Job ID = 16439297 SRX = SRX15206464 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: 00:04:04 7450557 reads; of these: 7450557 (100.00%) were unpaired; of these: 140566 (1.89%) aligned 0 times 2531927 (33.98%) aligned exactly 1 time 4778064 (64.13%) aligned >1 times 98.11% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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] 1078437 / 7309991 = 0.1475 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:58:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.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 @ Tue, 02 Aug 2022 14:58:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:58:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:58:17: 1000000 INFO @ Tue, 02 Aug 2022 14:58:23: 2000000 INFO @ Tue, 02 Aug 2022 14:58:29: 3000000 INFO @ Tue, 02 Aug 2022 14:58:36: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.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 @ Tue, 02 Aug 2022 14:58:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:58:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:58:44: 5000000 INFO @ Tue, 02 Aug 2022 14:58:47: 1000000 INFO @ Tue, 02 Aug 2022 14:58:52: 6000000 INFO @ Tue, 02 Aug 2022 14:58:54: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:58:54: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:58:54: #1 total tags in treatment: 6231554 INFO @ Tue, 02 Aug 2022 14:58:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:58:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:58:55: 2000000 INFO @ Tue, 02 Aug 2022 14:58:55: #1 tags after filtering in treatment: 6231473 INFO @ Tue, 02 Aug 2022 14:58:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:58:55: #1 finished! INFO @ Tue, 02 Aug 2022 14:58:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:58:56: #2 number of paired peaks: 6756 INFO @ Tue, 02 Aug 2022 14:58:56: start model_add_line... INFO @ Tue, 02 Aug 2022 14:58:56: start X-correlation... INFO @ Tue, 02 Aug 2022 14:58:56: end of X-cor INFO @ Tue, 02 Aug 2022 14:58:56: #2 finished! INFO @ Tue, 02 Aug 2022 14:58:56: #2 predicted fragment length is 109 bps INFO @ Tue, 02 Aug 2022 14:58:56: #2 alternative fragment length(s) may be 4,109 bps INFO @ Tue, 02 Aug 2022 14:58:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.05_model.r WARNING @ Tue, 02 Aug 2022 14:58:56: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:58:56: #2 You may need to consider one of the other alternative d(s): 4,109 WARNING @ Tue, 02 Aug 2022 14:58:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:58:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:58:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:59:02: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:59:09: 4000000 INFO @ Tue, 02 Aug 2022 14:59:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.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 @ Tue, 02 Aug 2022 14:59:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:59:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:59:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:59:18: 5000000 INFO @ Tue, 02 Aug 2022 14:59:18: 1000000 INFO @ Tue, 02 Aug 2022 14:59:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:59:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:59:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.05_summits.bed INFO @ Tue, 02 Aug 2022 14:59:20: Done! pass1 - making usageList (923 chroms): 2 millis pass2 - checking and writing primary data (3583 records, 4 fields): 121 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:59:25: 2000000 INFO @ Tue, 02 Aug 2022 14:59:26: 6000000 INFO @ Tue, 02 Aug 2022 14:59:27: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:59:27: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:59:27: #1 total tags in treatment: 6231554 INFO @ Tue, 02 Aug 2022 14:59:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:59:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:59:28: #1 tags after filtering in treatment: 6231473 INFO @ Tue, 02 Aug 2022 14:59:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:59:28: #1 finished! INFO @ Tue, 02 Aug 2022 14:59:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:59:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:59:29: #2 number of paired peaks: 6756 INFO @ Tue, 02 Aug 2022 14:59:29: start model_add_line... INFO @ Tue, 02 Aug 2022 14:59:29: start X-correlation... INFO @ Tue, 02 Aug 2022 14:59:29: end of X-cor INFO @ Tue, 02 Aug 2022 14:59:29: #2 finished! INFO @ Tue, 02 Aug 2022 14:59:29: #2 predicted fragment length is 109 bps INFO @ Tue, 02 Aug 2022 14:59:29: #2 alternative fragment length(s) may be 4,109 bps INFO @ Tue, 02 Aug 2022 14:59:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.10_model.r WARNING @ Tue, 02 Aug 2022 14:59:29: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:59:29: #2 You may need to consider one of the other alternative d(s): 4,109 WARNING @ Tue, 02 Aug 2022 14:59:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:59:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:59:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:59:32: 3000000 INFO @ Tue, 02 Aug 2022 14:59:38: 4000000 INFO @ Tue, 02 Aug 2022 14:59:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:59:46: 5000000 INFO @ Tue, 02 Aug 2022 14:59:53: 6000000 INFO @ Tue, 02 Aug 2022 14:59:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:59:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:59:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.10_summits.bed INFO @ Tue, 02 Aug 2022 14:59:53: Done! pass1 - making usageList (726 chroms): 2 millis pass2 - checking and writing primary data (2021 records, 4 fields): 100 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:59:54: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:59:54: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:59:54: #1 total tags in treatment: 6231554 INFO @ Tue, 02 Aug 2022 14:59:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:59:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:59:55: #1 tags after filtering in treatment: 6231473 INFO @ Tue, 02 Aug 2022 14:59:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:59:55: #1 finished! INFO @ Tue, 02 Aug 2022 14:59:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:59:56: #2 number of paired peaks: 6756 INFO @ Tue, 02 Aug 2022 14:59:56: start model_add_line... INFO @ Tue, 02 Aug 2022 14:59:56: start X-correlation... INFO @ Tue, 02 Aug 2022 14:59:56: end of X-cor INFO @ Tue, 02 Aug 2022 14:59:56: #2 finished! INFO @ Tue, 02 Aug 2022 14:59:56: #2 predicted fragment length is 109 bps INFO @ Tue, 02 Aug 2022 14:59:56: #2 alternative fragment length(s) may be 4,109 bps INFO @ Tue, 02 Aug 2022 14:59:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.20_model.r WARNING @ Tue, 02 Aug 2022 14:59:56: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:59:56: #2 You may need to consider one of the other alternative d(s): 4,109 WARNING @ Tue, 02 Aug 2022 14:59:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:59:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:00:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:00:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:00:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:00:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206464/SRX15206464.20_summits.bed INFO @ Tue, 02 Aug 2022 15:00:18: Done! pass1 - making usageList (512 chroms): 1 millis pass2 - checking and writing primary data (1098 records, 4 fields): 33 millis CompletedMACS2peakCalling