Job ID = 14170022 SRX = SRX8556352 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28682179 spots for SRR12024962/SRR12024962.sra Written 28682179 spots for SRR12024962/SRR12024962.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170643 ("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: 00:11:46 28682179 reads; of these: 28682179 (100.00%) were paired; of these: 27534441 (96.00%) aligned concordantly 0 times 737830 (2.57%) aligned concordantly exactly 1 time 409908 (1.43%) aligned concordantly >1 times ---- 27534441 pairs aligned concordantly 0 times; of these: 188352 (0.68%) aligned discordantly 1 time ---- 27346089 pairs aligned 0 times concordantly or discordantly; of these: 54692178 mates make up the pairs; of these: 54416481 (99.50%) aligned 0 times 61689 (0.11%) aligned exactly 1 time 214008 (0.39%) aligned >1 times 5.14% overall alignment rate Time searching: 00:11:46 Overall time: 00:11:46 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] 806052 / 1322365 = 0.6096 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 04:58:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.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 04:58:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:58:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:58:43: 1000000 INFO @ Sat, 11 Dec 2021 04:58:46: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 04:58:46: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 04:58:46: #1 total tags in treatment: 433735 INFO @ Sat, 11 Dec 2021 04:58:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:58:46: #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 04:58:46: #1 tags after filtering in treatment: 406790 INFO @ Sat, 11 Dec 2021 04:58:46: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 04:58:46: #1 finished! INFO @ Sat, 11 Dec 2021 04:58:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:58:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:58:46: #2 number of paired peaks: 2036 INFO @ Sat, 11 Dec 2021 04:58:46: start model_add_line... INFO @ Sat, 11 Dec 2021 04:58:46: start X-correlation... INFO @ Sat, 11 Dec 2021 04:58:46: end of X-cor INFO @ Sat, 11 Dec 2021 04:58:46: #2 finished! INFO @ Sat, 11 Dec 2021 04:58:46: #2 predicted fragment length is 180 bps INFO @ Sat, 11 Dec 2021 04:58:46: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 11 Dec 2021 04:58:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.05_model.r WARNING @ Sat, 11 Dec 2021 04:58:46: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:58:46: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Sat, 11 Dec 2021 04:58:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 04:58:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:58:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:58:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:58:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.05_peaks.xls INFO @ Sat, 11 Dec 2021 04:58:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:58:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.05_summits.bed INFO @ Sat, 11 Dec 2021 04:58:47: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 3 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 04:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.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 04:59:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:59:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:59:13: 1000000 INFO @ Sat, 11 Dec 2021 04:59:16: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 04:59:16: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 04:59:16: #1 total tags in treatment: 433735 INFO @ Sat, 11 Dec 2021 04:59:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:59:16: #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 04:59:16: #1 tags after filtering in treatment: 406790 INFO @ Sat, 11 Dec 2021 04:59:16: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 04:59:16: #1 finished! INFO @ Sat, 11 Dec 2021 04:59:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:59:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:59:16: #2 number of paired peaks: 2036 INFO @ Sat, 11 Dec 2021 04:59:16: start model_add_line... INFO @ Sat, 11 Dec 2021 04:59:16: start X-correlation... INFO @ Sat, 11 Dec 2021 04:59:16: end of X-cor INFO @ Sat, 11 Dec 2021 04:59:16: #2 finished! INFO @ Sat, 11 Dec 2021 04:59:16: #2 predicted fragment length is 180 bps INFO @ Sat, 11 Dec 2021 04:59:16: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 11 Dec 2021 04:59:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.10_model.r WARNING @ Sat, 11 Dec 2021 04:59:16: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:59:16: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Sat, 11 Dec 2021 04:59:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 04:59:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:59:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:59:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.10_peaks.xls INFO @ Sat, 11 Dec 2021 04:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.10_summits.bed INFO @ Sat, 11 Dec 2021 04:59:17: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (178 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 04:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.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 04:59:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:59:35: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 04:59:43: 1000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 04:59:46: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 04:59:46: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 04:59:46: #1 total tags in treatment: 433735 INFO @ Sat, 11 Dec 2021 04:59:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:59:46: #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 04:59:46: #1 tags after filtering in treatment: 406790 INFO @ Sat, 11 Dec 2021 04:59:46: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 04:59:46: #1 finished! INFO @ Sat, 11 Dec 2021 04:59:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:59:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:59:46: #2 number of paired peaks: 2036 INFO @ Sat, 11 Dec 2021 04:59:46: start model_add_line... INFO @ Sat, 11 Dec 2021 04:59:46: start X-correlation... INFO @ Sat, 11 Dec 2021 04:59:46: end of X-cor INFO @ Sat, 11 Dec 2021 04:59:46: #2 finished! INFO @ Sat, 11 Dec 2021 04:59:46: #2 predicted fragment length is 180 bps INFO @ Sat, 11 Dec 2021 04:59:46: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 11 Dec 2021 04:59:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.20_model.r WARNING @ Sat, 11 Dec 2021 04:59:46: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:59:46: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Sat, 11 Dec 2021 04:59:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 04:59:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:59:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:59:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:59:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.20_peaks.xls INFO @ Sat, 11 Dec 2021 04:59:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:59:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556352/SRX8556352.20_summits.bed INFO @ Sat, 11 Dec 2021 04:59:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 1 millis CompletedMACS2peakCalling