Job ID = 14167210 SRX = SRX6407590 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4822856 spots for SRR9645781/SRR9645781.sra Written 4822856 spots for SRR9645781/SRR9645781.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167749 ("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: 00:02:27 4822856 reads; of these: 4822856 (100.00%) were unpaired; of these: 591183 (12.26%) aligned 0 times 3294847 (68.32%) aligned exactly 1 time 936826 (19.42%) aligned >1 times 87.74% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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_rmdupse_core] 297143 / 4231673 = 0.0702 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 @ Fri, 10 Dec 2021 11:07:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.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 @ Fri, 10 Dec 2021 11:07:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:07:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:07:20: 1000000 INFO @ Fri, 10 Dec 2021 11:07:27: 2000000 INFO @ Fri, 10 Dec 2021 11:07:34: 3000000 INFO @ Fri, 10 Dec 2021 11:07:40: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 11:07:40: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 11:07:40: #1 total tags in treatment: 3934530 INFO @ Fri, 10 Dec 2021 11:07:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:07:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:07:40: #1 tags after filtering in treatment: 3934530 INFO @ Fri, 10 Dec 2021 11:07:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:07:40: #1 finished! INFO @ Fri, 10 Dec 2021 11:07:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:07:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:07:40: #2 number of paired peaks: 261 WARNING @ Fri, 10 Dec 2021 11:07:40: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 10 Dec 2021 11:07:40: start model_add_line... INFO @ Fri, 10 Dec 2021 11:07:40: start X-correlation... INFO @ Fri, 10 Dec 2021 11:07:40: end of X-cor INFO @ Fri, 10 Dec 2021 11:07:40: #2 finished! INFO @ Fri, 10 Dec 2021 11:07:40: #2 predicted fragment length is 102 bps INFO @ Fri, 10 Dec 2021 11:07:40: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 10 Dec 2021 11:07:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.05_model.r WARNING @ Fri, 10 Dec 2021 11:07:40: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:07:40: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Fri, 10 Dec 2021 11:07:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:07:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:07:40: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 10 Dec 2021 11:07:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.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 @ Fri, 10 Dec 2021 11:07:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:07:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:07:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:07:51: 1000000 INFO @ Fri, 10 Dec 2021 11:07:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:07:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:07:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.05_summits.bed INFO @ Fri, 10 Dec 2021 11:07:53: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (544 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:07:59: 2000000 INFO @ Fri, 10 Dec 2021 11:08:07: 3000000 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 @ Fri, 10 Dec 2021 11:08:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.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 @ Fri, 10 Dec 2021 11:08:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:08:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:08:14: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 11:08:14: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 11:08:14: #1 total tags in treatment: 3934530 INFO @ Fri, 10 Dec 2021 11:08:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:08:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:08:14: #1 tags after filtering in treatment: 3934530 INFO @ Fri, 10 Dec 2021 11:08:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:08:14: #1 finished! INFO @ Fri, 10 Dec 2021 11:08:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:08:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:08:15: #2 number of paired peaks: 261 WARNING @ Fri, 10 Dec 2021 11:08:15: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 10 Dec 2021 11:08:15: start model_add_line... INFO @ Fri, 10 Dec 2021 11:08:15: start X-correlation... INFO @ Fri, 10 Dec 2021 11:08:15: end of X-cor INFO @ Fri, 10 Dec 2021 11:08:15: #2 finished! INFO @ Fri, 10 Dec 2021 11:08:15: #2 predicted fragment length is 102 bps INFO @ Fri, 10 Dec 2021 11:08:15: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 10 Dec 2021 11:08:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.10_model.r WARNING @ Fri, 10 Dec 2021 11:08:15: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:08:15: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Fri, 10 Dec 2021 11:08:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:08:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:08:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:08:21: 1000000 INFO @ Fri, 10 Dec 2021 11:08:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:08:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:08:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:08:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.10_summits.bed INFO @ Fri, 10 Dec 2021 11:08:28: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (261 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:08:29: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:08:37: 3000000 INFO @ Fri, 10 Dec 2021 11:08:45: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 11:08:45: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 11:08:45: #1 total tags in treatment: 3934530 INFO @ Fri, 10 Dec 2021 11:08:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:08:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:08:45: #1 tags after filtering in treatment: 3934530 INFO @ Fri, 10 Dec 2021 11:08:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:08:45: #1 finished! INFO @ Fri, 10 Dec 2021 11:08:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:08:45: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:08:45: #2 number of paired peaks: 261 WARNING @ Fri, 10 Dec 2021 11:08:45: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 10 Dec 2021 11:08:45: start model_add_line... INFO @ Fri, 10 Dec 2021 11:08:45: start X-correlation... INFO @ Fri, 10 Dec 2021 11:08:45: end of X-cor INFO @ Fri, 10 Dec 2021 11:08:45: #2 finished! INFO @ Fri, 10 Dec 2021 11:08:45: #2 predicted fragment length is 102 bps INFO @ Fri, 10 Dec 2021 11:08:45: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 10 Dec 2021 11:08:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.20_model.r WARNING @ Fri, 10 Dec 2021 11:08:45: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:08:45: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Fri, 10 Dec 2021 11:08:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:08:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:08:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:08:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:08:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:08:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:08:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6407590/SRX6407590.20_summits.bed INFO @ Fri, 10 Dec 2021 11:08:58: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (134 records, 4 fields): 2 millis CompletedMACS2peakCalling