Job ID = 6452978 SRX = SRX085399 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:47:45 prefetch.2.10.7: 1) Downloading 'SRR317177'... 2020-06-21T07:47:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:50:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:50:12 prefetch.2.10.7: 'SRR317177' is valid 2020-06-21T07:50:12 prefetch.2.10.7: 1) 'SRR317177' was downloaded successfully Read 21327048 spots for SRR317177/SRR317177.sra Written 21327048 spots for SRR317177/SRR317177.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: 00:04:51 21327048 reads; of these: 21327048 (100.00%) were unpaired; of these: 7653105 (35.88%) aligned 0 times 11936320 (55.97%) aligned exactly 1 time 1737623 (8.15%) aligned >1 times 64.12% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 9087735 / 13673943 = 0.6646 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 16:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.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 16:59:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:59:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:59:08: 1000000 INFO @ Sun, 21 Jun 2020 16:59:14: 2000000 INFO @ Sun, 21 Jun 2020 16:59:21: 3000000 INFO @ Sun, 21 Jun 2020 16:59:27: 4000000 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 16:59:31: #1 tag size is determined as 54 bps INFO @ Sun, 21 Jun 2020 16:59:31: #1 tag size = 54 INFO @ Sun, 21 Jun 2020 16:59:31: #1 total tags in treatment: 4586208 INFO @ Sun, 21 Jun 2020 16:59:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:59:31: #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 16:59:32: #1 tags after filtering in treatment: 4586027 INFO @ Sun, 21 Jun 2020 16:59:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:59:32: #1 finished! INFO @ Sun, 21 Jun 2020 16:59:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:59:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.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 16:59:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:59:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:59:32: #2 number of paired peaks: 6038 INFO @ Sun, 21 Jun 2020 16:59:32: start model_add_line... INFO @ Sun, 21 Jun 2020 16:59:32: start X-correlation... INFO @ Sun, 21 Jun 2020 16:59:32: end of X-cor INFO @ Sun, 21 Jun 2020 16:59:32: #2 finished! INFO @ Sun, 21 Jun 2020 16:59:32: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 16:59:32: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 16:59:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.05_model.r WARNING @ Sun, 21 Jun 2020 16:59:32: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:59:32: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 16:59:32: #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 16:59:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:59:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:59:39: 1000000 INFO @ Sun, 21 Jun 2020 16:59:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:59:45: 2000000 INFO @ Sun, 21 Jun 2020 16:59:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:59:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:59:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.05_summits.bed INFO @ Sun, 21 Jun 2020 16:59:49: Done! pass1 - making usageList (531 chroms): 2 millis pass2 - checking and writing primary data (11966 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:59:52: 3000000 INFO @ Sun, 21 Jun 2020 16:59:59: 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 @ Sun, 21 Jun 2020 17:00:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.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 17:00:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:00:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:00:03: #1 tag size is determined as 54 bps INFO @ Sun, 21 Jun 2020 17:00:03: #1 tag size = 54 INFO @ Sun, 21 Jun 2020 17:00:03: #1 total tags in treatment: 4586208 INFO @ Sun, 21 Jun 2020 17:00:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:00:03: #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 17:00:03: #1 tags after filtering in treatment: 4586027 INFO @ Sun, 21 Jun 2020 17:00:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:00:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:00:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:00:04: #2 number of paired peaks: 6038 INFO @ Sun, 21 Jun 2020 17:00:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:00:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:00:04: end of X-cor INFO @ Sun, 21 Jun 2020 17:00:04: #2 finished! INFO @ Sun, 21 Jun 2020 17:00:04: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 17:00:04: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 17:00:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.10_model.r WARNING @ Sun, 21 Jun 2020 17:00:04: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:00:04: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 17:00:04: #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 17:00:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:00:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:00:08: 1000000 INFO @ Sun, 21 Jun 2020 17:00:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:15: 2000000 INFO @ Sun, 21 Jun 2020 17:00:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.10_summits.bed INFO @ Sun, 21 Jun 2020 17:00:20: Done! pass1 - making usageList (310 chroms): 2 millis pass2 - checking and writing primary data (9324 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:00:21: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:00:28: 4000000 INFO @ Sun, 21 Jun 2020 17:00:32: #1 tag size is determined as 54 bps INFO @ Sun, 21 Jun 2020 17:00:32: #1 tag size = 54 INFO @ Sun, 21 Jun 2020 17:00:32: #1 total tags in treatment: 4586208 INFO @ Sun, 21 Jun 2020 17:00:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:00:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:00:32: #1 tags after filtering in treatment: 4586027 INFO @ Sun, 21 Jun 2020 17:00:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:00:32: #1 finished! INFO @ Sun, 21 Jun 2020 17:00:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:00:33: #2 number of paired peaks: 6038 INFO @ Sun, 21 Jun 2020 17:00:33: start model_add_line... INFO @ Sun, 21 Jun 2020 17:00:33: start X-correlation... INFO @ Sun, 21 Jun 2020 17:00:33: end of X-cor INFO @ Sun, 21 Jun 2020 17:00:33: #2 finished! INFO @ Sun, 21 Jun 2020 17:00:33: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 17:00:33: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 17:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.20_model.r WARNING @ Sun, 21 Jun 2020 17:00:33: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:00:33: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 17:00:33: #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 17:00:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:00:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:00:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085399/SRX085399.20_summits.bed INFO @ Sun, 21 Jun 2020 17:00:48: Done! pass1 - making usageList (197 chroms): 1 millis pass2 - checking and writing primary data (6994 records, 4 fields): 15 millis CompletedMACS2peakCalling