Job ID = 16436376 SRX = SRX15369014 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: 00:10:04 20502489 reads; of these: 20502489 (100.00%) were unpaired; of these: 1024087 (4.99%) aligned 0 times 12128012 (59.15%) aligned exactly 1 time 7350390 (35.85%) aligned >1 times 95.01% overall alignment rate Time searching: 00:10:04 Overall time: 00:10:04 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_sort_core] merging from 8 files... [bam_rmdupse_core] 11246079 / 19478402 = 0.5774 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 11:42:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.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 11:42:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:42:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:42:53: 1000000 INFO @ Tue, 02 Aug 2022 11:43:00: 2000000 INFO @ Tue, 02 Aug 2022 11:43:06: 3000000 INFO @ Tue, 02 Aug 2022 11:43:13: 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 11:43:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.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 11:43:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:43:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:43:20: 5000000 INFO @ Tue, 02 Aug 2022 11:43:22: 1000000 INFO @ Tue, 02 Aug 2022 11:43:28: 6000000 INFO @ Tue, 02 Aug 2022 11:43:29: 2000000 INFO @ Tue, 02 Aug 2022 11:43:35: 7000000 INFO @ Tue, 02 Aug 2022 11:43:36: 3000000 INFO @ Tue, 02 Aug 2022 11:43:43: 8000000 INFO @ Tue, 02 Aug 2022 11:43:43: 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 11:43:44: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:43:44: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:43:44: #1 total tags in treatment: 8232323 INFO @ Tue, 02 Aug 2022 11:43:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:43:44: #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 11:43:45: #1 tags after filtering in treatment: 8232282 INFO @ Tue, 02 Aug 2022 11:43:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:43:45: #1 finished! INFO @ Tue, 02 Aug 2022 11:43:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:43:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:43:45: #2 number of paired peaks: 1236 INFO @ Tue, 02 Aug 2022 11:43:45: start model_add_line... INFO @ Tue, 02 Aug 2022 11:43:46: start X-correlation... INFO @ Tue, 02 Aug 2022 11:43:46: end of X-cor INFO @ Tue, 02 Aug 2022 11:43:46: #2 finished! INFO @ Tue, 02 Aug 2022 11:43:46: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 11:43:46: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 02 Aug 2022 11:43:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.05_model.r WARNING @ Tue, 02 Aug 2022 11:43:46: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:43:46: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 02 Aug 2022 11:43:46: #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 11:43:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:43:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:43:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.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 11:43:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:43:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:43:50: 5000000 INFO @ Tue, 02 Aug 2022 11:43:54: 1000000 INFO @ Tue, 02 Aug 2022 11:43:57: 6000000 INFO @ Tue, 02 Aug 2022 11:44:01: 2000000 INFO @ Tue, 02 Aug 2022 11:44:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:44:04: 7000000 INFO @ Tue, 02 Aug 2022 11:44:08: 3000000 INFO @ Tue, 02 Aug 2022 11:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.05_summits.bed INFO @ Tue, 02 Aug 2022 11:44:11: Done! INFO @ Tue, 02 Aug 2022 11:44:11: 8000000 pass1 - making usageList (709 chroms): 2 millis pass2 - checking and writing primary data (2881 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:44:13: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:44:13: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:44:13: #1 total tags in treatment: 8232323 INFO @ Tue, 02 Aug 2022 11:44:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:44:13: #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 11:44:13: #1 tags after filtering in treatment: 8232282 INFO @ Tue, 02 Aug 2022 11:44:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:44:13: #1 finished! INFO @ Tue, 02 Aug 2022 11:44:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:44:14: #2 number of paired peaks: 1236 INFO @ Tue, 02 Aug 2022 11:44:14: start model_add_line... INFO @ Tue, 02 Aug 2022 11:44:14: start X-correlation... INFO @ Tue, 02 Aug 2022 11:44:14: end of X-cor INFO @ Tue, 02 Aug 2022 11:44:14: #2 finished! INFO @ Tue, 02 Aug 2022 11:44:14: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 11:44:14: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 02 Aug 2022 11:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.10_model.r WARNING @ Tue, 02 Aug 2022 11:44:14: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:44:14: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 02 Aug 2022 11:44:14: #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 11:44:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:44:14: 4000000 INFO @ Tue, 02 Aug 2022 11:44:20: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:44:26: 6000000 INFO @ Tue, 02 Aug 2022 11:44:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:44:33: 7000000 INFO @ Tue, 02 Aug 2022 11:44:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:44:38: 8000000 INFO @ Tue, 02 Aug 2022 11:44:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:44:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.10_summits.bed INFO @ Tue, 02 Aug 2022 11:44:39: Done! pass1 - making usageList (615 chroms): 1 millis pass2 - checking and writing primary data (1820 records, 4 fields): 136 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:44:40: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:44:40: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:44:40: #1 total tags in treatment: 8232323 INFO @ Tue, 02 Aug 2022 11:44:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:44:40: #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 11:44:40: #1 tags after filtering in treatment: 8232282 INFO @ Tue, 02 Aug 2022 11:44:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:44:40: #1 finished! INFO @ Tue, 02 Aug 2022 11:44:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:44:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:44:41: #2 number of paired peaks: 1236 INFO @ Tue, 02 Aug 2022 11:44:41: start model_add_line... INFO @ Tue, 02 Aug 2022 11:44:41: start X-correlation... INFO @ Tue, 02 Aug 2022 11:44:41: end of X-cor INFO @ Tue, 02 Aug 2022 11:44:41: #2 finished! INFO @ Tue, 02 Aug 2022 11:44:41: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 11:44:41: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 02 Aug 2022 11:44:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.20_model.r WARNING @ Tue, 02 Aug 2022 11:44:41: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:44:41: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 02 Aug 2022 11:44:41: #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 11:44:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:44:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:44:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:45:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:45:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:45:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369014/SRX15369014.20_summits.bed INFO @ Tue, 02 Aug 2022 11:45:06: Done! pass1 - making usageList (498 chroms): 1 millis pass2 - checking and writing primary data (1378 records, 4 fields): 46 millis CompletedMACS2peakCalling