Job ID = 16438074 SRX = SRX14148453 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: 00:05:31 16622084 reads; of these: 16622084 (100.00%) were unpaired; of these: 1956141 (11.77%) aligned 0 times 10589612 (63.71%) aligned exactly 1 time 4076331 (24.52%) aligned >1 times 88.23% overall alignment rate Time searching: 00:05:31 Overall time: 00:05:31 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1647050 / 14665943 = 0.1123 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 13:38:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.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 13:38:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:38:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:38:47: 1000000 INFO @ Tue, 02 Aug 2022 13:38:55: 2000000 INFO @ Tue, 02 Aug 2022 13:39:02: 3000000 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 13:39:09: 4000000 INFO @ Tue, 02 Aug 2022 13:39:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.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 13:39:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:39:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:39:16: 1000000 INFO @ Tue, 02 Aug 2022 13:39:16: 5000000 INFO @ Tue, 02 Aug 2022 13:39:23: 2000000 INFO @ Tue, 02 Aug 2022 13:39:23: 6000000 INFO @ Tue, 02 Aug 2022 13:39:29: 3000000 INFO @ Tue, 02 Aug 2022 13:39:31: 7000000 INFO @ Tue, 02 Aug 2022 13:39:36: 4000000 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 13:39:38: 8000000 INFO @ Tue, 02 Aug 2022 13:39:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.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 13:39:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:39:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:39:43: 5000000 INFO @ Tue, 02 Aug 2022 13:39:45: 9000000 INFO @ Tue, 02 Aug 2022 13:39:46: 1000000 INFO @ Tue, 02 Aug 2022 13:39:49: 6000000 INFO @ Tue, 02 Aug 2022 13:39:52: 10000000 INFO @ Tue, 02 Aug 2022 13:39:53: 2000000 INFO @ Tue, 02 Aug 2022 13:39:56: 7000000 INFO @ Tue, 02 Aug 2022 13:39:58: 11000000 INFO @ Tue, 02 Aug 2022 13:40:00: 3000000 INFO @ Tue, 02 Aug 2022 13:40:03: 8000000 INFO @ Tue, 02 Aug 2022 13:40:06: 12000000 INFO @ Tue, 02 Aug 2022 13:40:07: 4000000 INFO @ Tue, 02 Aug 2022 13:40:09: 9000000 INFO @ Tue, 02 Aug 2022 13:40:12: 13000000 INFO @ Tue, 02 Aug 2022 13:40:13: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:40:13: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:40:13: #1 total tags in treatment: 13018893 INFO @ Tue, 02 Aug 2022 13:40:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:40:13: #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 13:40:13: #1 tags after filtering in treatment: 13018749 INFO @ Tue, 02 Aug 2022 13:40:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:40:13: #1 finished! INFO @ Tue, 02 Aug 2022 13:40:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:40:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:40:14: 5000000 INFO @ Tue, 02 Aug 2022 13:40:14: #2 number of paired peaks: 1182 INFO @ Tue, 02 Aug 2022 13:40:14: start model_add_line... INFO @ Tue, 02 Aug 2022 13:40:14: start X-correlation... INFO @ Tue, 02 Aug 2022 13:40:14: end of X-cor INFO @ Tue, 02 Aug 2022 13:40:14: #2 finished! INFO @ Tue, 02 Aug 2022 13:40:14: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 13:40:14: #2 alternative fragment length(s) may be 3,77 bps INFO @ Tue, 02 Aug 2022 13:40:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.05_model.r WARNING @ Tue, 02 Aug 2022 13:40:14: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:40:14: #2 You may need to consider one of the other alternative d(s): 3,77 WARNING @ Tue, 02 Aug 2022 13:40:14: #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 13:40:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:40:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:40:16: 10000000 INFO @ Tue, 02 Aug 2022 13:40:21: 6000000 INFO @ Tue, 02 Aug 2022 13:40:22: 11000000 INFO @ Tue, 02 Aug 2022 13:40:27: 7000000 INFO @ Tue, 02 Aug 2022 13:40:29: 12000000 INFO @ Tue, 02 Aug 2022 13:40:34: 8000000 INFO @ Tue, 02 Aug 2022 13:40:35: 13000000 INFO @ Tue, 02 Aug 2022 13:40:36: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:40:36: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:40:36: #1 total tags in treatment: 13018893 INFO @ Tue, 02 Aug 2022 13:40:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:40:36: #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 13:40:36: #1 tags after filtering in treatment: 13018749 INFO @ Tue, 02 Aug 2022 13:40:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:40:36: #1 finished! INFO @ Tue, 02 Aug 2022 13:40:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:40:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:40:37: #2 number of paired peaks: 1182 INFO @ Tue, 02 Aug 2022 13:40:37: start model_add_line... INFO @ Tue, 02 Aug 2022 13:40:37: start X-correlation... INFO @ Tue, 02 Aug 2022 13:40:37: end of X-cor INFO @ Tue, 02 Aug 2022 13:40:37: #2 finished! INFO @ Tue, 02 Aug 2022 13:40:37: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 13:40:37: #2 alternative fragment length(s) may be 3,77 bps INFO @ Tue, 02 Aug 2022 13:40:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.10_model.r WARNING @ Tue, 02 Aug 2022 13:40:37: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:40:37: #2 You may need to consider one of the other alternative d(s): 3,77 WARNING @ Tue, 02 Aug 2022 13:40:37: #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 13:40:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:40:37: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:40:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:40:40: 9000000 INFO @ Tue, 02 Aug 2022 13:40:46: 10000000 INFO @ Tue, 02 Aug 2022 13:40:52: 11000000 INFO @ Tue, 02 Aug 2022 13:40:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:40:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:40:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.05_summits.bed INFO @ Tue, 02 Aug 2022 13:40:53: Done! pass1 - making usageList (541 chroms): 1 millis pass2 - checking and writing primary data (2205 records, 4 fields): 103 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:40:58: 12000000 INFO @ Tue, 02 Aug 2022 13:41:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:41:04: 13000000 INFO @ Tue, 02 Aug 2022 13:41:04: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:41:04: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:41:04: #1 total tags in treatment: 13018893 INFO @ Tue, 02 Aug 2022 13:41:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:41:04: #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 13:41:05: #1 tags after filtering in treatment: 13018749 INFO @ Tue, 02 Aug 2022 13:41:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:41:05: #1 finished! INFO @ Tue, 02 Aug 2022 13:41:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:41:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:41:06: #2 number of paired peaks: 1182 INFO @ Tue, 02 Aug 2022 13:41:06: start model_add_line... INFO @ Tue, 02 Aug 2022 13:41:06: start X-correlation... INFO @ Tue, 02 Aug 2022 13:41:06: end of X-cor INFO @ Tue, 02 Aug 2022 13:41:06: #2 finished! INFO @ Tue, 02 Aug 2022 13:41:06: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 13:41:06: #2 alternative fragment length(s) may be 3,77 bps INFO @ Tue, 02 Aug 2022 13:41:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.20_model.r WARNING @ Tue, 02 Aug 2022 13:41:06: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:41:06: #2 You may need to consider one of the other alternative d(s): 3,77 WARNING @ Tue, 02 Aug 2022 13:41:06: #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 13:41:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:41:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:41:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.10_summits.bed INFO @ Tue, 02 Aug 2022 13:41:16: Done! pass1 - making usageList (378 chroms): 1 millis pass2 - checking and writing primary data (1080 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:41:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:41:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:41:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:41:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX14148453/SRX14148453.20_summits.bed INFO @ Tue, 02 Aug 2022 13:41:45: Done! pass1 - making usageList (218 chroms): 1 millis pass2 - checking and writing primary data (504 records, 4 fields): 32 millis CompletedMACS2peakCalling