.77% overall alignment rate Time searching: 00:11:20 Overall time: 00:11:20 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_sort_core] merging from 8 files... [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] 296654 / 5986341 = 0.0496 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 15:25:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.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 15:25:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:25:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:26:03: 1000000 INFO @ Sat, 11 Dec 2021 15:26:08: 2000000 INFO @ Sat, 11 Dec 2021 15:26:14: 3000000 INFO @ Sat, 11 Dec 2021 15:26:20: 4000000 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 15:26:26: 5000000 INFO @ Sat, 11 Dec 2021 15:26:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.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 15:26:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:26:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:26:31: 6000000 INFO @ Sat, 11 Dec 2021 15:26:32: 1000000 INFO @ Sat, 11 Dec 2021 15:26:37: 7000000 INFO @ Sat, 11 Dec 2021 15:26:38: 2000000 INFO @ Sat, 11 Dec 2021 15:26:43: 8000000 INFO @ Sat, 11 Dec 2021 15:26:44: 3000000 INFO @ Sat, 11 Dec 2021 15:26:49: 9000000 INFO @ Sat, 11 Dec 2021 15:26:50: 4000000 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 15:26:55: 10000000 INFO @ Sat, 11 Dec 2021 15:26:57: 5000000 INFO @ Sat, 11 Dec 2021 15:26:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.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 15:26:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:26:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:27:01: 11000000 INFO @ Sat, 11 Dec 2021 15:27:02: 6000000 INFO @ Sat, 11 Dec 2021 15:27:03: 1000000 INFO @ Sat, 11 Dec 2021 15:27:07: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 15:27:07: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 15:27:07: #1 total tags in treatment: 5283944 INFO @ Sat, 11 Dec 2021 15:27:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:27:07: #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 15:27:07: #1 tags after filtering in treatment: 4704323 INFO @ Sat, 11 Dec 2021 15:27:07: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 11 Dec 2021 15:27:07: #1 finished! INFO @ Sat, 11 Dec 2021 15:27:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:27:07: #2 number of paired peaks: 3552 INFO @ Sat, 11 Dec 2021 15:27:07: start model_add_line... INFO @ Sat, 11 Dec 2021 15:27:07: start X-correlation... INFO @ Sat, 11 Dec 2021 15:27:07: end of X-cor INFO @ Sat, 11 Dec 2021 15:27:07: #2 finished! INFO @ Sat, 11 Dec 2021 15:27:07: #2 predicted fragment length is 232 bps INFO @ Sat, 11 Dec 2021 15:27:07: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 11 Dec 2021 15:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.05_model.r INFO @ Sat, 11 Dec 2021 15:27:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:27:08: 7000000 INFO @ Sat, 11 Dec 2021 15:27:10: 2000000 INFO @ Sat, 11 Dec 2021 15:27:14: 8000000 INFO @ Sat, 11 Dec 2021 15:27:16: 3000000 INFO @ Sat, 11 Dec 2021 15:27:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:27:20: 9000000 INFO @ Sat, 11 Dec 2021 15:27:22: 4000000 INFO @ Sat, 11 Dec 2021 15:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:27:26: 10000000 INFO @ Sat, 11 Dec 2021 15:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.05_summits.bed INFO @ Sat, 11 Dec 2021 15:27:26: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12338 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:27:28: 5000000 INFO @ Sat, 11 Dec 2021 15:27:31: 11000000 INFO @ Sat, 11 Dec 2021 15:27:35: 6000000 INFO @ Sat, 11 Dec 2021 15:27:37: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 15:27:37: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 15:27:37: #1 total tags in treatment: 5283944 INFO @ Sat, 11 Dec 2021 15:27:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:27:37: #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 15:27:37: #1 tags after filtering in treatment: 4704323 INFO @ Sat, 11 Dec 2021 15:27:37: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 11 Dec 2021 15:27:37: #1 finished! INFO @ Sat, 11 Dec 2021 15:27:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:27:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:27:38: #2 number of paired peaks: 3552 INFO @ Sat, 11 Dec 2021 15:27:38: start model_add_line... INFO @ Sat, 11 Dec 2021 15:27:38: start X-correlation... INFO @ Sat, 11 Dec 2021 15:27:38: end of X-cor INFO @ Sat, 11 Dec 2021 15:27:38: #2 finished! INFO @ Sat, 11 Dec 2021 15:27:38: #2 predicted fragment length is 232 bps INFO @ Sat, 11 Dec 2021 15:27:38: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 11 Dec 2021 15:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.10_model.r INFO @ Sat, 11 Dec 2021 15:27:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:27:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:27:42: 7000000 INFO @ Sat, 11 Dec 2021 15:27:48: 8000000 INFO @ Sat, 11 Dec 2021 15:27:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:27:54: 9000000 INFO @ Sat, 11 Dec 2021 15:27:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:27:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:27:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.10_summits.bed INFO @ Sat, 11 Dec 2021 15:27:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5151 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:28:02: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:28:07: 11000000 INFO @ Sat, 11 Dec 2021 15:28:13: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 15:28:13: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 15:28:13: #1 total tags in treatment: 5283944 INFO @ Sat, 11 Dec 2021 15:28:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:28:13: #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 15:28:13: #1 tags after filtering in treatment: 4704323 INFO @ Sat, 11 Dec 2021 15:28:13: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 11 Dec 2021 15:28:13: #1 finished! INFO @ Sat, 11 Dec 2021 15:28:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:28:14: #2 number of paired peaks: 3552 INFO @ Sat, 11 Dec 2021 15:28:14: start model_add_line... INFO @ Sat, 11 Dec 2021 15:28:14: start X-correlation... INFO @ Sat, 11 Dec 2021 15:28:14: end of X-cor INFO @ Sat, 11 Dec 2021 15:28:14: #2 finished! INFO @ Sat, 11 Dec 2021 15:28:14: #2 predicted fragment length is 232 bps INFO @ Sat, 11 Dec 2021 15:28:14: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 11 Dec 2021 15:28:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.20_model.r INFO @ Sat, 11 Dec 2021 15:28:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:28:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:28:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.20_summits.bed INFO @ Sat, 11 Dec 2021 15:28:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1166 records, 4 fields): 3 millis CompletedMACS2peakCalling