Job ID = 14171119 SRX = SRX9555309 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7395726 spots for SRR13110423/SRR13110423.sra Written 7395726 spots for SRR13110423/SRR13110423.sra Read 7340893 spots for SRR13110424/SRR13110424.sra Written 7340893 spots for SRR13110424/SRR13110424.sra Read 7536782 spots for SRR13110425/SRR13110425.sra Written 7536782 spots for SRR13110425/SRR13110425.sra Read 7421518 spots for SRR13110426/SRR13110426.sra Written 7421518 spots for SRR13110426/SRR13110426.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171580 ("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: 00:04:39 29694919 reads; of these: 29694919 (100.00%) were paired; of these: 28297657 (95.29%) aligned concordantly 0 times 1129641 (3.80%) aligned concordantly exactly 1 time 267621 (0.90%) aligned concordantly >1 times ---- 28297657 pairs aligned concordantly 0 times; of these: 6977 (0.02%) aligned discordantly 1 time ---- 28290680 pairs aligned 0 times concordantly or discordantly; of these: 56581360 mates make up the pairs; of these: 56353740 (99.60%) aligned 0 times 93487 (0.17%) aligned exactly 1 time 134133 (0.24%) aligned >1 times 5.11% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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] 42580 / 1403488 = 0.0303 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 09:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.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 09:47:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:47:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:47:19: 1000000 INFO @ Sat, 11 Dec 2021 09:47:23: 2000000 INFO @ Sat, 11 Dec 2021 09:47:28: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:47:28: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:47:28: #1 total tags in treatment: 1354779 INFO @ Sat, 11 Dec 2021 09:47:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:47:28: #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 09:47:28: #1 tags after filtering in treatment: 1268936 INFO @ Sat, 11 Dec 2021 09:47:28: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 09:47:28: #1 finished! INFO @ Sat, 11 Dec 2021 09:47:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:47:28: #2 number of paired peaks: 6316 INFO @ Sat, 11 Dec 2021 09:47:28: start model_add_line... INFO @ Sat, 11 Dec 2021 09:47:28: start X-correlation... INFO @ Sat, 11 Dec 2021 09:47:28: end of X-cor INFO @ Sat, 11 Dec 2021 09:47:28: #2 finished! INFO @ Sat, 11 Dec 2021 09:47:28: #2 predicted fragment length is 188 bps INFO @ Sat, 11 Dec 2021 09:47:28: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 11 Dec 2021 09:47:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.05_model.r INFO @ Sat, 11 Dec 2021 09:47:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:47:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:47:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.05_summits.bed INFO @ Sat, 11 Dec 2021 09:47:33: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1016 records, 4 fields): 2 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 09:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.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 09:47:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:47:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:47:50: 1000000 INFO @ Sat, 11 Dec 2021 09:47:56: 2000000 INFO @ Sat, 11 Dec 2021 09:48:02: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:48:02: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:48:02: #1 total tags in treatment: 1354779 INFO @ Sat, 11 Dec 2021 09:48:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:48:02: #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 09:48:02: #1 tags after filtering in treatment: 1268936 INFO @ Sat, 11 Dec 2021 09:48:02: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 09:48:02: #1 finished! INFO @ Sat, 11 Dec 2021 09:48:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:48:02: #2 number of paired peaks: 6316 INFO @ Sat, 11 Dec 2021 09:48:02: start model_add_line... INFO @ Sat, 11 Dec 2021 09:48:02: start X-correlation... INFO @ Sat, 11 Dec 2021 09:48:02: end of X-cor INFO @ Sat, 11 Dec 2021 09:48:02: #2 finished! INFO @ Sat, 11 Dec 2021 09:48:02: #2 predicted fragment length is 188 bps INFO @ Sat, 11 Dec 2021 09:48:02: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 11 Dec 2021 09:48:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.10_model.r INFO @ Sat, 11 Dec 2021 09:48:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:48:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:48:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:48:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:48:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:48:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.10_summits.bed INFO @ Sat, 11 Dec 2021 09:48:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (353 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 09:48:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.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 09:48:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:48:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:48:19: 1000000 INFO @ Sat, 11 Dec 2021 09:48:23: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:48:28: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:48:28: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:48:28: #1 total tags in treatment: 1354779 INFO @ Sat, 11 Dec 2021 09:48:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:48:28: #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 09:48:28: #1 tags after filtering in treatment: 1268936 INFO @ Sat, 11 Dec 2021 09:48:28: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 09:48:28: #1 finished! INFO @ Sat, 11 Dec 2021 09:48:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:48:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:48:29: #2 number of paired peaks: 6316 INFO @ Sat, 11 Dec 2021 09:48:29: start model_add_line... INFO @ Sat, 11 Dec 2021 09:48:29: start X-correlation... INFO @ Sat, 11 Dec 2021 09:48:29: end of X-cor INFO @ Sat, 11 Dec 2021 09:48:29: #2 finished! INFO @ Sat, 11 Dec 2021 09:48:29: #2 predicted fragment length is 188 bps INFO @ Sat, 11 Dec 2021 09:48:29: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 11 Dec 2021 09:48:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.20_model.r INFO @ Sat, 11 Dec 2021 09:48:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:48:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:48:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:48:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:48:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:48:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555309/SRX9555309.20_summits.bed INFO @ Sat, 11 Dec 2021 09:48:33: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 1 millis CompletedMACS2peakCalling