Job ID = 14171276 SRX = SRX9555340 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2126958 spots for SRR13110865/SRR13110865.sra Written 2126958 spots for SRR13110865/SRR13110865.sra Read 2004799 spots for SRR13110866/SRR13110866.sra Written 2004799 spots for SRR13110866/SRR13110866.sra Read 2025951 spots for SRR13110867/SRR13110867.sra Written 2025951 spots for SRR13110867/SRR13110867.sra Read 1951473 spots for SRR13110868/SRR13110868.sra Written 1951473 spots for SRR13110868/SRR13110868.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171719 ("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: 00:01:29 8109181 reads; of these: 8109181 (100.00%) were paired; of these: 7896573 (97.38%) aligned concordantly 0 times 145948 (1.80%) aligned concordantly exactly 1 time 66660 (0.82%) aligned concordantly >1 times ---- 7896573 pairs aligned concordantly 0 times; of these: 1612 (0.02%) aligned discordantly 1 time ---- 7894961 pairs aligned 0 times concordantly or discordantly; of these: 15789922 mates make up the pairs; of these: 15763320 (99.83%) aligned 0 times 6791 (0.04%) aligned exactly 1 time 19811 (0.13%) aligned >1 times 2.81% overall alignment rate Time searching: 00:01:29 Overall time: 00:01:29 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] 1563 / 63345 = 0.0247 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 10:53:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.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 10:53:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:53:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:53:56: #1 tag size is determined as 65 bps INFO @ Sat, 11 Dec 2021 10:53:56: #1 tag size = 65 INFO @ Sat, 11 Dec 2021 10:53:56: #1 total tags in treatment: 211050 INFO @ Sat, 11 Dec 2021 10:53:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:53:56: #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 10:53:56: #1 tags after filtering in treatment: 204866 INFO @ Sat, 11 Dec 2021 10:53:56: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:53:56: #1 finished! INFO @ Sat, 11 Dec 2021 10:53:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:53:56: #2 number of paired peaks: 900 WARNING @ Sat, 11 Dec 2021 10:53:56: Fewer paired peaks (900) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 900 pairs to build model! INFO @ Sat, 11 Dec 2021 10:53:56: start model_add_line... INFO @ Sat, 11 Dec 2021 10:53:56: start X-correlation... INFO @ Sat, 11 Dec 2021 10:53:56: end of X-cor INFO @ Sat, 11 Dec 2021 10:53:56: #2 finished! INFO @ Sat, 11 Dec 2021 10:53:56: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 10:53:56: #2 alternative fragment length(s) may be 45,508,568 bps INFO @ Sat, 11 Dec 2021 10:53:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.05_model.r WARNING @ Sat, 11 Dec 2021 10:53:56: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:53:56: #2 You may need to consider one of the other alternative d(s): 45,508,568 WARNING @ Sat, 11 Dec 2021 10:53:56: #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 10:53:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:53:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:53:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:53:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:53:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:53:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.05_summits.bed INFO @ Sat, 11 Dec 2021 10:53:57: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (169 records, 4 fields): 6 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 10:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.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 10:54:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:54:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:54:26: #1 tag size is determined as 65 bps INFO @ Sat, 11 Dec 2021 10:54:26: #1 tag size = 65 INFO @ Sat, 11 Dec 2021 10:54:26: #1 total tags in treatment: 211050 INFO @ Sat, 11 Dec 2021 10:54:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:54:26: #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 10:54:26: #1 tags after filtering in treatment: 204866 INFO @ Sat, 11 Dec 2021 10:54:26: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:54:26: #1 finished! INFO @ Sat, 11 Dec 2021 10:54:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:54:26: #2 number of paired peaks: 900 WARNING @ Sat, 11 Dec 2021 10:54:26: Fewer paired peaks (900) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 900 pairs to build model! INFO @ Sat, 11 Dec 2021 10:54:26: start model_add_line... INFO @ Sat, 11 Dec 2021 10:54:26: start X-correlation... INFO @ Sat, 11 Dec 2021 10:54:26: end of X-cor INFO @ Sat, 11 Dec 2021 10:54:26: #2 finished! INFO @ Sat, 11 Dec 2021 10:54:26: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 10:54:26: #2 alternative fragment length(s) may be 45,508,568 bps INFO @ Sat, 11 Dec 2021 10:54:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.10_model.r WARNING @ Sat, 11 Dec 2021 10:54:26: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:54:26: #2 You may need to consider one of the other alternative d(s): 45,508,568 WARNING @ Sat, 11 Dec 2021 10:54:26: #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 10:54:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:54:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:54:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.10_summits.bed INFO @ Sat, 11 Dec 2021 10:54:27: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (76 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 10:54:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.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 10:54:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:54:54: #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 10:54:56: #1 tag size is determined as 65 bps INFO @ Sat, 11 Dec 2021 10:54:56: #1 tag size = 65 INFO @ Sat, 11 Dec 2021 10:54:56: #1 total tags in treatment: 211050 INFO @ Sat, 11 Dec 2021 10:54:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:54:56: #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 10:54:56: #1 tags after filtering in treatment: 204866 INFO @ Sat, 11 Dec 2021 10:54:56: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:54:56: #1 finished! INFO @ Sat, 11 Dec 2021 10:54:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:54:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:54:56: #2 number of paired peaks: 900 WARNING @ Sat, 11 Dec 2021 10:54:56: Fewer paired peaks (900) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 900 pairs to build model! INFO @ Sat, 11 Dec 2021 10:54:56: start model_add_line... INFO @ Sat, 11 Dec 2021 10:54:56: start X-correlation... INFO @ Sat, 11 Dec 2021 10:54:56: end of X-cor INFO @ Sat, 11 Dec 2021 10:54:56: #2 finished! INFO @ Sat, 11 Dec 2021 10:54:56: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 10:54:56: #2 alternative fragment length(s) may be 45,508,568 bps INFO @ Sat, 11 Dec 2021 10:54:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.20_model.r WARNING @ Sat, 11 Dec 2021 10:54:56: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:54:56: #2 You may need to consider one of the other alternative d(s): 45,508,568 WARNING @ Sat, 11 Dec 2021 10:54:56: #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 10:54:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:54:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:54:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:54:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:54:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:54:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555340/SRX9555340.20_summits.bed INFO @ Sat, 11 Dec 2021 10:54:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 1 millis CompletedMACS2peakCalling