Job ID = 14171408 SRX = SRX9555270 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1995693 spots for SRR13110651/SRR13110651.sra Written 1995693 spots for SRR13110651/SRR13110651.sra Read 2007430 spots for SRR13110652/SRR13110652.sra Written 2007430 spots for SRR13110652/SRR13110652.sra Read 2038155 spots for SRR13110653/SRR13110653.sra Written 2038155 spots for SRR13110653/SRR13110653.sra Read 2029620 spots for SRR13110654/SRR13110654.sra Written 2029620 spots for SRR13110654/SRR13110654.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171874 ("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: 00:01:11 8070898 reads; of these: 8070898 (100.00%) were paired; of these: 7808146 (96.74%) aligned concordantly 0 times 185885 (2.30%) aligned concordantly exactly 1 time 76867 (0.95%) aligned concordantly >1 times ---- 7808146 pairs aligned concordantly 0 times; of these: 2142 (0.03%) aligned discordantly 1 time ---- 7806004 pairs aligned 0 times concordantly or discordantly; of these: 15612008 mates make up the pairs; of these: 15560564 (99.67%) aligned 0 times 17539 (0.11%) aligned exactly 1 time 33905 (0.22%) aligned >1 times 3.60% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 5659 / 264658 = 0.0214 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 11:37:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.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 11:37:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:37:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:37:06: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 11:37:06: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 11:37:06: #1 total tags in treatment: 257130 INFO @ Sat, 11 Dec 2021 11:37:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:37:06: #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 11:37:06: #1 tags after filtering in treatment: 253480 INFO @ Sat, 11 Dec 2021 11:37:06: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:37:06: #1 finished! INFO @ Sat, 11 Dec 2021 11:37:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:37:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:37:07: #2 number of paired peaks: 1154 INFO @ Sat, 11 Dec 2021 11:37:07: start model_add_line... INFO @ Sat, 11 Dec 2021 11:37:07: start X-correlation... INFO @ Sat, 11 Dec 2021 11:37:07: end of X-cor INFO @ Sat, 11 Dec 2021 11:37:07: #2 finished! INFO @ Sat, 11 Dec 2021 11:37:07: #2 predicted fragment length is 174 bps INFO @ Sat, 11 Dec 2021 11:37:07: #2 alternative fragment length(s) may be 84,174 bps INFO @ Sat, 11 Dec 2021 11:37:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.05_model.r INFO @ Sat, 11 Dec 2021 11:37:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:37:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:37:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:37:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:37:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:37:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.05_summits.bed INFO @ Sat, 11 Dec 2021 11:37:08: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (61 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 11:37:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.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 11:37:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:37:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:37:36: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 11:37:36: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 11:37:36: #1 total tags in treatment: 257130 INFO @ Sat, 11 Dec 2021 11:37:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:37:36: #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 11:37:36: #1 tags after filtering in treatment: 253480 INFO @ Sat, 11 Dec 2021 11:37:36: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:37:36: #1 finished! INFO @ Sat, 11 Dec 2021 11:37:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:37:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:37:36: #2 number of paired peaks: 1154 INFO @ Sat, 11 Dec 2021 11:37:36: start model_add_line... INFO @ Sat, 11 Dec 2021 11:37:36: start X-correlation... INFO @ Sat, 11 Dec 2021 11:37:36: end of X-cor INFO @ Sat, 11 Dec 2021 11:37:36: #2 finished! INFO @ Sat, 11 Dec 2021 11:37:36: #2 predicted fragment length is 174 bps INFO @ Sat, 11 Dec 2021 11:37:36: #2 alternative fragment length(s) may be 84,174 bps INFO @ Sat, 11 Dec 2021 11:37:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.10_model.r INFO @ Sat, 11 Dec 2021 11:37:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:37:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:37:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:37:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:37:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:37:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.10_summits.bed INFO @ Sat, 11 Dec 2021 11:37:37: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (41 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 11:38:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.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 11:38:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:38:03: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:38:06: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 11:38:06: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 11:38:06: #1 total tags in treatment: 257130 INFO @ Sat, 11 Dec 2021 11:38:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:38:06: #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 11:38:06: #1 tags after filtering in treatment: 253480 INFO @ Sat, 11 Dec 2021 11:38:06: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:38:06: #1 finished! INFO @ Sat, 11 Dec 2021 11:38:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:38:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:38:06: #2 number of paired peaks: 1154 INFO @ Sat, 11 Dec 2021 11:38:06: start model_add_line... INFO @ Sat, 11 Dec 2021 11:38:06: start X-correlation... INFO @ Sat, 11 Dec 2021 11:38:06: end of X-cor INFO @ Sat, 11 Dec 2021 11:38:06: #2 finished! INFO @ Sat, 11 Dec 2021 11:38:06: #2 predicted fragment length is 174 bps INFO @ Sat, 11 Dec 2021 11:38:06: #2 alternative fragment length(s) may be 84,174 bps INFO @ Sat, 11 Dec 2021 11:38:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.20_model.r INFO @ Sat, 11 Dec 2021 11:38:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:38:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:38:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:38:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:38:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:38:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555270/SRX9555270.20_summits.bed INFO @ Sat, 11 Dec 2021 11:38:07: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (28 records, 4 fields): 2 millis CompletedMACS2peakCalling