Job ID = 14171132 SRX = SRX9555314 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1822350 spots for SRR13110443/SRR13110443.sra Written 1822350 spots for SRR13110443/SRR13110443.sra Read 1794984 spots for SRR13110444/SRR13110444.sra Written 1794984 spots for SRR13110444/SRR13110444.sra Read 1822782 spots for SRR13110445/SRR13110445.sra Written 1822782 spots for SRR13110445/SRR13110445.sra Read 1806420 spots for SRR13110446/SRR13110446.sra Written 1806420 spots for SRR13110446/SRR13110446.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171576 ("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: 00:01:20 7246536 reads; of these: 7246536 (100.00%) were paired; of these: 6850759 (94.54%) aligned concordantly 0 times 279243 (3.85%) aligned concordantly exactly 1 time 116534 (1.61%) aligned concordantly >1 times ---- 6850759 pairs aligned concordantly 0 times; of these: 683 (0.01%) aligned discordantly 1 time ---- 6850076 pairs aligned 0 times concordantly or discordantly; of these: 13700152 mates make up the pairs; of these: 13659298 (99.70%) aligned 0 times 16579 (0.12%) aligned exactly 1 time 24275 (0.18%) aligned >1 times 5.75% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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] 8762 / 396172 = 0.0221 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 09:45:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.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 09:45:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:45:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:45:30: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:45:30: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:45:30: #1 total tags in treatment: 387023 INFO @ Sat, 11 Dec 2021 09:45:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:45:30: #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 09:45:30: #1 tags after filtering in treatment: 381000 INFO @ Sat, 11 Dec 2021 09:45:30: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 09:45:30: #1 finished! INFO @ Sat, 11 Dec 2021 09:45:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:45:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:45:30: #2 number of paired peaks: 713 WARNING @ Sat, 11 Dec 2021 09:45:30: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sat, 11 Dec 2021 09:45:30: start model_add_line... INFO @ Sat, 11 Dec 2021 09:45:30: start X-correlation... INFO @ Sat, 11 Dec 2021 09:45:30: end of X-cor INFO @ Sat, 11 Dec 2021 09:45:30: #2 finished! INFO @ Sat, 11 Dec 2021 09:45:30: #2 predicted fragment length is 77 bps INFO @ Sat, 11 Dec 2021 09:45:30: #2 alternative fragment length(s) may be 77,581 bps INFO @ Sat, 11 Dec 2021 09:45:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.05_model.r WARNING @ Sat, 11 Dec 2021 09:45:31: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:45:31: #2 You may need to consider one of the other alternative d(s): 77,581 WARNING @ Sat, 11 Dec 2021 09:45:31: #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 09:45:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:45:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:45:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:45:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:45:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.05_summits.bed INFO @ Sat, 11 Dec 2021 09:45:32: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (65 records, 4 fields): 1 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 09:45:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.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 09:45:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:45:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:46:02: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:46:02: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:46:02: #1 total tags in treatment: 387023 INFO @ Sat, 11 Dec 2021 09:46:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:46:02: #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 09:46:02: #1 tags after filtering in treatment: 381000 INFO @ Sat, 11 Dec 2021 09:46:02: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 09:46:02: #1 finished! INFO @ Sat, 11 Dec 2021 09:46:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:46:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:46:02: #2 number of paired peaks: 713 WARNING @ Sat, 11 Dec 2021 09:46:02: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sat, 11 Dec 2021 09:46:02: start model_add_line... INFO @ Sat, 11 Dec 2021 09:46:02: start X-correlation... INFO @ Sat, 11 Dec 2021 09:46:02: end of X-cor INFO @ Sat, 11 Dec 2021 09:46:02: #2 finished! INFO @ Sat, 11 Dec 2021 09:46:02: #2 predicted fragment length is 77 bps INFO @ Sat, 11 Dec 2021 09:46:02: #2 alternative fragment length(s) may be 77,581 bps INFO @ Sat, 11 Dec 2021 09:46:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.10_model.r WARNING @ Sat, 11 Dec 2021 09:46:02: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:46:02: #2 You may need to consider one of the other alternative d(s): 77,581 WARNING @ Sat, 11 Dec 2021 09:46:02: #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 09:46:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:46:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:46:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:46:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:46:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:46:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.10_summits.bed INFO @ Sat, 11 Dec 2021 09:46:03: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (46 records, 4 fields): 1 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 09:46:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.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 09:46:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:46:26: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:46:32: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:46:32: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:46:32: #1 total tags in treatment: 387023 INFO @ Sat, 11 Dec 2021 09:46:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:46:32: #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 09:46:32: #1 tags after filtering in treatment: 381000 INFO @ Sat, 11 Dec 2021 09:46:32: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 09:46:32: #1 finished! INFO @ Sat, 11 Dec 2021 09:46:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:46:32: #2 number of paired peaks: 713 WARNING @ Sat, 11 Dec 2021 09:46:32: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sat, 11 Dec 2021 09:46:32: start model_add_line... INFO @ Sat, 11 Dec 2021 09:46:32: start X-correlation... INFO @ Sat, 11 Dec 2021 09:46:32: end of X-cor INFO @ Sat, 11 Dec 2021 09:46:32: #2 finished! INFO @ Sat, 11 Dec 2021 09:46:32: #2 predicted fragment length is 77 bps INFO @ Sat, 11 Dec 2021 09:46:32: #2 alternative fragment length(s) may be 77,581 bps INFO @ Sat, 11 Dec 2021 09:46:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.20_model.r WARNING @ Sat, 11 Dec 2021 09:46:32: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:46:32: #2 You may need to consider one of the other alternative d(s): 77,581 WARNING @ Sat, 11 Dec 2021 09:46:32: #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 09:46:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:46:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:46:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:46:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:46:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:46:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555314/SRX9555314.20_summits.bed INFO @ Sat, 11 Dec 2021 09:46:33: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 1 millis CompletedMACS2peakCalling