Job ID = 14171410 SRX = SRX9555272 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9015899 spots for SRR13110659/SRR13110659.sra Written 9015899 spots for SRR13110659/SRR13110659.sra Read 8742534 spots for SRR13110660/SRR13110660.sra Written 8742534 spots for SRR13110660/SRR13110660.sra Read 9220361 spots for SRR13110661/SRR13110661.sra Written 9220361 spots for SRR13110661/SRR13110661.sra Read 8922841 spots for SRR13110662/SRR13110662.sra Written 8922841 spots for SRR13110662/SRR13110662.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171941 ("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: 00:08:45 35901635 reads; of these: 35901635 (100.00%) were paired; of these: 34788837 (96.90%) aligned concordantly 0 times 892609 (2.49%) aligned concordantly exactly 1 time 220189 (0.61%) aligned concordantly >1 times ---- 34788837 pairs aligned concordantly 0 times; of these: 3135 (0.01%) aligned discordantly 1 time ---- 34785702 pairs aligned 0 times concordantly or discordantly; of these: 69571404 mates make up the pairs; of these: 68879834 (99.01%) aligned 0 times 153956 (0.22%) aligned exactly 1 time 537614 (0.77%) aligned >1 times 4.07% overall alignment rate Time searching: 00:08:45 Overall time: 00:08:45 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] 56719 / 1113510 = 0.0509 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 11:49:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.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 11:49:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:49:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:49:08: 1000000 INFO @ Sat, 11 Dec 2021 11:49:14: 2000000 INFO @ Sat, 11 Dec 2021 11:49:18: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:49:18: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:49:18: #1 total tags in treatment: 1056243 INFO @ Sat, 11 Dec 2021 11:49:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:49:18: #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 11:49:18: #1 tags after filtering in treatment: 1026718 INFO @ Sat, 11 Dec 2021 11:49:18: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:49:18: #1 finished! INFO @ Sat, 11 Dec 2021 11:49:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:49:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:49:18: #2 number of paired peaks: 3554 INFO @ Sat, 11 Dec 2021 11:49:18: start model_add_line... INFO @ Sat, 11 Dec 2021 11:49:18: start X-correlation... INFO @ Sat, 11 Dec 2021 11:49:18: end of X-cor INFO @ Sat, 11 Dec 2021 11:49:18: #2 finished! INFO @ Sat, 11 Dec 2021 11:49:18: #2 predicted fragment length is 148 bps INFO @ Sat, 11 Dec 2021 11:49:18: #2 alternative fragment length(s) may be 4,148,183,228 bps INFO @ Sat, 11 Dec 2021 11:49:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.05_model.r INFO @ Sat, 11 Dec 2021 11:49:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:49:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:49:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:49:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:49:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:49:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.05_summits.bed INFO @ Sat, 11 Dec 2021 11:49:22: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (181 records, 4 fields): 7 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 11:49:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.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 11:49:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:49:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:49:38: 1000000 INFO @ Sat, 11 Dec 2021 11:49:44: 2000000 INFO @ Sat, 11 Dec 2021 11:49:49: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:49:49: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:49:49: #1 total tags in treatment: 1056243 INFO @ Sat, 11 Dec 2021 11:49:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:49:49: #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 11:49:49: #1 tags after filtering in treatment: 1026718 INFO @ Sat, 11 Dec 2021 11:49:49: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:49:49: #1 finished! INFO @ Sat, 11 Dec 2021 11:49:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:49:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:49:49: #2 number of paired peaks: 3554 INFO @ Sat, 11 Dec 2021 11:49:49: start model_add_line... INFO @ Sat, 11 Dec 2021 11:49:49: start X-correlation... INFO @ Sat, 11 Dec 2021 11:49:49: end of X-cor INFO @ Sat, 11 Dec 2021 11:49:49: #2 finished! INFO @ Sat, 11 Dec 2021 11:49:49: #2 predicted fragment length is 148 bps INFO @ Sat, 11 Dec 2021 11:49:49: #2 alternative fragment length(s) may be 4,148,183,228 bps INFO @ Sat, 11 Dec 2021 11:49:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.10_model.r INFO @ Sat, 11 Dec 2021 11:49:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:49:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:49:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:49:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:49:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:49:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.10_summits.bed INFO @ Sat, 11 Dec 2021 11:49:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 2 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 11:50:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.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 11:50:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:50:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:50:08: 1000000 INFO @ Sat, 11 Dec 2021 11:50:14: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:50:19: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:50:19: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:50:19: #1 total tags in treatment: 1056243 INFO @ Sat, 11 Dec 2021 11:50:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:50:19: #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 11:50:19: #1 tags after filtering in treatment: 1026718 INFO @ Sat, 11 Dec 2021 11:50:19: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:50:19: #1 finished! INFO @ Sat, 11 Dec 2021 11:50:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:50:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:50:19: #2 number of paired peaks: 3554 INFO @ Sat, 11 Dec 2021 11:50:19: start model_add_line... INFO @ Sat, 11 Dec 2021 11:50:19: start X-correlation... INFO @ Sat, 11 Dec 2021 11:50:19: end of X-cor INFO @ Sat, 11 Dec 2021 11:50:19: #2 finished! INFO @ Sat, 11 Dec 2021 11:50:19: #2 predicted fragment length is 148 bps INFO @ Sat, 11 Dec 2021 11:50:19: #2 alternative fragment length(s) may be 4,148,183,228 bps INFO @ Sat, 11 Dec 2021 11:50:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.20_model.r INFO @ Sat, 11 Dec 2021 11:50:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:50:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:50:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:50:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:50:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:50:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555272/SRX9555272.20_summits.bed INFO @ Sat, 11 Dec 2021 11:50:23: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (27 records, 4 fields): 1 millis CompletedMACS2peakCalling