Job ID = 14167812 SRX = SRX8688909 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:21 7722577 reads; of these: 7722577 (100.00%) were unpaired; of these: 328001 (4.25%) aligned 0 times 5368891 (69.52%) aligned exactly 1 time 2025685 (26.23%) aligned >1 times 95.75% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 595528 / 7394576 = 0.0805 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 13:35:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.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 13:35:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:35:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:35:22: 1000000 INFO @ Fri, 10 Dec 2021 13:35:28: 2000000 INFO @ Fri, 10 Dec 2021 13:35:33: 3000000 INFO @ Fri, 10 Dec 2021 13:35:39: 4000000 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 13:35:44: 5000000 INFO @ Fri, 10 Dec 2021 13:35:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.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 13:35:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:35:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:35:50: 6000000 INFO @ Fri, 10 Dec 2021 13:35:52: 1000000 INFO @ Fri, 10 Dec 2021 13:35:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:35:55: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:35:55: #1 total tags in treatment: 6799048 INFO @ Fri, 10 Dec 2021 13:35:55: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:35:55: #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 13:35:56: #1 tags after filtering in treatment: 6798880 INFO @ Fri, 10 Dec 2021 13:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:35:56: #1 finished! INFO @ Fri, 10 Dec 2021 13:35:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:35:56: #2 number of paired peaks: 934 WARNING @ Fri, 10 Dec 2021 13:35:56: Fewer paired peaks (934) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 934 pairs to build model! INFO @ Fri, 10 Dec 2021 13:35:56: start model_add_line... INFO @ Fri, 10 Dec 2021 13:35:56: start X-correlation... INFO @ Fri, 10 Dec 2021 13:35:56: end of X-cor INFO @ Fri, 10 Dec 2021 13:35:56: #2 finished! INFO @ Fri, 10 Dec 2021 13:35:56: #2 predicted fragment length is 53 bps INFO @ Fri, 10 Dec 2021 13:35:56: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 10 Dec 2021 13:35:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.05_model.r WARNING @ Fri, 10 Dec 2021 13:35:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:35:56: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 10 Dec 2021 13:35:56: #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 13:35:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:35:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:35:58: 2000000 INFO @ Fri, 10 Dec 2021 13:36:04: 3000000 INFO @ Fri, 10 Dec 2021 13:36:10: 4000000 INFO @ Fri, 10 Dec 2021 13:36:12: #3 Call peaks for each chromosome... 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 13:36:15: 5000000 INFO @ Fri, 10 Dec 2021 13:36:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.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 13:36:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:36:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:36:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.05_summits.bed INFO @ Fri, 10 Dec 2021 13:36:20: Done! pass1 - making usageList (597 chroms): 1 millis pass2 - checking and writing primary data (2366 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:36:21: 6000000 INFO @ Fri, 10 Dec 2021 13:36:22: 1000000 INFO @ Fri, 10 Dec 2021 13:36:26: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:36:26: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:36:26: #1 total tags in treatment: 6799048 INFO @ Fri, 10 Dec 2021 13:36:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:36:26: #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 13:36:27: #1 tags after filtering in treatment: 6798880 INFO @ Fri, 10 Dec 2021 13:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:36:27: #1 finished! INFO @ Fri, 10 Dec 2021 13:36:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:36:27: #2 number of paired peaks: 934 WARNING @ Fri, 10 Dec 2021 13:36:27: Fewer paired peaks (934) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 934 pairs to build model! INFO @ Fri, 10 Dec 2021 13:36:27: start model_add_line... INFO @ Fri, 10 Dec 2021 13:36:27: start X-correlation... INFO @ Fri, 10 Dec 2021 13:36:27: end of X-cor INFO @ Fri, 10 Dec 2021 13:36:27: #2 finished! INFO @ Fri, 10 Dec 2021 13:36:27: #2 predicted fragment length is 53 bps INFO @ Fri, 10 Dec 2021 13:36:27: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 10 Dec 2021 13:36:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.10_model.r WARNING @ Fri, 10 Dec 2021 13:36:27: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:36:27: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 10 Dec 2021 13:36:27: #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 13:36:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:36:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:36:28: 2000000 INFO @ Fri, 10 Dec 2021 13:36:34: 3000000 INFO @ Fri, 10 Dec 2021 13:36:39: 4000000 INFO @ Fri, 10 Dec 2021 13:36:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:36:45: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:36:50: 6000000 INFO @ Fri, 10 Dec 2021 13:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:36:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.10_summits.bed INFO @ Fri, 10 Dec 2021 13:36:50: Done! pass1 - making usageList (468 chroms): 1 millis pass2 - checking and writing primary data (1215 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:36:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:36:55: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:36:55: #1 total tags in treatment: 6799048 INFO @ Fri, 10 Dec 2021 13:36:55: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:36:55: #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 13:36:55: #1 tags after filtering in treatment: 6798880 INFO @ Fri, 10 Dec 2021 13:36:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:36:55: #1 finished! INFO @ Fri, 10 Dec 2021 13:36:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:36:56: #2 number of paired peaks: 934 WARNING @ Fri, 10 Dec 2021 13:36:56: Fewer paired peaks (934) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 934 pairs to build model! INFO @ Fri, 10 Dec 2021 13:36:56: start model_add_line... INFO @ Fri, 10 Dec 2021 13:36:56: start X-correlation... INFO @ Fri, 10 Dec 2021 13:36:56: end of X-cor INFO @ Fri, 10 Dec 2021 13:36:56: #2 finished! INFO @ Fri, 10 Dec 2021 13:36:56: #2 predicted fragment length is 53 bps INFO @ Fri, 10 Dec 2021 13:36:56: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 10 Dec 2021 13:36:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.20_model.r WARNING @ Fri, 10 Dec 2021 13:36:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:36:56: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 10 Dec 2021 13:36:56: #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 13:36:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:36:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:37:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688909/SRX8688909.20_summits.bed INFO @ Fri, 10 Dec 2021 13:37:20: Done! pass1 - making usageList (180 chroms): 1 millis pass2 - checking and writing primary data (298 records, 4 fields): 7 millis CompletedMACS2peakCalling