Job ID = 12265048 SRX = SRX3032280 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: 00:02:55 14146139 reads; of these: 14146139 (100.00%) were unpaired; of these: 2344464 (16.57%) aligned 0 times 10885489 (76.95%) aligned exactly 1 time 916186 (6.48%) aligned >1 times 83.43% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 4676210 / 11801675 = 0.3962 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:11:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.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 @ Sat, 03 Apr 2021 06:11:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:11:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:11:31: 1000000 INFO @ Sat, 03 Apr 2021 06:11:37: 2000000 INFO @ Sat, 03 Apr 2021 06:11:44: 3000000 INFO @ Sat, 03 Apr 2021 06:11:50: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.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 @ Sat, 03 Apr 2021 06:11:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:11:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:11:56: 5000000 INFO @ Sat, 03 Apr 2021 06:12:00: 1000000 INFO @ Sat, 03 Apr 2021 06:12:03: 6000000 INFO @ Sat, 03 Apr 2021 06:12:06: 2000000 INFO @ Sat, 03 Apr 2021 06:12:10: 7000000 INFO @ Sat, 03 Apr 2021 06:12:11: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:12:11: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:12:11: #1 total tags in treatment: 7125465 INFO @ Sat, 03 Apr 2021 06:12:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:12:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:12:11: #1 tags after filtering in treatment: 7125332 INFO @ Sat, 03 Apr 2021 06:12:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:12:11: #1 finished! INFO @ Sat, 03 Apr 2021 06:12:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:12:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:12:12: #2 number of paired peaks: 3062 INFO @ Sat, 03 Apr 2021 06:12:12: start model_add_line... INFO @ Sat, 03 Apr 2021 06:12:12: start X-correlation... INFO @ Sat, 03 Apr 2021 06:12:12: end of X-cor INFO @ Sat, 03 Apr 2021 06:12:12: #2 finished! INFO @ Sat, 03 Apr 2021 06:12:12: #2 predicted fragment length is 96 bps INFO @ Sat, 03 Apr 2021 06:12:12: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 03 Apr 2021 06:12:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.05_model.r WARNING @ Sat, 03 Apr 2021 06:12:12: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:12:12: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 03 Apr 2021 06:12:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:12:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:12:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:12:12: 3000000 INFO @ Sat, 03 Apr 2021 06:12:18: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:12:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.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 @ Sat, 03 Apr 2021 06:12:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:12:24: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:12:24: 5000000 INFO @ Sat, 03 Apr 2021 06:12:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:12:31: 1000000 INFO @ Sat, 03 Apr 2021 06:12:31: 6000000 INFO @ Sat, 03 Apr 2021 06:12:38: 2000000 INFO @ Sat, 03 Apr 2021 06:12:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:12:38: 7000000 INFO @ Sat, 03 Apr 2021 06:12:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:12:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.05_summits.bed INFO @ Sat, 03 Apr 2021 06:12:38: Done! pass1 - making usageList (119 chroms): 3 millis pass2 - checking and writing primary data (17491 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:12:39: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:12:39: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:12:39: #1 total tags in treatment: 7125465 INFO @ Sat, 03 Apr 2021 06:12:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:12:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:12:40: #1 tags after filtering in treatment: 7125332 INFO @ Sat, 03 Apr 2021 06:12:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:12:40: #1 finished! INFO @ Sat, 03 Apr 2021 06:12:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:12:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:12:40: #2 number of paired peaks: 3062 INFO @ Sat, 03 Apr 2021 06:12:40: start model_add_line... INFO @ Sat, 03 Apr 2021 06:12:40: start X-correlation... INFO @ Sat, 03 Apr 2021 06:12:40: end of X-cor INFO @ Sat, 03 Apr 2021 06:12:40: #2 finished! INFO @ Sat, 03 Apr 2021 06:12:40: #2 predicted fragment length is 96 bps INFO @ Sat, 03 Apr 2021 06:12:40: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 03 Apr 2021 06:12:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.10_model.r WARNING @ Sat, 03 Apr 2021 06:12:40: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:12:40: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 03 Apr 2021 06:12:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:12:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:12:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:12:44: 3000000 INFO @ Sat, 03 Apr 2021 06:12:50: 4000000 INFO @ Sat, 03 Apr 2021 06:12:56: 5000000 INFO @ Sat, 03 Apr 2021 06:12:56: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:13:03: 6000000 INFO @ Sat, 03 Apr 2021 06:13:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:13:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:13:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.10_summits.bed INFO @ Sat, 03 Apr 2021 06:13:06: Done! pass1 - making usageList (82 chroms): 2 millis pass2 - checking and writing primary data (9779 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:13:09: 7000000 INFO @ Sat, 03 Apr 2021 06:13:11: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:13:11: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:13:11: #1 total tags in treatment: 7125465 INFO @ Sat, 03 Apr 2021 06:13:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:13:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:13:11: #1 tags after filtering in treatment: 7125332 INFO @ Sat, 03 Apr 2021 06:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:13:11: #1 finished! INFO @ Sat, 03 Apr 2021 06:13:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:13:12: #2 number of paired peaks: 3062 INFO @ Sat, 03 Apr 2021 06:13:12: start model_add_line... INFO @ Sat, 03 Apr 2021 06:13:12: start X-correlation... INFO @ Sat, 03 Apr 2021 06:13:12: end of X-cor INFO @ Sat, 03 Apr 2021 06:13:12: #2 finished! INFO @ Sat, 03 Apr 2021 06:13:12: #2 predicted fragment length is 96 bps INFO @ Sat, 03 Apr 2021 06:13:12: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 03 Apr 2021 06:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.20_model.r WARNING @ Sat, 03 Apr 2021 06:13:12: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:13:12: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 03 Apr 2021 06:13:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:13:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:13:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:13:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:13:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:13:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:13:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3032280/SRX3032280.20_summits.bed INFO @ Sat, 03 Apr 2021 06:13:36: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (3321 records, 4 fields): 7 millis CompletedMACS2peakCalling