Job ID = 6454268 SRX = SRX193626 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:04:08 prefetch.2.10.7: 1) Downloading 'SRR586004'... 2020-06-21T09:04:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:05:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:05:50 prefetch.2.10.7: 'SRR586004' is valid 2020-06-21T09:05:50 prefetch.2.10.7: 1) 'SRR586004' was downloaded successfully Read 10951532 spots for SRR586004/SRR586004.sra Written 10951532 spots for SRR586004/SRR586004.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: 00:01:58 10951532 reads; of these: 10951532 (100.00%) were unpaired; of these: 5688282 (51.94%) aligned 0 times 4211754 (38.46%) aligned exactly 1 time 1051496 (9.60%) aligned >1 times 48.06% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 2607588 / 5263250 = 0.4954 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 18:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.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 18:09:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:03: 1000000 INFO @ Sun, 21 Jun 2020 18:10:10: 2000000 INFO @ Sun, 21 Jun 2020 18:10:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:10:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:10:14: #1 total tags in treatment: 2655662 INFO @ Sun, 21 Jun 2020 18:10:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:14: #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 18:10:14: #1 tags after filtering in treatment: 2655390 INFO @ Sun, 21 Jun 2020 18:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:15: #2 number of paired peaks: 1451 INFO @ Sun, 21 Jun 2020 18:10:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:15: #2 predicted fragment length is 177 bps INFO @ Sun, 21 Jun 2020 18:10:15: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 21 Jun 2020 18:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.05_model.r INFO @ Sun, 21 Jun 2020 18:10:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:10:22: #3 Call peaks for each chromosome... 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 18:10:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.05_summits.bed INFO @ Sun, 21 Jun 2020 18:10:25: Done! pass1 - making usageList (314 chroms): 2 millis pass2 - checking and writing primary data (974 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:10:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.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 18:10:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:33: 1000000 INFO @ Sun, 21 Jun 2020 18:10:39: 2000000 INFO @ Sun, 21 Jun 2020 18:10:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:10:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:10:43: #1 total tags in treatment: 2655662 INFO @ Sun, 21 Jun 2020 18:10:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:43: #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 18:10:43: #1 tags after filtering in treatment: 2655390 INFO @ Sun, 21 Jun 2020 18:10:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:44: #2 number of paired peaks: 1451 INFO @ Sun, 21 Jun 2020 18:10:44: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:44: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:44: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:44: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:44: #2 predicted fragment length is 177 bps INFO @ Sun, 21 Jun 2020 18:10:44: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 21 Jun 2020 18:10:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.10_model.r INFO @ Sun, 21 Jun 2020 18:10:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:10:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.10_summits.bed INFO @ Sun, 21 Jun 2020 18:10:54: Done! pass1 - making usageList (158 chroms): 1 millis pass2 - checking and writing primary data (382 records, 4 fields): 8 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 18:10:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.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 18:10:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:11:04: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:11:11: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:11:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:11:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:11:17: #1 total tags in treatment: 2655662 INFO @ Sun, 21 Jun 2020 18:11:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:11:17: #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 18:11:17: #1 tags after filtering in treatment: 2655390 INFO @ Sun, 21 Jun 2020 18:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:11:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:11:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:11:17: #2 number of paired peaks: 1451 INFO @ Sun, 21 Jun 2020 18:11:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:11:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:11:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:11:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:11:17: #2 predicted fragment length is 177 bps INFO @ Sun, 21 Jun 2020 18:11:17: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 21 Jun 2020 18:11:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.20_model.r INFO @ Sun, 21 Jun 2020 18:11:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:11:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:11:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:11:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:11:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193626/SRX193626.20_summits.bed INFO @ Sun, 21 Jun 2020 18:11:28: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (160 records, 4 fields): 8 millis CompletedMACS2peakCalling