Job ID = 6459095 SRX = SRX6386767 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:53:37 prefetch.2.10.7: 1) Downloading 'SRR9624499'... 2020-06-21T12:53:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:57:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:57:28 prefetch.2.10.7: 1) 'SRR9624499' was downloaded successfully Read 20920661 spots for SRR9624499/SRR9624499.sra Written 20920661 spots for SRR9624499/SRR9624499.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: 00:04:36 20920661 reads; of these: 20920661 (100.00%) were unpaired; of these: 7025163 (33.58%) aligned 0 times 9960171 (47.61%) aligned exactly 1 time 3935327 (18.81%) aligned >1 times 66.42% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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] 7170279 / 13895498 = 0.5160 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 22:06:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.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 22:06:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:22: 1000000 INFO @ Sun, 21 Jun 2020 22:06:27: 2000000 INFO @ Sun, 21 Jun 2020 22:06:32: 3000000 INFO @ Sun, 21 Jun 2020 22:06:37: 4000000 INFO @ Sun, 21 Jun 2020 22:06:43: 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 @ Sun, 21 Jun 2020 22:06:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.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 22:06:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:48: 6000000 INFO @ Sun, 21 Jun 2020 22:06:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:06:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:06:52: #1 total tags in treatment: 6725219 INFO @ Sun, 21 Jun 2020 22:06:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:52: #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 22:06:52: #1 tags after filtering in treatment: 6725195 INFO @ Sun, 21 Jun 2020 22:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:52: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:52: 1000000 INFO @ Sun, 21 Jun 2020 22:06:53: #2 number of paired peaks: 1504 INFO @ Sun, 21 Jun 2020 22:06:53: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:53: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:53: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:53: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:53: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 22:06:53: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 21 Jun 2020 22:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.05_model.r WARNING @ Sun, 21 Jun 2020 22:06:53: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:06:53: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 21 Jun 2020 22:06:53: #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 22:06:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:06:58: 2000000 INFO @ Sun, 21 Jun 2020 22:07:04: 3000000 INFO @ Sun, 21 Jun 2020 22:07:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:07:10: 4000000 INFO @ Sun, 21 Jun 2020 22:07:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:07:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:07:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.05_summits.bed INFO @ Sun, 21 Jun 2020 22:07:13: Done! pass1 - making usageList (675 chroms): 2 millis pass2 - checking and writing primary data (2671 records, 4 fields): 19 millis CompletedMACS2peakCalling 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 22:07:16: 5000000 INFO @ Sun, 21 Jun 2020 22:07:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.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 22:07:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:22: 6000000 INFO @ Sun, 21 Jun 2020 22:07:22: 1000000 INFO @ Sun, 21 Jun 2020 22:07:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:07:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:07:26: #1 total tags in treatment: 6725219 INFO @ Sun, 21 Jun 2020 22:07:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:07:26: #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 22:07:26: #1 tags after filtering in treatment: 6725195 INFO @ Sun, 21 Jun 2020 22:07:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:07:26: #1 finished! INFO @ Sun, 21 Jun 2020 22:07:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:07:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:07:27: #2 number of paired peaks: 1504 INFO @ Sun, 21 Jun 2020 22:07:27: start model_add_line... INFO @ Sun, 21 Jun 2020 22:07:27: start X-correlation... INFO @ Sun, 21 Jun 2020 22:07:27: end of X-cor INFO @ Sun, 21 Jun 2020 22:07:27: #2 finished! INFO @ Sun, 21 Jun 2020 22:07:27: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 22:07:27: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 21 Jun 2020 22:07:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.10_model.r WARNING @ Sun, 21 Jun 2020 22:07:27: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:07:27: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 21 Jun 2020 22:07:27: #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 22:07:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:07:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:07:28: 2000000 INFO @ Sun, 21 Jun 2020 22:07:33: 3000000 INFO @ Sun, 21 Jun 2020 22:07:38: 4000000 INFO @ Sun, 21 Jun 2020 22:07:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:07:43: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:07:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:07:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:07:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.10_summits.bed INFO @ Sun, 21 Jun 2020 22:07:48: Done! INFO @ Sun, 21 Jun 2020 22:07:48: 6000000 pass1 - making usageList (570 chroms): 1 millis pass2 - checking and writing primary data (2158 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:07:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:07:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:07:52: #1 total tags in treatment: 6725219 INFO @ Sun, 21 Jun 2020 22:07:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:07:52: #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 22:07:53: #1 tags after filtering in treatment: 6725195 INFO @ Sun, 21 Jun 2020 22:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:07:53: #1 finished! INFO @ Sun, 21 Jun 2020 22:07:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:07:53: #2 number of paired peaks: 1504 INFO @ Sun, 21 Jun 2020 22:07:53: start model_add_line... INFO @ Sun, 21 Jun 2020 22:07:53: start X-correlation... INFO @ Sun, 21 Jun 2020 22:07:53: end of X-cor INFO @ Sun, 21 Jun 2020 22:07:53: #2 finished! INFO @ Sun, 21 Jun 2020 22:07:53: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 22:07:53: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 21 Jun 2020 22:07:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.20_model.r WARNING @ Sun, 21 Jun 2020 22:07:53: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:07:53: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 21 Jun 2020 22:07:53: #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 22:07:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:07:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:08:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386767/SRX6386767.20_summits.bed INFO @ Sun, 21 Jun 2020 22:08:15: Done! pass1 - making usageList (440 chroms): 1 millis pass2 - checking and writing primary data (1275 records, 4 fields): 13 millis CompletedMACS2peakCalling