Job ID = 14171181 SRX = SRX9555328 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8549944 spots for SRR13110817/SRR13110817.sra Written 8549944 spots for SRR13110817/SRR13110817.sra Read 8298738 spots for SRR13110818/SRR13110818.sra Written 8298738 spots for SRR13110818/SRR13110818.sra Read 8517671 spots for SRR13110819/SRR13110819.sra Written 8517671 spots for SRR13110819/SRR13110819.sra Read 8319859 spots for SRR13110820/SRR13110820.sra Written 8319859 spots for SRR13110820/SRR13110820.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171664 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:04 33686212 reads; of these: 33686212 (100.00%) were paired; of these: 32784028 (97.32%) aligned concordantly 0 times 652111 (1.94%) aligned concordantly exactly 1 time 250073 (0.74%) aligned concordantly >1 times ---- 32784028 pairs aligned concordantly 0 times; of these: 14064 (0.04%) aligned discordantly 1 time ---- 32769964 pairs aligned 0 times concordantly or discordantly; of these: 65539928 mates make up the pairs; of these: 65442510 (99.85%) aligned 0 times 27482 (0.04%) aligned exactly 1 time 69936 (0.11%) aligned >1 times 2.86% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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] 16920 / 666177 = 0.0254 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 10:34:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.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 10:34:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:34:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:34:31: 1000000 INFO @ Sat, 11 Dec 2021 10:34:38: #1 tag size is determined as 72 bps INFO @ Sat, 11 Dec 2021 10:34:38: #1 tag size = 72 INFO @ Sat, 11 Dec 2021 10:34:38: #1 total tags in treatment: 885378 INFO @ Sat, 11 Dec 2021 10:34:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:34:38: #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 10:34:38: #1 tags after filtering in treatment: 826532 INFO @ Sat, 11 Dec 2021 10:34:38: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 10:34:38: #1 finished! INFO @ Sat, 11 Dec 2021 10:34:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:34:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:34:38: #2 number of paired peaks: 3839 INFO @ Sat, 11 Dec 2021 10:34:38: start model_add_line... INFO @ Sat, 11 Dec 2021 10:34:38: start X-correlation... INFO @ Sat, 11 Dec 2021 10:34:38: end of X-cor INFO @ Sat, 11 Dec 2021 10:34:38: #2 finished! INFO @ Sat, 11 Dec 2021 10:34:38: #2 predicted fragment length is 108 bps INFO @ Sat, 11 Dec 2021 10:34:38: #2 alternative fragment length(s) may be 108 bps INFO @ Sat, 11 Dec 2021 10:34:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.05_model.r WARNING @ Sat, 11 Dec 2021 10:34:38: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:34:38: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Sat, 11 Dec 2021 10:34:38: #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 10:34:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:34:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:34:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:34:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:34:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.05_summits.bed INFO @ Sat, 11 Dec 2021 10:34:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1508 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 10:34:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.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 10:34:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:34:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:35:01: 1000000 INFO @ Sat, 11 Dec 2021 10:35:08: #1 tag size is determined as 72 bps INFO @ Sat, 11 Dec 2021 10:35:08: #1 tag size = 72 INFO @ Sat, 11 Dec 2021 10:35:08: #1 total tags in treatment: 885378 INFO @ Sat, 11 Dec 2021 10:35:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:35:08: #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 10:35:08: #1 tags after filtering in treatment: 826532 INFO @ Sat, 11 Dec 2021 10:35:08: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 10:35:08: #1 finished! INFO @ Sat, 11 Dec 2021 10:35:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:35:08: #2 number of paired peaks: 3839 INFO @ Sat, 11 Dec 2021 10:35:08: start model_add_line... INFO @ Sat, 11 Dec 2021 10:35:08: start X-correlation... INFO @ Sat, 11 Dec 2021 10:35:08: end of X-cor INFO @ Sat, 11 Dec 2021 10:35:08: #2 finished! INFO @ Sat, 11 Dec 2021 10:35:08: #2 predicted fragment length is 108 bps INFO @ Sat, 11 Dec 2021 10:35:08: #2 alternative fragment length(s) may be 108 bps INFO @ Sat, 11 Dec 2021 10:35:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.10_model.r WARNING @ Sat, 11 Dec 2021 10:35:08: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:35:08: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Sat, 11 Dec 2021 10:35:08: #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 10:35:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:35:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:35:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:35:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:35:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:35:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.10_summits.bed INFO @ Sat, 11 Dec 2021 10:35:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (358 records, 4 fields): 12 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 10:35:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.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 10:35:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:35:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:35:29: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 10:35:34: #1 tag size is determined as 72 bps INFO @ Sat, 11 Dec 2021 10:35:34: #1 tag size = 72 INFO @ Sat, 11 Dec 2021 10:35:34: #1 total tags in treatment: 885378 INFO @ Sat, 11 Dec 2021 10:35:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:35:34: #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 10:35:34: #1 tags after filtering in treatment: 826532 INFO @ Sat, 11 Dec 2021 10:35:34: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 10:35:34: #1 finished! INFO @ Sat, 11 Dec 2021 10:35:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:35:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:35:35: #2 number of paired peaks: 3839 INFO @ Sat, 11 Dec 2021 10:35:35: start model_add_line... INFO @ Sat, 11 Dec 2021 10:35:35: start X-correlation... INFO @ Sat, 11 Dec 2021 10:35:35: end of X-cor INFO @ Sat, 11 Dec 2021 10:35:35: #2 finished! INFO @ Sat, 11 Dec 2021 10:35:35: #2 predicted fragment length is 108 bps INFO @ Sat, 11 Dec 2021 10:35:35: #2 alternative fragment length(s) may be 108 bps INFO @ Sat, 11 Dec 2021 10:35:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.20_model.r WARNING @ Sat, 11 Dec 2021 10:35:35: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:35:35: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Sat, 11 Dec 2021 10:35:35: #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 10:35:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:35:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 10:35:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:35:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:35:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:35:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555328/SRX9555328.20_summits.bed INFO @ Sat, 11 Dec 2021 10:35:37: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (120 records, 4 fields): 2 millis CompletedMACS2peakCalling