Job ID = 6454091 SRX = SRX181433 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:47:02 prefetch.2.10.7: 1) Downloading 'SRR548170'... 2020-06-21T08:47:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:53:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:53:03 prefetch.2.10.7: 1) 'SRR548170' was downloaded successfully Read 29151113 spots for SRR548170/SRR548170.sra Written 29151113 spots for SRR548170/SRR548170.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: 00:04:10 29151113 reads; of these: 29151113 (100.00%) were unpaired; of these: 8637835 (29.63%) aligned 0 times 18720473 (64.22%) aligned exactly 1 time 1792805 (6.15%) aligned >1 times 70.37% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 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] 17747346 / 20513278 = 0.8652 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 18:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.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 18:01:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:30: 1000000 INFO @ Sun, 21 Jun 2020 18:01:35: 2000000 INFO @ Sun, 21 Jun 2020 18:01:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:01:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:01:40: #1 total tags in treatment: 2765932 INFO @ Sun, 21 Jun 2020 18:01:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:40: #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 18:01:40: #1 tags after filtering in treatment: 2765825 INFO @ Sun, 21 Jun 2020 18:01:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:41: #2 number of paired peaks: 1364 INFO @ Sun, 21 Jun 2020 18:01:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:41: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 18:01:41: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 21 Jun 2020 18:01:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.05_model.r INFO @ Sun, 21 Jun 2020 18:01:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:01:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.05_summits.bed INFO @ Sun, 21 Jun 2020 18:01:50: Done! pass1 - making usageList (401 chroms): 2 millis pass2 - checking and writing primary data (1591 records, 4 fields): 13 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 18:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.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 18:01:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:00: 1000000 INFO @ Sun, 21 Jun 2020 18:02:05: 2000000 INFO @ Sun, 21 Jun 2020 18:02:10: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:02:10: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:02:10: #1 total tags in treatment: 2765932 INFO @ Sun, 21 Jun 2020 18:02:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:10: #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 18:02:10: #1 tags after filtering in treatment: 2765825 INFO @ Sun, 21 Jun 2020 18:02:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:10: #2 number of paired peaks: 1364 INFO @ Sun, 21 Jun 2020 18:02:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:10: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 18:02:10: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 21 Jun 2020 18:02:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.10_model.r INFO @ Sun, 21 Jun 2020 18:02:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.10_summits.bed INFO @ Sun, 21 Jun 2020 18:02:20: Done! pass1 - making usageList (198 chroms): 0 millis pass2 - checking and writing primary data (501 records, 4 fields): 7 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 18:02:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.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 18:02:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:30: 1000000 INFO @ Sun, 21 Jun 2020 18:02:35: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:02:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:02:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:02:40: #1 total tags in treatment: 2765932 INFO @ Sun, 21 Jun 2020 18:02:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:40: #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 18:02:40: #1 tags after filtering in treatment: 2765825 INFO @ Sun, 21 Jun 2020 18:02:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:40: #2 number of paired peaks: 1364 INFO @ Sun, 21 Jun 2020 18:02:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:40: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 18:02:40: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 21 Jun 2020 18:02:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.20_model.r INFO @ Sun, 21 Jun 2020 18:02:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:02:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181433/SRX181433.20_summits.bed INFO @ Sun, 21 Jun 2020 18:02:50: Done! pass1 - making usageList (85 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 5 millis CompletedMACS2peakCalling