Job ID = 6454136 SRX = SRX183882 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:13:39 prefetch.2.10.7: 1) Downloading 'SRR557677'... 2020-06-21T09:13:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:16:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:16:14 prefetch.2.10.7: 'SRR557677' is valid 2020-06-21T09:16:14 prefetch.2.10.7: 1) 'SRR557677' was downloaded successfully Read 10657102 spots for SRR557677/SRR557677.sra Written 10657102 spots for SRR557677/SRR557677.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: 00:01:13 10657102 reads; of these: 10657102 (100.00%) were unpaired; of these: 122400 (1.15%) aligned 0 times 10346720 (97.09%) aligned exactly 1 time 187982 (1.76%) aligned >1 times 98.85% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 3463644 / 10534702 = 0.3288 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 18:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.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 18:20:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:34: 1000000 INFO @ Sun, 21 Jun 2020 18:20:39: 2000000 INFO @ Sun, 21 Jun 2020 18:20:45: 3000000 INFO @ Sun, 21 Jun 2020 18:20:51: 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 18:20:56: 5000000 INFO @ Sun, 21 Jun 2020 18:20:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.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 18:20:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:02: 6000000 INFO @ Sun, 21 Jun 2020 18:21:04: 1000000 INFO @ Sun, 21 Jun 2020 18:21:09: 7000000 INFO @ Sun, 21 Jun 2020 18:21:09: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:21:09: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:21:09: #1 total tags in treatment: 7071058 INFO @ Sun, 21 Jun 2020 18:21:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:09: #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 18:21:10: #1 tags after filtering in treatment: 7070262 INFO @ Sun, 21 Jun 2020 18:21:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:10: 2000000 INFO @ Sun, 21 Jun 2020 18:21:10: #2 number of paired peaks: 1069 INFO @ Sun, 21 Jun 2020 18:21:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:10: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 18:21:10: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 21 Jun 2020 18:21:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.05_model.r INFO @ Sun, 21 Jun 2020 18:21:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:16: 3000000 INFO @ Sun, 21 Jun 2020 18:21:21: 4000000 INFO @ Sun, 21 Jun 2020 18:21:26: #3 Call peaks for each chromosome... 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 18:21:27: 5000000 INFO @ Sun, 21 Jun 2020 18:21:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.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 18:21:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:33: 6000000 INFO @ Sun, 21 Jun 2020 18:21:33: 1000000 INFO @ Sun, 21 Jun 2020 18:21:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.05_summits.bed INFO @ Sun, 21 Jun 2020 18:21:34: Done! pass1 - making usageList (19 chroms): 1 millis pass2 - checking and writing primary data (8589 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:38: 2000000 INFO @ Sun, 21 Jun 2020 18:21:39: 7000000 INFO @ Sun, 21 Jun 2020 18:21:40: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:21:40: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:21:40: #1 total tags in treatment: 7071058 INFO @ Sun, 21 Jun 2020 18:21:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:40: #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 18:21:40: #1 tags after filtering in treatment: 7070262 INFO @ Sun, 21 Jun 2020 18:21:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:41: #2 number of paired peaks: 1069 INFO @ Sun, 21 Jun 2020 18:21:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:41: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 18:21:41: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 21 Jun 2020 18:21:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.10_model.r INFO @ Sun, 21 Jun 2020 18:21:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:43: 3000000 INFO @ Sun, 21 Jun 2020 18:21:49: 4000000 INFO @ Sun, 21 Jun 2020 18:21:54: 5000000 INFO @ Sun, 21 Jun 2020 18:21:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:59: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:22:04: 7000000 INFO @ Sun, 21 Jun 2020 18:22:04: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:22:04: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:22:04: #1 total tags in treatment: 7071058 INFO @ Sun, 21 Jun 2020 18:22:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:04: #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 18:22:04: #1 tags after filtering in treatment: 7070262 INFO @ Sun, 21 Jun 2020 18:22:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.10_summits.bed INFO @ Sun, 21 Jun 2020 18:22:05: Done! pass1 - making usageList (14 chroms): 1 millis INFO @ Sun, 21 Jun 2020 18:22:05: #2 number of paired peaks: 1069 INFO @ Sun, 21 Jun 2020 18:22:05: start model_add_line... pass2 - checking and writing primary data (3847 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:22:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:05: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 18:22:05: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 21 Jun 2020 18:22:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.20_model.r INFO @ Sun, 21 Jun 2020 18:22:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:22:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183882/SRX183882.20_summits.bed INFO @ Sun, 21 Jun 2020 18:22:28: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1714 records, 4 fields): 3 millis CompletedMACS2peakCalling