Job ID = 6456588 SRX = SRX365705 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:09:24 prefetch.2.10.7: 1) Downloading 'SRR1013783'... 2020-06-21T11:09:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:11:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:11:52 prefetch.2.10.7: 'SRR1013783' is valid 2020-06-21T11:11:52 prefetch.2.10.7: 1) 'SRR1013783' was downloaded successfully Read 14973157 spots for SRR1013783/SRR1013783.sra Written 14973157 spots for SRR1013783/SRR1013783.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: 00:02:49 14973157 reads; of these: 14973157 (100.00%) were unpaired; of these: 3623513 (24.20%) aligned 0 times 8011363 (53.50%) aligned exactly 1 time 3338281 (22.30%) aligned >1 times 75.80% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 4255157 / 11349644 = 0.3749 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 20:18:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.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 20:18:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:18:49: 1000000 INFO @ Sun, 21 Jun 2020 20:18:54: 2000000 INFO @ Sun, 21 Jun 2020 20:18:59: 3000000 INFO @ Sun, 21 Jun 2020 20:19:03: 4000000 INFO @ Sun, 21 Jun 2020 20:19:08: 5000000 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 20:19:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.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 20:19:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:19:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:19:14: 6000000 INFO @ Sun, 21 Jun 2020 20:19:19: 1000000 INFO @ Sun, 21 Jun 2020 20:19:19: 7000000 INFO @ Sun, 21 Jun 2020 20:19:20: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:19:20: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:19:20: #1 total tags in treatment: 7094487 INFO @ Sun, 21 Jun 2020 20:19:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:19:20: #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 20:19:21: #1 tags after filtering in treatment: 7094432 INFO @ Sun, 21 Jun 2020 20:19:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:19:21: #1 finished! INFO @ Sun, 21 Jun 2020 20:19:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:19:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:19:21: #2 number of paired peaks: 2177 INFO @ Sun, 21 Jun 2020 20:19:21: start model_add_line... INFO @ Sun, 21 Jun 2020 20:19:21: start X-correlation... INFO @ Sun, 21 Jun 2020 20:19:21: end of X-cor INFO @ Sun, 21 Jun 2020 20:19:21: #2 finished! INFO @ Sun, 21 Jun 2020 20:19:21: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 20:19:21: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 20:19:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.05_model.r INFO @ Sun, 21 Jun 2020 20:19:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:19:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:19:24: 2000000 INFO @ Sun, 21 Jun 2020 20:19:29: 3000000 INFO @ Sun, 21 Jun 2020 20:19:34: 4000000 INFO @ Sun, 21 Jun 2020 20:19:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:19:39: 5000000 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 20:19:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.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 20:19:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:19:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:19:45: 6000000 INFO @ Sun, 21 Jun 2020 20:19:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:19:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:19:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.05_summits.bed INFO @ Sun, 21 Jun 2020 20:19:45: Done! pass1 - making usageList (615 chroms): 3 millis pass2 - checking and writing primary data (5401 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:19:49: 1000000 INFO @ Sun, 21 Jun 2020 20:19:50: 7000000 INFO @ Sun, 21 Jun 2020 20:19:50: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:19:50: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:19:50: #1 total tags in treatment: 7094487 INFO @ Sun, 21 Jun 2020 20:19:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:19:50: #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 20:19:51: #1 tags after filtering in treatment: 7094432 INFO @ Sun, 21 Jun 2020 20:19:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:19:51: #1 finished! INFO @ Sun, 21 Jun 2020 20:19:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:19:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:19:52: #2 number of paired peaks: 2177 INFO @ Sun, 21 Jun 2020 20:19:52: start model_add_line... INFO @ Sun, 21 Jun 2020 20:19:52: start X-correlation... INFO @ Sun, 21 Jun 2020 20:19:52: end of X-cor INFO @ Sun, 21 Jun 2020 20:19:52: #2 finished! INFO @ Sun, 21 Jun 2020 20:19:52: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 20:19:52: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 20:19:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.10_model.r INFO @ Sun, 21 Jun 2020 20:19:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:19:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:19:54: 2000000 INFO @ Sun, 21 Jun 2020 20:19:59: 3000000 INFO @ Sun, 21 Jun 2020 20:20:04: 4000000 INFO @ Sun, 21 Jun 2020 20:20:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:20:09: 5000000 INFO @ Sun, 21 Jun 2020 20:20:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:20:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:20:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.10_summits.bed INFO @ Sun, 21 Jun 2020 20:20:15: Done! INFO @ Sun, 21 Jun 2020 20:20:15: 6000000 pass1 - making usageList (556 chroms): 2 millis pass2 - checking and writing primary data (3636 records, 4 fields): 34 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:20:21: 7000000 INFO @ Sun, 21 Jun 2020 20:20:21: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:20:21: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:20:21: #1 total tags in treatment: 7094487 INFO @ Sun, 21 Jun 2020 20:20:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:20:21: #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 20:20:22: #1 tags after filtering in treatment: 7094432 INFO @ Sun, 21 Jun 2020 20:20:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:20:22: #1 finished! INFO @ Sun, 21 Jun 2020 20:20:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:20:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:20:22: #2 number of paired peaks: 2177 INFO @ Sun, 21 Jun 2020 20:20:22: start model_add_line... INFO @ Sun, 21 Jun 2020 20:20:23: start X-correlation... INFO @ Sun, 21 Jun 2020 20:20:23: end of X-cor INFO @ Sun, 21 Jun 2020 20:20:23: #2 finished! INFO @ Sun, 21 Jun 2020 20:20:23: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 20:20:23: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 20:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.20_model.r INFO @ Sun, 21 Jun 2020 20:20:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:20:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:20:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:20:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:20:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365705/SRX365705.20_summits.bed INFO @ Sun, 21 Jun 2020 20:20:46: Done! pass1 - making usageList (443 chroms): 1 millis pass2 - checking and writing primary data (2189 records, 4 fields): 27 millis CompletedMACS2peakCalling