Job ID = 6626959 SRX = SRX7262567 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: 00:16:15 103639389 reads; of these: 103639389 (100.00%) were unpaired; of these: 93404090 (90.12%) aligned 0 times 7649661 (7.38%) aligned exactly 1 time 2585638 (2.49%) aligned >1 times 9.88% overall alignment rate Time searching: 00:16:15 Overall time: 00:16:15 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] 1328781 / 10235299 = 0.1298 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 09:20:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.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, 14 Jul 2020 09:20:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:20:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:20:16: 1000000 INFO @ Tue, 14 Jul 2020 09:20:21: 2000000 INFO @ Tue, 14 Jul 2020 09:20:27: 3000000 INFO @ Tue, 14 Jul 2020 09:20:32: 4000000 INFO @ Tue, 14 Jul 2020 09:20:38: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 09:20:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.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, 14 Jul 2020 09:20:40: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:20:40: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:20:44: 6000000 INFO @ Tue, 14 Jul 2020 09:20:47: 1000000 INFO @ Tue, 14 Jul 2020 09:20:50: 7000000 INFO @ Tue, 14 Jul 2020 09:20:54: 2000000 INFO @ Tue, 14 Jul 2020 09:20:56: 8000000 INFO @ Tue, 14 Jul 2020 09:21:01: 3000000 INFO @ Tue, 14 Jul 2020 09:21:02: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:21:02: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:21:02: #1 total tags in treatment: 8906518 INFO @ Tue, 14 Jul 2020 09:21:02: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:21:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:21:02: #1 tags after filtering in treatment: 8906352 INFO @ Tue, 14 Jul 2020 09:21:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:21:02: #1 finished! INFO @ Tue, 14 Jul 2020 09:21:02: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:21:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:21:03: #2 number of paired peaks: 1730 INFO @ Tue, 14 Jul 2020 09:21:03: start model_add_line... INFO @ Tue, 14 Jul 2020 09:21:03: start X-correlation... INFO @ Tue, 14 Jul 2020 09:21:03: end of X-cor INFO @ Tue, 14 Jul 2020 09:21:03: #2 finished! INFO @ Tue, 14 Jul 2020 09:21:03: #2 predicted fragment length is 77 bps INFO @ Tue, 14 Jul 2020 09:21:03: #2 alternative fragment length(s) may be 3,77,582 bps INFO @ Tue, 14 Jul 2020 09:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.05_model.r WARNING @ Tue, 14 Jul 2020 09:21:03: #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, 14 Jul 2020 09:21:03: #2 You may need to consider one of the other alternative d(s): 3,77,582 WARNING @ Tue, 14 Jul 2020 09:21:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:21:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:21:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:21:07: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 09:21:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.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, 14 Jul 2020 09:21:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:21:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:21:14: 5000000 INFO @ Tue, 14 Jul 2020 09:21:17: 1000000 INFO @ Tue, 14 Jul 2020 09:21:21: 6000000 INFO @ Tue, 14 Jul 2020 09:21:21: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:21:23: 2000000 INFO @ Tue, 14 Jul 2020 09:21:28: 7000000 INFO @ Tue, 14 Jul 2020 09:21:29: 3000000 INFO @ Tue, 14 Jul 2020 09:21:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:21:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:21:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.05_summits.bed INFO @ Tue, 14 Jul 2020 09:21:31: Done! pass1 - making usageList (515 chroms): 1 millis pass2 - checking and writing primary data (2086 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:21:35: 4000000 INFO @ Tue, 14 Jul 2020 09:21:35: 8000000 INFO @ Tue, 14 Jul 2020 09:21:41: 5000000 INFO @ Tue, 14 Jul 2020 09:21:42: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:21:42: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:21:42: #1 total tags in treatment: 8906518 INFO @ Tue, 14 Jul 2020 09:21:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:21:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:21:42: #1 tags after filtering in treatment: 8906352 INFO @ Tue, 14 Jul 2020 09:21:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:21:42: #1 finished! INFO @ Tue, 14 Jul 2020 09:21:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:21:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:21:43: #2 number of paired peaks: 1730 INFO @ Tue, 14 Jul 2020 09:21:43: start model_add_line... INFO @ Tue, 14 Jul 2020 09:21:43: start X-correlation... INFO @ Tue, 14 Jul 2020 09:21:43: end of X-cor INFO @ Tue, 14 Jul 2020 09:21:43: #2 finished! INFO @ Tue, 14 Jul 2020 09:21:43: #2 predicted fragment length is 77 bps INFO @ Tue, 14 Jul 2020 09:21:43: #2 alternative fragment length(s) may be 3,77,582 bps INFO @ Tue, 14 Jul 2020 09:21:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.10_model.r WARNING @ Tue, 14 Jul 2020 09:21:43: #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, 14 Jul 2020 09:21:43: #2 You may need to consider one of the other alternative d(s): 3,77,582 WARNING @ Tue, 14 Jul 2020 09:21:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:21:43: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:21:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:21:47: 6000000 INFO @ Tue, 14 Jul 2020 09:21:53: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:21:59: 8000000 INFO @ Tue, 14 Jul 2020 09:22:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:22:04: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:22:04: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:22:04: #1 total tags in treatment: 8906518 INFO @ Tue, 14 Jul 2020 09:22:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:22:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:22:05: #1 tags after filtering in treatment: 8906352 INFO @ Tue, 14 Jul 2020 09:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:22:05: #1 finished! INFO @ Tue, 14 Jul 2020 09:22:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:22:05: #2 number of paired peaks: 1730 INFO @ Tue, 14 Jul 2020 09:22:05: start model_add_line... INFO @ Tue, 14 Jul 2020 09:22:05: start X-correlation... INFO @ Tue, 14 Jul 2020 09:22:05: end of X-cor INFO @ Tue, 14 Jul 2020 09:22:05: #2 finished! INFO @ Tue, 14 Jul 2020 09:22:05: #2 predicted fragment length is 77 bps INFO @ Tue, 14 Jul 2020 09:22:05: #2 alternative fragment length(s) may be 3,77,582 bps INFO @ Tue, 14 Jul 2020 09:22:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.20_model.r WARNING @ Tue, 14 Jul 2020 09:22:05: #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, 14 Jul 2020 09:22:05: #2 You may need to consider one of the other alternative d(s): 3,77,582 WARNING @ Tue, 14 Jul 2020 09:22:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:22:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:22:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:22:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:22:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.10_summits.bed INFO @ Tue, 14 Jul 2020 09:22:12: Done! pass1 - making usageList (386 chroms): 1 millis pass2 - checking and writing primary data (1013 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:22:25: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:22:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:22:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:22:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7262567/SRX7262567.20_summits.bed INFO @ Tue, 14 Jul 2020 09:22:34: Done! pass1 - making usageList (175 chroms): 1 millis pass2 - checking and writing primary data (340 records, 4 fields): 5 millis CompletedMACS2peakCalling