Job ID = 6454104 SRX = SRX182775 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:17:09 prefetch.2.10.7: 1) Downloading 'SRR553569'... 2020-06-21T09:17:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:20:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:20:42 prefetch.2.10.7: 1) 'SRR553569' was downloaded successfully Read 25805249 spots for SRR553569/SRR553569.sra Written 25805249 spots for SRR553569/SRR553569.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: 00:04:46 25805249 reads; of these: 25805249 (100.00%) were unpaired; of these: 10799075 (41.85%) aligned 0 times 10117471 (39.21%) aligned exactly 1 time 4888703 (18.94%) aligned >1 times 58.15% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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_rmdupse_core] 7683487 / 15006174 = 0.5120 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 18:29:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.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 18:29:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:29:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:29:48: 1000000 INFO @ Sun, 21 Jun 2020 18:29:53: 2000000 INFO @ Sun, 21 Jun 2020 18:29:57: 3000000 INFO @ Sun, 21 Jun 2020 18:30:02: 4000000 INFO @ Sun, 21 Jun 2020 18:30:06: 5000000 INFO @ Sun, 21 Jun 2020 18:30:11: 6000000 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 18:30:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.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 18:30:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:16: 7000000 INFO @ Sun, 21 Jun 2020 18:30:18: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:30:18: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:30:18: #1 total tags in treatment: 7322687 INFO @ Sun, 21 Jun 2020 18:30:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:30:18: #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 18:30:18: #1 tags after filtering in treatment: 7322682 INFO @ Sun, 21 Jun 2020 18:30:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:30:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:30:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:30:19: #2 number of paired peaks: 1230 INFO @ Sun, 21 Jun 2020 18:30:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:30:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:30:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:30:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:30:19: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 18:30:19: #2 alternative fragment length(s) may be 3,38,566 bps INFO @ Sun, 21 Jun 2020 18:30:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.05_model.r WARNING @ Sun, 21 Jun 2020 18:30:19: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:30:19: #2 You may need to consider one of the other alternative d(s): 3,38,566 WARNING @ Sun, 21 Jun 2020 18:30:19: #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 18:30:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:30:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:30:19: 1000000 INFO @ Sun, 21 Jun 2020 18:30:24: 2000000 INFO @ Sun, 21 Jun 2020 18:30:29: 3000000 INFO @ Sun, 21 Jun 2020 18:30:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:30:35: 4000000 INFO @ Sun, 21 Jun 2020 18:30:40: 5000000 INFO @ Sun, 21 Jun 2020 18:30:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:30:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:30:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.05_summits.bed INFO @ Sun, 21 Jun 2020 18:30:41: Done! pass1 - making usageList (648 chroms): 1 millis pass2 - checking and writing primary data (2951 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 18:30:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.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 18:30:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:46: 6000000 INFO @ Sun, 21 Jun 2020 18:30:48: 1000000 INFO @ Sun, 21 Jun 2020 18:30:51: 7000000 INFO @ Sun, 21 Jun 2020 18:30:53: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:30:53: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:30:53: #1 total tags in treatment: 7322687 INFO @ Sun, 21 Jun 2020 18:30:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:30:53: #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 18:30:53: 2000000 INFO @ Sun, 21 Jun 2020 18:30:53: #1 tags after filtering in treatment: 7322682 INFO @ Sun, 21 Jun 2020 18:30:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:30:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:30:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:30:54: #2 number of paired peaks: 1230 INFO @ Sun, 21 Jun 2020 18:30:54: start model_add_line... INFO @ Sun, 21 Jun 2020 18:30:54: start X-correlation... INFO @ Sun, 21 Jun 2020 18:30:54: end of X-cor INFO @ Sun, 21 Jun 2020 18:30:54: #2 finished! INFO @ Sun, 21 Jun 2020 18:30:54: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 18:30:54: #2 alternative fragment length(s) may be 3,38,566 bps INFO @ Sun, 21 Jun 2020 18:30:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.10_model.r WARNING @ Sun, 21 Jun 2020 18:30:54: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:30:54: #2 You may need to consider one of the other alternative d(s): 3,38,566 WARNING @ Sun, 21 Jun 2020 18:30:54: #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 18:30:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:30:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:30:58: 3000000 INFO @ Sun, 21 Jun 2020 18:31:02: 4000000 INFO @ Sun, 21 Jun 2020 18:31:07: 5000000 INFO @ Sun, 21 Jun 2020 18:31:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:31:12: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:31:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:31:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:31:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.10_summits.bed INFO @ Sun, 21 Jun 2020 18:31:16: Done! INFO @ Sun, 21 Jun 2020 18:31:16: 7000000 pass1 - making usageList (519 chroms): 2 millis pass2 - checking and writing primary data (2302 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:31:18: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:31:18: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:31:18: #1 total tags in treatment: 7322687 INFO @ Sun, 21 Jun 2020 18:31:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:31:18: #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 18:31:18: #1 tags after filtering in treatment: 7322682 INFO @ Sun, 21 Jun 2020 18:31:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:31:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:31:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:31:19: #2 number of paired peaks: 1230 INFO @ Sun, 21 Jun 2020 18:31:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:31:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:31:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:31:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:31:19: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 18:31:19: #2 alternative fragment length(s) may be 3,38,566 bps INFO @ Sun, 21 Jun 2020 18:31:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.20_model.r WARNING @ Sun, 21 Jun 2020 18:31:19: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:31:19: #2 You may need to consider one of the other alternative d(s): 3,38,566 WARNING @ Sun, 21 Jun 2020 18:31:19: #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 18:31:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:31:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:31:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:31:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:31:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:31:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX182775/SRX182775.20_summits.bed INFO @ Sun, 21 Jun 2020 18:31:42: Done! pass1 - making usageList (442 chroms): 1 millis pass2 - checking and writing primary data (1530 records, 4 fields): 14 millis CompletedMACS2peakCalling