Job ID = 14171176 SRX = SRX9555327 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6317404 spots for SRR13110813/SRR13110813.sra Written 6317404 spots for SRR13110813/SRR13110813.sra Read 6129086 spots for SRR13110814/SRR13110814.sra Written 6129086 spots for SRR13110814/SRR13110814.sra Read 6303878 spots for SRR13110815/SRR13110815.sra Written 6303878 spots for SRR13110815/SRR13110815.sra Read 6205060 spots for SRR13110816/SRR13110816.sra Written 6205060 spots for SRR13110816/SRR13110816.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171654 ("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: 00:06:07 24955428 reads; of these: 24955428 (100.00%) were paired; of these: 24126061 (96.68%) aligned concordantly 0 times 613463 (2.46%) aligned concordantly exactly 1 time 215904 (0.87%) aligned concordantly >1 times ---- 24126061 pairs aligned concordantly 0 times; of these: 17353 (0.07%) aligned discordantly 1 time ---- 24108708 pairs aligned 0 times concordantly or discordantly; of these: 48217416 mates make up the pairs; of these: 48145075 (99.85%) aligned 0 times 25008 (0.05%) aligned exactly 1 time 47333 (0.10%) aligned >1 times 3.54% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 16547 / 635819 = 0.0260 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 10:31:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.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 10:31:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:31:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:32:02: 1000000 INFO @ Sat, 11 Dec 2021 10:32:07: #1 tag size is determined as 71 bps INFO @ Sat, 11 Dec 2021 10:32:07: #1 tag size = 71 INFO @ Sat, 11 Dec 2021 10:32:07: #1 total tags in treatment: 812990 INFO @ Sat, 11 Dec 2021 10:32:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:32:07: #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 10:32:07: #1 tags after filtering in treatment: 757140 INFO @ Sat, 11 Dec 2021 10:32:07: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 10:32:07: #1 finished! INFO @ Sat, 11 Dec 2021 10:32:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:32:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:32:07: #2 number of paired peaks: 4952 INFO @ Sat, 11 Dec 2021 10:32:07: start model_add_line... INFO @ Sat, 11 Dec 2021 10:32:07: start X-correlation... INFO @ Sat, 11 Dec 2021 10:32:07: end of X-cor INFO @ Sat, 11 Dec 2021 10:32:07: #2 finished! INFO @ Sat, 11 Dec 2021 10:32:07: #2 predicted fragment length is 123 bps INFO @ Sat, 11 Dec 2021 10:32:07: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 11 Dec 2021 10:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.05_model.r WARNING @ Sat, 11 Dec 2021 10:32:07: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:32:07: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 11 Dec 2021 10:32:07: #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 10:32:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:32:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:32:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:32:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:32:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:32:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.05_summits.bed INFO @ Sat, 11 Dec 2021 10:32:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1714 records, 4 fields): 4 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 10:32:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.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 10:32:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:32:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:32:31: 1000000 INFO @ Sat, 11 Dec 2021 10:32:36: #1 tag size is determined as 71 bps INFO @ Sat, 11 Dec 2021 10:32:36: #1 tag size = 71 INFO @ Sat, 11 Dec 2021 10:32:36: #1 total tags in treatment: 812990 INFO @ Sat, 11 Dec 2021 10:32:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:32:36: #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 10:32:36: #1 tags after filtering in treatment: 757140 INFO @ Sat, 11 Dec 2021 10:32:36: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 10:32:36: #1 finished! INFO @ Sat, 11 Dec 2021 10:32:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:32:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:32:36: #2 number of paired peaks: 4952 INFO @ Sat, 11 Dec 2021 10:32:36: start model_add_line... INFO @ Sat, 11 Dec 2021 10:32:36: start X-correlation... INFO @ Sat, 11 Dec 2021 10:32:36: end of X-cor INFO @ Sat, 11 Dec 2021 10:32:36: #2 finished! INFO @ Sat, 11 Dec 2021 10:32:36: #2 predicted fragment length is 123 bps INFO @ Sat, 11 Dec 2021 10:32:36: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 11 Dec 2021 10:32:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.10_model.r WARNING @ Sat, 11 Dec 2021 10:32:36: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:32:36: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 11 Dec 2021 10:32:36: #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 10:32:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:32:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:32:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:32:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:32:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:32:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.10_summits.bed INFO @ Sat, 11 Dec 2021 10:32:39: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (391 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 10:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.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 10:32:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:32:55: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 10:33:02: 1000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 10:33:07: #1 tag size is determined as 71 bps INFO @ Sat, 11 Dec 2021 10:33:07: #1 tag size = 71 INFO @ Sat, 11 Dec 2021 10:33:07: #1 total tags in treatment: 812990 INFO @ Sat, 11 Dec 2021 10:33:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:33:07: #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 10:33:07: #1 tags after filtering in treatment: 757140 INFO @ Sat, 11 Dec 2021 10:33:07: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 10:33:07: #1 finished! INFO @ Sat, 11 Dec 2021 10:33:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:33:07: #2 number of paired peaks: 4952 INFO @ Sat, 11 Dec 2021 10:33:07: start model_add_line... INFO @ Sat, 11 Dec 2021 10:33:07: start X-correlation... INFO @ Sat, 11 Dec 2021 10:33:07: end of X-cor INFO @ Sat, 11 Dec 2021 10:33:07: #2 finished! INFO @ Sat, 11 Dec 2021 10:33:07: #2 predicted fragment length is 123 bps INFO @ Sat, 11 Dec 2021 10:33:07: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 11 Dec 2021 10:33:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.20_model.r WARNING @ Sat, 11 Dec 2021 10:33:07: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:33:07: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 11 Dec 2021 10:33:07: #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 10:33:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:33:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:33:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:33:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:33:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:33:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555327/SRX9555327.20_summits.bed INFO @ Sat, 11 Dec 2021 10:33:10: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 1 millis CompletedMACS2peakCalling