Job ID = 6456624 SRX = SRX373354 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:54:46 prefetch.2.10.7: 1) Downloading 'SRR1024310'... 2020-06-21T10:54:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:07 prefetch.2.10.7: 1) 'SRR1024310' was downloaded successfully Read 152966819 spots for SRR1024310/SRR1024310.sra Written 152966819 spots for SRR1024310/SRR1024310.sra 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: 00:17:59 152966819 reads; of these: 152966819 (100.00%) were unpaired; of these: 116697675 (76.29%) aligned 0 times 29514567 (19.29%) aligned exactly 1 time 6754577 (4.42%) aligned >1 times 23.71% overall alignment rate Time searching: 00:17:59 Overall time: 00:17:59 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 16 files... [bam_rmdupse_core] 30416346 / 36269144 = 0.8386 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 @ Sun, 21 Jun 2020 20:57:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.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 @ Sun, 21 Jun 2020 20:57:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:57:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:57:24: 1000000 INFO @ Sun, 21 Jun 2020 20:57:32: 2000000 INFO @ Sun, 21 Jun 2020 20:57:40: 3000000 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 @ Sun, 21 Jun 2020 20:57:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.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 @ Sun, 21 Jun 2020 20:57:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:57:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:57:49: 4000000 INFO @ Sun, 21 Jun 2020 20:57:54: 1000000 INFO @ Sun, 21 Jun 2020 20:57:58: 5000000 INFO @ Sun, 21 Jun 2020 20:58:02: 2000000 INFO @ Sun, 21 Jun 2020 20:58:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:58:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:58:05: #1 total tags in treatment: 5852798 INFO @ Sun, 21 Jun 2020 20:58:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:58:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:58:06: #1 tags after filtering in treatment: 5852720 INFO @ Sun, 21 Jun 2020 20:58:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:58:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:58:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:58:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:58:07: #2 number of paired peaks: 3018 INFO @ Sun, 21 Jun 2020 20:58:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:58:07: start X-correlation... INFO @ Sun, 21 Jun 2020 20:58:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:58:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:58:07: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 20:58:07: #2 alternative fragment length(s) may be 3,77,583,585 bps INFO @ Sun, 21 Jun 2020 20:58:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.05_model.r WARNING @ Sun, 21 Jun 2020 20:58:07: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:58:07: #2 You may need to consider one of the other alternative d(s): 3,77,583,585 WARNING @ Sun, 21 Jun 2020 20:58:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:58:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:58:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:58:10: 3000000 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 @ Sun, 21 Jun 2020 20:58:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.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 @ Sun, 21 Jun 2020 20:58:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:58:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:58:18: 4000000 INFO @ Sun, 21 Jun 2020 20:58:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:58:25: 1000000 INFO @ Sun, 21 Jun 2020 20:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:58:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:58:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.05_summits.bed INFO @ Sun, 21 Jun 2020 20:58:27: Done! INFO @ Sun, 21 Jun 2020 20:58:28: 5000000 pass1 - making usageList (776 chroms): 2 millis pass2 - checking and writing primary data (3748 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:58:34: 2000000 INFO @ Sun, 21 Jun 2020 20:58:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:58:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:58:35: #1 total tags in treatment: 5852798 INFO @ Sun, 21 Jun 2020 20:58:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:58:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:58:36: #1 tags after filtering in treatment: 5852720 INFO @ Sun, 21 Jun 2020 20:58:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:58:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:58:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:58:37: #2 number of paired peaks: 3018 INFO @ Sun, 21 Jun 2020 20:58:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:58:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:58:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:58:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:58:37: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 20:58:37: #2 alternative fragment length(s) may be 3,77,583,585 bps INFO @ Sun, 21 Jun 2020 20:58:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.10_model.r WARNING @ Sun, 21 Jun 2020 20:58:37: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:58:37: #2 You may need to consider one of the other alternative d(s): 3,77,583,585 WARNING @ Sun, 21 Jun 2020 20:58:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:58:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:58:44: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:58:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:58:53: 4000000 INFO @ Sun, 21 Jun 2020 20:58:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:58:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:58:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.10_summits.bed INFO @ Sun, 21 Jun 2020 20:58:57: Done! pass1 - making usageList (610 chroms): 2 millis pass2 - checking and writing primary data (2127 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:59:03: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:59:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:59:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:59:12: #1 total tags in treatment: 5852798 INFO @ Sun, 21 Jun 2020 20:59:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:59:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:59:13: #1 tags after filtering in treatment: 5852720 INFO @ Sun, 21 Jun 2020 20:59:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:59:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:59:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:59:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:59:13: #2 number of paired peaks: 3018 INFO @ Sun, 21 Jun 2020 20:59:13: start model_add_line... INFO @ Sun, 21 Jun 2020 20:59:13: start X-correlation... INFO @ Sun, 21 Jun 2020 20:59:13: end of X-cor INFO @ Sun, 21 Jun 2020 20:59:13: #2 finished! INFO @ Sun, 21 Jun 2020 20:59:13: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 20:59:13: #2 alternative fragment length(s) may be 3,77,583,585 bps INFO @ Sun, 21 Jun 2020 20:59:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.20_model.r WARNING @ Sun, 21 Jun 2020 20:59:13: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:59:13: #2 You may need to consider one of the other alternative d(s): 3,77,583,585 WARNING @ Sun, 21 Jun 2020 20:59:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:59:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:59:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:59:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:59:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:59:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:59:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX373354/SRX373354.20_summits.bed INFO @ Sun, 21 Jun 2020 20:59:34: Done! pass1 - making usageList (339 chroms): 1 millis pass2 - checking and writing primary data (770 records, 4 fields): 38 millis CompletedMACS2peakCalling