Job ID = 16440848 SRX = SRX15369007 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: 00:10:18 26419843 reads; of these: 26419843 (100.00%) were unpaired; of these: 1215117 (4.60%) aligned 0 times 17697018 (66.98%) aligned exactly 1 time 7507708 (28.42%) aligned >1 times 95.40% overall alignment rate Time searching: 00:10:18 Overall time: 00:10:18 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 12 files... [bam_rmdupse_core] 10916359 / 25204726 = 0.4331 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 18:16:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.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 18:16:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:16:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:16:20: 1000000 INFO @ Tue, 02 Aug 2022 18:16:27: 2000000 INFO @ Tue, 02 Aug 2022 18:16:33: 3000000 INFO @ Tue, 02 Aug 2022 18:16:40: 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 18:16:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.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 18:16:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:16:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:16:46: 5000000 INFO @ Tue, 02 Aug 2022 18:16:50: 1000000 INFO @ Tue, 02 Aug 2022 18:16:53: 6000000 INFO @ Tue, 02 Aug 2022 18:16:56: 2000000 INFO @ Tue, 02 Aug 2022 18:17:00: 7000000 INFO @ Tue, 02 Aug 2022 18:17:03: 3000000 INFO @ Tue, 02 Aug 2022 18:17:07: 8000000 INFO @ Tue, 02 Aug 2022 18:17:10: 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 18:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.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 18:17:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:17:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:17:14: 9000000 INFO @ Tue, 02 Aug 2022 18:17:17: 5000000 INFO @ Tue, 02 Aug 2022 18:17:19: 1000000 INFO @ Tue, 02 Aug 2022 18:17:21: 10000000 INFO @ Tue, 02 Aug 2022 18:17:24: 6000000 INFO @ Tue, 02 Aug 2022 18:17:26: 2000000 INFO @ Tue, 02 Aug 2022 18:17:28: 11000000 INFO @ Tue, 02 Aug 2022 18:17:31: 7000000 INFO @ Tue, 02 Aug 2022 18:17:32: 3000000 INFO @ Tue, 02 Aug 2022 18:17:35: 12000000 INFO @ Tue, 02 Aug 2022 18:17:38: 8000000 INFO @ Tue, 02 Aug 2022 18:17:39: 4000000 INFO @ Tue, 02 Aug 2022 18:17:42: 13000000 INFO @ Tue, 02 Aug 2022 18:17:45: 5000000 INFO @ Tue, 02 Aug 2022 18:17:45: 9000000 INFO @ Tue, 02 Aug 2022 18:17:49: 14000000 INFO @ Tue, 02 Aug 2022 18:17:51: 6000000 INFO @ Tue, 02 Aug 2022 18:17:51: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 18:17:51: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 18:17:51: #1 total tags in treatment: 14288367 INFO @ Tue, 02 Aug 2022 18:17:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:17:51: #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 18:17:52: #1 tags after filtering in treatment: 14288364 INFO @ Tue, 02 Aug 2022 18:17:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 18:17:52: #1 finished! INFO @ Tue, 02 Aug 2022 18:17:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:17:52: 10000000 INFO @ Tue, 02 Aug 2022 18:17:53: #2 number of paired peaks: 1131 INFO @ Tue, 02 Aug 2022 18:17:53: start model_add_line... INFO @ Tue, 02 Aug 2022 18:17:53: start X-correlation... INFO @ Tue, 02 Aug 2022 18:17:53: end of X-cor INFO @ Tue, 02 Aug 2022 18:17:53: #2 finished! INFO @ Tue, 02 Aug 2022 18:17:53: #2 predicted fragment length is 92 bps INFO @ Tue, 02 Aug 2022 18:17:53: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 02 Aug 2022 18:17:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.05_model.r WARNING @ Tue, 02 Aug 2022 18:17:53: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:17:53: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Tue, 02 Aug 2022 18:17:53: #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 18:17:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:17:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:17:58: 7000000 INFO @ Tue, 02 Aug 2022 18:17:59: 11000000 INFO @ Tue, 02 Aug 2022 18:18:04: 8000000 INFO @ Tue, 02 Aug 2022 18:18:07: 12000000 INFO @ Tue, 02 Aug 2022 18:18:10: 9000000 INFO @ Tue, 02 Aug 2022 18:18:14: 13000000 INFO @ Tue, 02 Aug 2022 18:18:16: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:18:21: 14000000 INFO @ Tue, 02 Aug 2022 18:18:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:18:23: 