Job ID = 12266657 SRX = SRX7806729 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6539950 spots for SRR11186395/SRR11186395.sra Written 6539950 spots for SRR11186395/SRR11186395.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266845 ("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: 00:06:09 6539950 reads; of these: 6539950 (100.00%) were paired; of these: 5298078 (81.01%) aligned concordantly 0 times 695113 (10.63%) aligned concordantly exactly 1 time 546759 (8.36%) aligned concordantly >1 times ---- 5298078 pairs aligned concordantly 0 times; of these: 167910 (3.17%) aligned discordantly 1 time ---- 5130168 pairs aligned 0 times concordantly or discordantly; of these: 10260336 mates make up the pairs; of these: 9986693 (97.33%) aligned 0 times 92013 (0.90%) aligned exactly 1 time 181630 (1.77%) aligned >1 times 23.65% overall alignment rate Time searching: 00:06:09 Overall time: 00:06:09 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] 175989 / 1400153 = 0.1257 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 09:12:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.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 09:12:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:12:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:12:18: 1000000 INFO @ Sat, 03 Apr 2021 09:12:24: 2000000 INFO @ Sat, 03 Apr 2021 09:12:28: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:12:28: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:12:28: #1 total tags in treatment: 1074238 INFO @ Sat, 03 Apr 2021 09:12:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:12:28: #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 09:12:28: #1 tags after filtering in treatment: 872976 INFO @ Sat, 03 Apr 2021 09:12:28: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 09:12:28: #1 finished! INFO @ Sat, 03 Apr 2021 09:12:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:12:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:12:28: #2 number of paired peaks: 3239 INFO @ Sat, 03 Apr 2021 09:12:28: start model_add_line... INFO @ Sat, 03 Apr 2021 09:12:28: start X-correlation... INFO @ Sat, 03 Apr 2021 09:12:28: end of X-cor INFO @ Sat, 03 Apr 2021 09:12:28: #2 finished! INFO @ Sat, 03 Apr 2021 09:12:28: #2 predicted fragment length is 179 bps INFO @ Sat, 03 Apr 2021 09:12:28: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 03 Apr 2021 09:12:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.05_model.r INFO @ Sat, 03 Apr 2021 09:12:28: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:12:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:12:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:12:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:12:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:12:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.05_summits.bed INFO @ Sat, 03 Apr 2021 09:12:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1616 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 09:12:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.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 09:12:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:12:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:12:47: 1000000 INFO @ Sat, 03 Apr 2021 09:12:54: 2000000 INFO @ Sat, 03 Apr 2021 09:12:59: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:12:59: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:12:59: #1 total tags in treatment: 1074238 INFO @ Sat, 03 Apr 2021 09:12:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:12:59: #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 09:12:59: #1 tags after filtering in treatment: 872976 INFO @ Sat, 03 Apr 2021 09:12:59: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 09:12:59: #1 finished! INFO @ Sat, 03 Apr 2021 09:12:59: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:12:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:12:59: #2 number of paired peaks: 3239 INFO @ Sat, 03 Apr 2021 09:12:59: start model_add_line... INFO @ Sat, 03 Apr 2021 09:12:59: start X-correlation... INFO @ Sat, 03 Apr 2021 09:12:59: end of X-cor INFO @ Sat, 03 Apr 2021 09:12:59: #2 finished! INFO @ Sat, 03 Apr 2021 09:12:59: #2 predicted fragment length is 179 bps INFO @ Sat, 03 Apr 2021 09:12:59: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 03 Apr 2021 09:12:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.10_model.r INFO @ Sat, 03 Apr 2021 09:12:59: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:12:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:13:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.10_summits.bed INFO @ Sat, 03 Apr 2021 09:13:02: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (373 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 09:13:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.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 09:13:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:13:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:13:16: 1000000 INFO @ Sat, 03 Apr 2021 09:13:22: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:13:26: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:13:26: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:13:26: #1 total tags in treatment: 1074238 INFO @ Sat, 03 Apr 2021 09:13:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:13:26: #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 09:13:26: #1 tags after filtering in treatment: 872976 INFO @ Sat, 03 Apr 2021 09:13:26: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 09:13:26: #1 finished! INFO @ Sat, 03 Apr 2021 09:13:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:13:26: #2 number of paired peaks: 3239 INFO @ Sat, 03 Apr 2021 09:13:26: start model_add_line... INFO @ Sat, 03 Apr 2021 09:13:26: start X-correlation... INFO @ Sat, 03 Apr 2021 09:13:26: end of X-cor INFO @ Sat, 03 Apr 2021 09:13:26: #2 finished! INFO @ Sat, 03 Apr 2021 09:13:26: #2 predicted fragment length is 179 bps INFO @ Sat, 03 Apr 2021 09:13:26: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 03 Apr 2021 09:13:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.20_model.r INFO @ Sat, 03 Apr 2021 09:13:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:13:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:13:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806729/SRX7806729.20_summits.bed INFO @ Sat, 03 Apr 2021 09:13:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (75 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。