Job ID = 6454264 SRX = SRX193337 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:02:04 prefetch.2.10.7: 1) Downloading 'SRR585070'... 2020-06-21T09:02:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:02:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:02:59 prefetch.2.10.7: 'SRR585070' is valid 2020-06-21T09:02:59 prefetch.2.10.7: 1) 'SRR585070' was downloaded successfully Read 8053237 spots for SRR585070/SRR585070.sra Written 8053237 spots for SRR585070/SRR585070.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: 00:01:52 8053237 reads; of these: 8053237 (100.00%) were unpaired; of these: 374047 (4.64%) aligned 0 times 6432335 (79.87%) aligned exactly 1 time 1246855 (15.48%) aligned >1 times 95.36% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 2055991 / 7679190 = 0.2677 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 18:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.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 18:07:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:07:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:07:27: 1000000 INFO @ Sun, 21 Jun 2020 18:07:33: 2000000 INFO @ Sun, 21 Jun 2020 18:07:39: 3000000 INFO @ Sun, 21 Jun 2020 18:07:44: 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 18:07:50: 5000000 INFO @ Sun, 21 Jun 2020 18:07:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.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 18:07:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:07:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:07:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:07:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:07:54: #1 total tags in treatment: 5623199 INFO @ Sun, 21 Jun 2020 18:07:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:54: #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 18:07:54: #1 tags after filtering in treatment: 5622907 INFO @ Sun, 21 Jun 2020 18:07:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:55: #2 number of paired peaks: 11410 INFO @ Sun, 21 Jun 2020 18:07:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:56: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 18:07:56: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 18:07:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.05_model.r INFO @ Sun, 21 Jun 2020 18:07:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:58: 1000000 INFO @ Sun, 21 Jun 2020 18:08:03: 2000000 INFO @ Sun, 21 Jun 2020 18:08:09: 3000000 INFO @ Sun, 21 Jun 2020 18:08:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:15: 4000000 INFO @ Sun, 21 Jun 2020 18:08:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.05_peaks.xls 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 18:08:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.05_summits.bed INFO @ Sun, 21 Jun 2020 18:08:20: Done! pass1 - making usageList (315 chroms): 2 millis pass2 - checking and writing primary data (8589 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:08:21: 5000000 INFO @ Sun, 21 Jun 2020 18:08:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.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 18:08:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:08:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:08:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:08:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:08:25: #1 total tags in treatment: 5623199 INFO @ Sun, 21 Jun 2020 18:08:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:25: #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 18:08:25: #1 tags after filtering in treatment: 5622907 INFO @ Sun, 21 Jun 2020 18:08:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:26: #2 number of paired peaks: 11410 INFO @ Sun, 21 Jun 2020 18:08:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:26: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 18:08:26: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 18:08:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.10_model.r INFO @ Sun, 21 Jun 2020 18:08:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:28: 1000000 INFO @ Sun, 21 Jun 2020 18:08:34: 2000000 INFO @ Sun, 21 Jun 2020 18:08:40: 3000000 INFO @ Sun, 21 Jun 2020 18:08:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:08:46: 4000000 INFO @ Sun, 21 Jun 2020 18:08:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.10_summits.bed INFO @ Sun, 21 Jun 2020 18:08:52: Done! pass1 - making usageList (226 chroms): 2 millis pass2 - checking and writing primary data (7796 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:08:52: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:08:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:08:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:08:56: #1 total tags in treatment: 5623199 INFO @ Sun, 21 Jun 2020 18:08:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:56: #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 18:08:56: #1 tags after filtering in treatment: 5622907 INFO @ Sun, 21 Jun 2020 18:08:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:57: #2 number of paired peaks: 11410 INFO @ Sun, 21 Jun 2020 18:08:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:57: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 18:08:57: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 18:08:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.20_model.r INFO @ Sun, 21 Jun 2020 18:08:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:09:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:09:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193337/SRX193337.20_summits.bed INFO @ Sun, 21 Jun 2020 18:09:22: Done! pass1 - making usageList (138 chroms): 2 millis pass2 - checking and writing primary data (6639 records, 4 fields): 11 millis CompletedMACS2peakCalling