11000000 INFO @ Tue, 02 Aug 2022 18:18:23: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 18:18:23: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 18:18:23: #1 total tags in treatment: 14288367 INFO @ Tue, 02 Aug 2022 18:18:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:18:23: #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 18:18:23: #1 tags after filtering in treatment: 14288364 INFO @ Tue, 02 Aug 2022 18:18:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 18:18:23: #1 finished! INFO @ Tue, 02 Aug 2022 18:18:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:18:24: #2 number of paired peaks: 1131 INFO @ Tue, 02 Aug 2022 18:18:24: start model_add_line... INFO @ Tue, 02 Aug 2022 18:18:24: start X-correlation... INFO @ Tue, 02 Aug 2022 18:18:24: end of X-cor INFO @ Tue, 02 Aug 2022 18:18:24: #2 finished! INFO @ Tue, 02 Aug 2022 18:18:24: #2 predicted fragment length is 92 bps INFO @ Tue, 02 Aug 2022 18:18:24: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 02 Aug 2022 18:18:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.10_model.r WARNING @ Tue, 02 Aug 2022 18:18:24: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:18:24: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Tue, 02 Aug 2022 18:18:24: #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 18:18:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:18:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:18:29: 12000000 INFO @ Tue, 02 Aug 2022 18:18:35: 13000000 INFO @ Tue, 02 Aug 2022 18:18:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:18:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:18:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.05_summits.bed INFO @ Tue, 02 Aug 2022 18:18:38: Done! pass1 - making usageList (732 chroms): 3 millis pass2 - checking and writing primary data (9365 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:18:41: 14000000 INFO @ Tue, 02 Aug 2022 18:18:43: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 18:18:43: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 18:18:43: #1 total tags in treatment: 14288367 INFO @ Tue, 02 Aug 2022 18:18:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:18:43: #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 18:18:44: #1 tags after filtering in treatment: 14288364 INFO @ Tue, 02 Aug 2022 18:18:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 18:18:44: #1 finished! INFO @ Tue, 02 Aug 2022 18:18:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:18:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:18:45: #2 number of paired peaks: 1131 INFO @ Tue, 02 Aug 2022 18:18:45: start model_add_line... INFO @ Tue, 02 Aug 2022 18:18:45: start X-correlation... INFO @ Tue, 02 Aug 2022 18:18:45: end of X-cor INFO @ Tue, 02 Aug 2022 18:18:45: #2 finished! INFO @ Tue, 02 Aug 2022 18:18:45: #2 predicted fragment length is 92 bps INFO @ Tue, 02 Aug 2022 18:18:45: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 02 Aug 2022 18:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.20_model.r WARNING @ Tue, 02 Aug 2022 18:18:45: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:18:45: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Tue, 02 Aug 2022 18:18:45: #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 18:18:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:18:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:18:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:19:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:19:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:19:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.10_summits.bed INFO @ Tue, 02 Aug 2022 18:19:06: Done! pass1 - making usageList (585 chroms): 2 millis pass2 - checking and writing primary data (5394 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:19:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:19:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:19:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:19:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369007/SRX15369007.20_summits.bed INFO @ Tue, 02 Aug 2022 18:19:27: Done! pass1 - making usageList (507 chroms): 2 millis pass2 - checking and writing primary data (2652 records, 4 fields): 31 millis CompletedMACS2peakCalling