Job ID = 14170119 SRX = SRX8556376 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28509514 spots for SRR12024932/SRR12024932.sra Written 28509514 spots for SRR12024932/SRR12024932.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170719 ("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: 00:31:08 28509514 reads; of these: 28509514 (100.00%) were paired; of these: 24315931 (85.29%) aligned concordantly 0 times 3125403 (10.96%) aligned concordantly exactly 1 time 1068180 (3.75%) aligned concordantly >1 times ---- 24315931 pairs aligned concordantly 0 times; of these: 512706 (2.11%) aligned discordantly 1 time ---- 23803225 pairs aligned 0 times concordantly or discordantly; of these: 47606450 mates make up the pairs; of these: 46015801 (96.66%) aligned 0 times 924953 (1.94%) aligned exactly 1 time 665696 (1.40%) aligned >1 times 19.30% overall alignment rate Time searching: 00:31:08 Overall time: 00:31:08 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_sort_core] merging from 8 files... [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] 3405178 / 4636171 = 0.7345 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 06:11:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.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 06:11:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:11:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:11:53: 1000000 INFO @ Sat, 11 Dec 2021 06:12:02: 2000000 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 06:12:12: 3000000 INFO @ Sat, 11 Dec 2021 06:12:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.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 06:12:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:12:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:12:22: 1000000 INFO @ Sat, 11 Dec 2021 06:12:22: 4000000 INFO @ Sat, 11 Dec 2021 06:12:24: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:12:24: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:12:24: #1 total tags in treatment: 1056223 INFO @ Sat, 11 Dec 2021 06:12:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:12:24: #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 06:12:24: #1 tags after filtering in treatment: 862442 INFO @ Sat, 11 Dec 2021 06:12:24: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 06:12:24: #1 finished! INFO @ Sat, 11 Dec 2021 06:12:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:12:24: #2 number of paired peaks: 3059 INFO @ Sat, 11 Dec 2021 06:12:24: start model_add_line... INFO @ Sat, 11 Dec 2021 06:12:24: start X-correlation... INFO @ Sat, 11 Dec 2021 06:12:24: end of X-cor INFO @ Sat, 11 Dec 2021 06:12:24: #2 finished! INFO @ Sat, 11 Dec 2021 06:12:24: #2 predicted fragment length is 172 bps INFO @ Sat, 11 Dec 2021 06:12:24: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 11 Dec 2021 06:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.05_model.r WARNING @ Sat, 11 Dec 2021 06:12:24: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:12:24: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 11 Dec 2021 06:12:24: #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 06:12:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:12:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.05_summits.bed INFO @ Sat, 11 Dec 2021 06:12:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2250 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:12:30: 2000000 INFO @ Sat, 11 Dec 2021 06:12:38: 3000000 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 06:12:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.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 06:12:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:12:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:12:47: 4000000 INFO @ Sat, 11 Dec 2021 06:12:48: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:12:48: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:12:48: #1 total tags in treatment: 1056223 INFO @ Sat, 11 Dec 2021 06:12:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:12:48: #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 06:12:48: #1 tags after filtering in treatment: 862442 INFO @ Sat, 11 Dec 2021 06:12:48: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 06:12:48: #1 finished! INFO @ Sat, 11 Dec 2021 06:12:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:12:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:12:48: #2 number of paired peaks: 3059 INFO @ Sat, 11 Dec 2021 06:12:48: start model_add_line... INFO @ Sat, 11 Dec 2021 06:12:48: start X-correlation... INFO @ Sat, 11 Dec 2021 06:12:48: end of X-cor INFO @ Sat, 11 Dec 2021 06:12:48: #2 finished! INFO @ Sat, 11 Dec 2021 06:12:48: #2 predicted fragment length is 172 bps INFO @ Sat, 11 Dec 2021 06:12:48: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 11 Dec 2021 06:12:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.10_model.r WARNING @ Sat, 11 Dec 2021 06:12:48: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:12:48: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 11 Dec 2021 06:12:48: #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 06:12:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:12:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:12:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:12:51: 1000000 INFO @ Sat, 11 Dec 2021 06:12:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:12:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:12:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.10_summits.bed INFO @ Sat, 11 Dec 2021 06:12:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1178 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:12:59: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:13:07: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:13:16: 4000000 INFO @ Sat, 11 Dec 2021 06:13:17: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:13:17: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:13:17: #1 total tags in treatment: 1056223 INFO @ Sat, 11 Dec 2021 06:13:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:13:17: #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 06:13:17: #1 tags after filtering in treatment: 862442 INFO @ Sat, 11 Dec 2021 06:13:17: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 06:13:17: #1 finished! INFO @ Sat, 11 Dec 2021 06:13:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:13:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:13:17: #2 number of paired peaks: 3059 INFO @ Sat, 11 Dec 2021 06:13:17: start model_add_line... INFO @ Sat, 11 Dec 2021 06:13:17: start X-correlation... INFO @ Sat, 11 Dec 2021 06:13:17: end of X-cor INFO @ Sat, 11 Dec 2021 06:13:17: #2 finished! INFO @ Sat, 11 Dec 2021 06:13:17: #2 predicted fragment length is 172 bps INFO @ Sat, 11 Dec 2021 06:13:17: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 11 Dec 2021 06:13:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.20_model.r WARNING @ Sat, 11 Dec 2021 06:13:17: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:13:17: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 11 Dec 2021 06:13:17: #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 06:13:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:13:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:13:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:13:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:13:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:13:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556376/SRX8556376.20_summits.bed INFO @ Sat, 11 Dec 2021 06:13:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (627 records, 4 fields): 8 millis CompletedMACS2peakCalling