Job ID = 6452471 SRX = SRX013084 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:37:27 prefetch.2.10.7: 1) Downloading 'SRR030350'... 2020-06-21T07:37:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:38:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:38:19 prefetch.2.10.7: 'SRR030350' is valid 2020-06-21T07:38:19 prefetch.2.10.7: 1) 'SRR030350' was downloaded successfully Read 4239797 spots for SRR030350/SRR030350.sra Written 4239797 spots for SRR030350/SRR030350.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: 00:00:38 4239797 reads; of these: 4239797 (100.00%) were unpaired; of these: 1385519 (32.68%) aligned 0 times 2365927 (55.80%) aligned exactly 1 time 488351 (11.52%) aligned >1 times 67.32% overall alignment rate Time searching: 00:00:38 Overall time: 00:00:38 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] 111318 / 2854278 = 0.0390 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 16:40:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.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 16:40:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:40:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:40:28: 1000000 INFO @ Sun, 21 Jun 2020 16:40:35: 2000000 INFO @ Sun, 21 Jun 2020 16:40:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:40:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:40:40: #1 total tags in treatment: 2742960 INFO @ Sun, 21 Jun 2020 16:40:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:40:40: #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 16:40:40: #1 tags after filtering in treatment: 2742811 INFO @ Sun, 21 Jun 2020 16:40:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:40:40: #1 finished! INFO @ Sun, 21 Jun 2020 16:40:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:40:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:40:40: #2 number of paired peaks: 351 WARNING @ Sun, 21 Jun 2020 16:40:40: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Sun, 21 Jun 2020 16:40:40: start model_add_line... INFO @ Sun, 21 Jun 2020 16:40:40: start X-correlation... INFO @ Sun, 21 Jun 2020 16:40:40: end of X-cor INFO @ Sun, 21 Jun 2020 16:40:40: #2 finished! INFO @ Sun, 21 Jun 2020 16:40:40: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 16:40:40: #2 alternative fragment length(s) may be 78 bps INFO @ Sun, 21 Jun 2020 16:40:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.05_model.r INFO @ Sun, 21 Jun 2020 16:40:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:40:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:40:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:40:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:40:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:40:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.05_summits.bed INFO @ Sun, 21 Jun 2020 16:40:50: Done! pass1 - making usageList (122 chroms): 1 millis pass2 - checking and writing primary data (304 records, 4 fields): 33 millis CompletedMACS2peakCalling 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 16:40:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.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 16:40:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:40:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:40:59: 1000000 INFO @ Sun, 21 Jun 2020 16:41:05: 2000000 INFO @ Sun, 21 Jun 2020 16:41:10: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:41:10: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:41:10: #1 total tags in treatment: 2742960 INFO @ Sun, 21 Jun 2020 16:41:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:41:10: #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 16:41:11: #1 tags after filtering in treatment: 2742811 INFO @ Sun, 21 Jun 2020 16:41:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:41:11: #1 finished! INFO @ Sun, 21 Jun 2020 16:41:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:41:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:41:11: #2 number of paired peaks: 351 WARNING @ Sun, 21 Jun 2020 16:41:11: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Sun, 21 Jun 2020 16:41:11: start model_add_line... INFO @ Sun, 21 Jun 2020 16:41:11: start X-correlation... INFO @ Sun, 21 Jun 2020 16:41:11: end of X-cor INFO @ Sun, 21 Jun 2020 16:41:11: #2 finished! INFO @ Sun, 21 Jun 2020 16:41:11: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 16:41:11: #2 alternative fragment length(s) may be 78 bps INFO @ Sun, 21 Jun 2020 16:41:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.10_model.r INFO @ Sun, 21 Jun 2020 16:41:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:41:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:41:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:41:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:41:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:41:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.10_summits.bed INFO @ Sun, 21 Jun 2020 16:41:20: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (135 records, 4 fields): 3 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 16:41:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.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 16:41:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:41:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:41:29: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:41:35: 2000000 INFO @ Sun, 21 Jun 2020 16:41:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:41:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:41:40: #1 total tags in treatment: 2742960 INFO @ Sun, 21 Jun 2020 16:41:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:41:40: #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 16:41:40: #1 tags after filtering in treatment: 2742811 INFO @ Sun, 21 Jun 2020 16:41:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:41:40: #1 finished! INFO @ Sun, 21 Jun 2020 16:41:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:41:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:41:40: #2 number of paired peaks: 351 WARNING @ Sun, 21 Jun 2020 16:41:40: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Sun, 21 Jun 2020 16:41:40: start model_add_line... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:41:40: start X-correlation... INFO @ Sun, 21 Jun 2020 16:41:40: end of X-cor INFO @ Sun, 21 Jun 2020 16:41:40: #2 finished! INFO @ Sun, 21 Jun 2020 16:41:40: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 16:41:40: #2 alternative fragment length(s) may be 78 bps INFO @ Sun, 21 Jun 2020 16:41:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.20_model.r INFO @ Sun, 21 Jun 2020 16:41:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:41:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:41:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:41:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:41:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:41:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013084/SRX013084.20_summits.bed INFO @ Sun, 21 Jun 2020 16:41:51: Done! pass1 - making usageList (41 chroms): 0 millis pass2 - checking and writing primary data (54 records, 4 fields): 2 millis CompletedMACS2peakCalling