Job ID = 14171387 SRX = SRX9555261 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6295487 spots for SRR13110398/SRR13110398.sra Written 6295487 spots for SRR13110398/SRR13110398.sra Read 6244436 spots for SRR13110399/SRR13110399.sra Written 6244436 spots for SRR13110399/SRR13110399.sra Read 6368647 spots for SRR13110400/SRR13110400.sra Written 6368647 spots for SRR13110400/SRR13110400.sra Read 6327833 spots for SRR13110401/SRR13110401.sra Written 6327833 spots for SRR13110401/SRR13110401.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171872 ("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: 00:03:49 25236403 reads; of these: 25236403 (100.00%) were paired; of these: 24240311 (96.05%) aligned concordantly 0 times 810083 (3.21%) aligned concordantly exactly 1 time 186009 (0.74%) aligned concordantly >1 times ---- 24240311 pairs aligned concordantly 0 times; of these: 2639 (0.01%) aligned discordantly 1 time ---- 24237672 pairs aligned 0 times concordantly or discordantly; of these: 48475344 mates make up the pairs; of these: 48328765 (99.70%) aligned 0 times 62181 (0.13%) aligned exactly 1 time 84398 (0.17%) aligned >1 times 4.25% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 22659 / 998027 = 0.0227 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 11:37:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.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 11:37:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:37:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:37:26: 1000000 INFO @ Sat, 11 Dec 2021 11:37:31: 2000000 INFO @ Sat, 11 Dec 2021 11:37:31: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:37:31: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:37:31: #1 total tags in treatment: 973478 INFO @ Sat, 11 Dec 2021 11:37:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:37:31: #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 11:37:31: #1 tags after filtering in treatment: 947362 INFO @ Sat, 11 Dec 2021 11:37:31: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:37:31: #1 finished! INFO @ Sat, 11 Dec 2021 11:37:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:37:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:37:31: #2 number of paired peaks: 1695 INFO @ Sat, 11 Dec 2021 11:37:31: start model_add_line... INFO @ Sat, 11 Dec 2021 11:37:31: start X-correlation... INFO @ Sat, 11 Dec 2021 11:37:31: end of X-cor INFO @ Sat, 11 Dec 2021 11:37:31: #2 finished! INFO @ Sat, 11 Dec 2021 11:37:31: #2 predicted fragment length is 175 bps INFO @ Sat, 11 Dec 2021 11:37:31: #2 alternative fragment length(s) may be 141,170,175 bps INFO @ Sat, 11 Dec 2021 11:37:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.05_model.r INFO @ Sat, 11 Dec 2021 11:37:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:37:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:37:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:37:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:37:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:37:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.05_summits.bed INFO @ Sat, 11 Dec 2021 11:37:35: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (309 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 11:37:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.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 11:37:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:37:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:37:56: 1000000 INFO @ Sat, 11 Dec 2021 11:38:01: 2000000 INFO @ Sat, 11 Dec 2021 11:38:01: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:38:01: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:38:01: #1 total tags in treatment: 973478 INFO @ Sat, 11 Dec 2021 11:38:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:38:01: #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 11:38:01: #1 tags after filtering in treatment: 947362 INFO @ Sat, 11 Dec 2021 11:38:01: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:38:01: #1 finished! INFO @ Sat, 11 Dec 2021 11:38:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:38:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:38:01: #2 number of paired peaks: 1695 INFO @ Sat, 11 Dec 2021 11:38:01: start model_add_line... INFO @ Sat, 11 Dec 2021 11:38:01: start X-correlation... INFO @ Sat, 11 Dec 2021 11:38:01: end of X-cor INFO @ Sat, 11 Dec 2021 11:38:01: #2 finished! INFO @ Sat, 11 Dec 2021 11:38:01: #2 predicted fragment length is 175 bps INFO @ Sat, 11 Dec 2021 11:38:01: #2 alternative fragment length(s) may be 141,170,175 bps INFO @ Sat, 11 Dec 2021 11:38:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.10_model.r INFO @ Sat, 11 Dec 2021 11:38:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:38:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:38:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:38:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:38:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:38:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.10_summits.bed INFO @ Sat, 11 Dec 2021 11:38:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 23 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 11:38:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.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 11:38:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:38:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:38:26: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:38:31: 2000000 INFO @ Sat, 11 Dec 2021 11:38:32: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:38:32: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:38:32: #1 total tags in treatment: 973478 INFO @ Sat, 11 Dec 2021 11:38:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:38:32: #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 11:38:32: #1 tags after filtering in treatment: 947362 INFO @ Sat, 11 Dec 2021 11:38:32: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:38:32: #1 finished! INFO @ Sat, 11 Dec 2021 11:38:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:38:32: #2 number of paired peaks: 1695 INFO @ Sat, 11 Dec 2021 11:38:32: start model_add_line... INFO @ Sat, 11 Dec 2021 11:38:32: start X-correlation... INFO @ Sat, 11 Dec 2021 11:38:32: end of X-cor INFO @ Sat, 11 Dec 2021 11:38:32: #2 finished! INFO @ Sat, 11 Dec 2021 11:38:32: #2 predicted fragment length is 175 bps INFO @ Sat, 11 Dec 2021 11:38:32: #2 alternative fragment length(s) may be 141,170,175 bps INFO @ Sat, 11 Dec 2021 11:38:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.20_model.r INFO @ Sat, 11 Dec 2021 11:38:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:38:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:38:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:38:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:38:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:38:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555261/SRX9555261.20_summits.bed INFO @ Sat, 11 Dec 2021 11:38:35: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (42 records, 4 fields): 1 millis CompletedMACS2peakCalling