Job ID = 14172254 SRX = SRX9281754 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5405833 spots for SRR12813495/SRR12813495.sra Written 5405833 spots for SRR12813495/SRR12813495.sra Read 5410969 spots for SRR12813496/SRR12813496.sra Written 5410969 spots for SRR12813496/SRR12813496.sra Read 5542192 spots for SRR12813497/SRR12813497.sra Written 5542192 spots for SRR12813497/SRR12813497.sra Read 5207068 spots for SRR12813498/SRR12813498.sra Written 5207068 spots for SRR12813498/SRR12813498.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172729 ("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: 00:06:15 21566062 reads; of these: 21566062 (100.00%) were paired; of these: 17551614 (81.39%) aligned concordantly 0 times 3625761 (16.81%) aligned concordantly exactly 1 time 388687 (1.80%) aligned concordantly >1 times ---- 17551614 pairs aligned concordantly 0 times; of these: 28455 (0.16%) aligned discordantly 1 time ---- 17523159 pairs aligned 0 times concordantly or discordantly; of these: 35046318 mates make up the pairs; of these: 34363021 (98.05%) aligned 0 times 385750 (1.10%) aligned exactly 1 time 297547 (0.85%) aligned >1 times 20.33% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 765588 / 4023137 = 0.1903 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 15:04:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.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 15:04:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:04:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:04:52: 1000000 INFO @ Sat, 11 Dec 2021 15:04:58: 2000000 INFO @ Sat, 11 Dec 2021 15:05:04: 3000000 INFO @ Sat, 11 Dec 2021 15:05:10: 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 15:05:16: 5000000 INFO @ Sat, 11 Dec 2021 15:05:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.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 15:05:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:05:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:05:23: 1000000 INFO @ Sat, 11 Dec 2021 15:05:23: 6000000 INFO @ Sat, 11 Dec 2021 15:05:29: 2000000 INFO @ Sat, 11 Dec 2021 15:05:29: 7000000 INFO @ Sat, 11 Dec 2021 15:05:31: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:05:31: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:05:31: #1 total tags in treatment: 3249094 INFO @ Sat, 11 Dec 2021 15:05:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:05:31: #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 15:05:31: #1 tags after filtering in treatment: 1992916 INFO @ Sat, 11 Dec 2021 15:05:31: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 11 Dec 2021 15:05:31: #1 finished! INFO @ Sat, 11 Dec 2021 15:05:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:05:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:05:31: #2 number of paired peaks: 11312 INFO @ Sat, 11 Dec 2021 15:05:31: start model_add_line... INFO @ Sat, 11 Dec 2021 15:05:31: start X-correlation... INFO @ Sat, 11 Dec 2021 15:05:31: end of X-cor INFO @ Sat, 11 Dec 2021 15:05:31: #2 finished! INFO @ Sat, 11 Dec 2021 15:05:31: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 15:05:31: #2 alternative fragment length(s) may be 149,305 bps INFO @ Sat, 11 Dec 2021 15:05:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.05_model.r INFO @ Sat, 11 Dec 2021 15:05:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:05:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:05:35: 3000000 INFO @ Sat, 11 Dec 2021 15:05:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:05:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:05:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:05:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.05_summits.bed INFO @ Sat, 11 Dec 2021 15:05:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8448 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:05:41: 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 15:05:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.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 15:05:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:05:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:05:47: 5000000 INFO @ Sat, 11 Dec 2021 15:05:53: 1000000 INFO @ Sat, 11 Dec 2021 15:05:54: 6000000 INFO @ Sat, 11 Dec 2021 15:06:00: 2000000 INFO @ Sat, 11 Dec 2021 15:06:00: 7000000 INFO @ Sat, 11 Dec 2021 15:06:01: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:06:01: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:06:01: #1 total tags in treatment: 3249094 INFO @ Sat, 11 Dec 2021 15:06:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:06:01: #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 15:06:01: #1 tags after filtering in treatment: 1992916 INFO @ Sat, 11 Dec 2021 15:06:01: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 11 Dec 2021 15:06:01: #1 finished! INFO @ Sat, 11 Dec 2021 15:06:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:06:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:06:02: #2 number of paired peaks: 11312 INFO @ Sat, 11 Dec 2021 15:06:02: start model_add_line... INFO @ Sat, 11 Dec 2021 15:06:02: start X-correlation... INFO @ Sat, 11 Dec 2021 15:06:02: end of X-cor INFO @ Sat, 11 Dec 2021 15:06:02: #2 finished! INFO @ Sat, 11 Dec 2021 15:06:02: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 15:06:02: #2 alternative fragment length(s) may be 149,305 bps INFO @ Sat, 11 Dec 2021 15:06:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.10_model.r INFO @ Sat, 11 Dec 2021 15:06:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:06:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:06:06: 3000000 INFO @ Sat, 11 Dec 2021 15:06:06: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:06:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:06:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:06:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.10_summits.bed INFO @ Sat, 11 Dec 2021 15:06:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6648 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:06:12: 4000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:06:18: 5000000 INFO @ Sat, 11 Dec 2021 15:06:24: 6000000 INFO @ Sat, 11 Dec 2021 15:06:31: 7000000 INFO @ Sat, 11 Dec 2021 15:06:32: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:06:32: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:06:32: #1 total tags in treatment: 3249094 INFO @ Sat, 11 Dec 2021 15:06:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:06:32: #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 15:06:32: #1 tags after filtering in treatment: 1992916 INFO @ Sat, 11 Dec 2021 15:06:32: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 11 Dec 2021 15:06:32: #1 finished! INFO @ Sat, 11 Dec 2021 15:06:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:06:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:06:32: #2 number of paired peaks: 11312 INFO @ Sat, 11 Dec 2021 15:06:32: start model_add_line... INFO @ Sat, 11 Dec 2021 15:06:32: start X-correlation... INFO @ Sat, 11 Dec 2021 15:06:32: end of X-cor INFO @ Sat, 11 Dec 2021 15:06:32: #2 finished! INFO @ Sat, 11 Dec 2021 15:06:32: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 15:06:32: #2 alternative fragment length(s) may be 149,305 bps INFO @ Sat, 11 Dec 2021 15:06:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.20_model.r INFO @ Sat, 11 Dec 2021 15:06:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:06:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:06:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:06:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:06:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:06:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281754/SRX9281754.20_summits.bed INFO @ Sat, 11 Dec 2021 15:06:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3235 records, 4 fields): 5 millis CompletedMACS2peakCalling