Job ID = 14171398 SRX = SRX9555269 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1927459 spots for SRR13110647/SRR13110647.sra Written 1927459 spots for SRR13110647/SRR13110647.sra Read 1929923 spots for SRR13110648/SRR13110648.sra Written 1929923 spots for SRR13110648/SRR13110648.sra Read 1965073 spots for SRR13110649/SRR13110649.sra Written 1965073 spots for SRR13110649/SRR13110649.sra Read 1953838 spots for SRR13110650/SRR13110650.sra Written 1953838 spots for SRR13110650/SRR13110650.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171859 ("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: 00:01:15 7776293 reads; of these: 7776293 (100.00%) were paired; of these: 7468400 (96.04%) aligned concordantly 0 times 221070 (2.84%) aligned concordantly exactly 1 time 86823 (1.12%) aligned concordantly >1 times ---- 7468400 pairs aligned concordantly 0 times; of these: 1887 (0.03%) aligned discordantly 1 time ---- 7466513 pairs aligned 0 times concordantly or discordantly; of these: 14933026 mates make up the pairs; of these: 14882669 (99.66%) aligned 0 times 18486 (0.12%) aligned exactly 1 time 31871 (0.21%) aligned >1 times 4.31% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 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] 6827 / 309508 = 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 11:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.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 11:34:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:34:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:35:00: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:35:00: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:35:00: #1 total tags in treatment: 301097 INFO @ Sat, 11 Dec 2021 11:35:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:35:00: #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 11:35:00: #1 tags after filtering in treatment: 297080 INFO @ Sat, 11 Dec 2021 11:35:00: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:35:00: #1 finished! INFO @ Sat, 11 Dec 2021 11:35:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:35:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:35:00: #2 number of paired peaks: 747 WARNING @ Sat, 11 Dec 2021 11:35:00: Fewer paired peaks (747) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 747 pairs to build model! INFO @ Sat, 11 Dec 2021 11:35:00: start model_add_line... INFO @ Sat, 11 Dec 2021 11:35:00: start X-correlation... INFO @ Sat, 11 Dec 2021 11:35:00: end of X-cor INFO @ Sat, 11 Dec 2021 11:35:00: #2 finished! INFO @ Sat, 11 Dec 2021 11:35:00: #2 predicted fragment length is 68 bps INFO @ Sat, 11 Dec 2021 11:35:00: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 11 Dec 2021 11:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.05_model.r WARNING @ Sat, 11 Dec 2021 11:35:00: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:35:00: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 11 Dec 2021 11:35:00: #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 11:35:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:35:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:35:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:35:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:35:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.05_summits.bed INFO @ Sat, 11 Dec 2021 11:35:01: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 9 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 11:35:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.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 11:35:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:35:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:35:30: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:35:30: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:35:30: #1 total tags in treatment: 301097 INFO @ Sat, 11 Dec 2021 11:35:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:35:30: #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 11:35:30: #1 tags after filtering in treatment: 297080 INFO @ Sat, 11 Dec 2021 11:35:30: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:35:30: #1 finished! INFO @ Sat, 11 Dec 2021 11:35:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:35:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:35:30: #2 number of paired peaks: 747 WARNING @ Sat, 11 Dec 2021 11:35:30: Fewer paired peaks (747) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 747 pairs to build model! INFO @ Sat, 11 Dec 2021 11:35:30: start model_add_line... INFO @ Sat, 11 Dec 2021 11:35:30: start X-correlation... INFO @ Sat, 11 Dec 2021 11:35:30: end of X-cor INFO @ Sat, 11 Dec 2021 11:35:30: #2 finished! INFO @ Sat, 11 Dec 2021 11:35:30: #2 predicted fragment length is 68 bps INFO @ Sat, 11 Dec 2021 11:35:30: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 11 Dec 2021 11:35:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.10_model.r WARNING @ Sat, 11 Dec 2021 11:35:30: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:35:30: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 11 Dec 2021 11:35:30: #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 11:35:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:35:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:35:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:35:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:35:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:35:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.10_summits.bed INFO @ Sat, 11 Dec 2021 11:35:31: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (43 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 11:35:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.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 11:35:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:35:57: #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 11:36:00: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:36:00: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:36:00: #1 total tags in treatment: 301097 INFO @ Sat, 11 Dec 2021 11:36:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:36:00: #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 11:36:00: #1 tags after filtering in treatment: 297080 INFO @ Sat, 11 Dec 2021 11:36:00: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:36:00: #1 finished! INFO @ Sat, 11 Dec 2021 11:36:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:36:00: #2 number of paired peaks: 747 WARNING @ Sat, 11 Dec 2021 11:36:00: Fewer paired peaks (747) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 747 pairs to build model! INFO @ Sat, 11 Dec 2021 11:36:00: start model_add_line... INFO @ Sat, 11 Dec 2021 11:36:00: start X-correlation... INFO @ Sat, 11 Dec 2021 11:36:00: end of X-cor INFO @ Sat, 11 Dec 2021 11:36:00: #2 finished! INFO @ Sat, 11 Dec 2021 11:36:00: #2 predicted fragment length is 68 bps INFO @ Sat, 11 Dec 2021 11:36:00: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 11 Dec 2021 11:36:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.20_model.r WARNING @ Sat, 11 Dec 2021 11:36:00: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:36:00: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 11 Dec 2021 11:36:00: #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 11:36:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:36:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:36:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:36:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:36:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:36:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555269/SRX9555269.20_summits.bed INFO @ Sat, 11 Dec 2021 11:36:01: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (33 records, 4 fields): 1 millis CompletedMACS2peakCalling