Job ID = 6452527 SRX = SRX016142 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:38:22 prefetch.2.10.7: 1) Downloading 'SRR034693'... 2020-06-21T07:38:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:40:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:40:50 prefetch.2.10.7: 'SRR034693' is valid 2020-06-21T07:40:50 prefetch.2.10.7: 1) 'SRR034693' was downloaded successfully Read 15245172 spots for SRR034693/SRR034693.sra Written 15245172 spots for SRR034693/SRR034693.sra 2020-06-21T07:41:38 prefetch.2.10.7: 1) Downloading 'SRR034694'... 2020-06-21T07:41:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:42:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:42:07 prefetch.2.10.7: 'SRR034694' is valid 2020-06-21T07:42:07 prefetch.2.10.7: 1) 'SRR034694' was downloaded successfully Read 4246371 spots for SRR034694/SRR034694.sra Written 4246371 spots for SRR034694/SRR034694.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:35 19491543 reads; of these: 19491543 (100.00%) were unpaired; of these: 820532 (4.21%) aligned 0 times 16039290 (82.29%) aligned exactly 1 time 2631721 (13.50%) aligned >1 times 95.79% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 13949534 / 18671011 = 0.7471 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 16:49:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.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 16:49:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:49:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:49:23: 1000000 INFO @ Sun, 21 Jun 2020 16:49:28: 2000000 INFO @ Sun, 21 Jun 2020 16:49:33: 3000000 INFO @ Sun, 21 Jun 2020 16:49:39: 4000000 INFO @ Sun, 21 Jun 2020 16:49:42: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:49:42: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:49:42: #1 total tags in treatment: 4721477 INFO @ Sun, 21 Jun 2020 16:49:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:49:42: #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 16:49:43: #1 tags after filtering in treatment: 4721425 INFO @ Sun, 21 Jun 2020 16:49:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:49:43: #1 finished! INFO @ Sun, 21 Jun 2020 16:49:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:49:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:49:43: #2 number of paired peaks: 1057 INFO @ Sun, 21 Jun 2020 16:49:43: start model_add_line... INFO @ Sun, 21 Jun 2020 16:49:43: start X-correlation... INFO @ Sun, 21 Jun 2020 16:49:43: end of X-cor INFO @ Sun, 21 Jun 2020 16:49:43: #2 finished! INFO @ Sun, 21 Jun 2020 16:49:43: #2 predicted fragment length is 259 bps INFO @ Sun, 21 Jun 2020 16:49:43: #2 alternative fragment length(s) may be 259 bps INFO @ Sun, 21 Jun 2020 16:49:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.05_model.r INFO @ Sun, 21 Jun 2020 16:49:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:49:43: #3 Pre-compute pvalue-qvalue table... 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 16:49:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.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 16:49:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:49:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:49:53: 1000000 INFO @ Sun, 21 Jun 2020 16:49:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:49:58: 2000000 INFO @ Sun, 21 Jun 2020 16:50:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:50:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:50:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.05_summits.bed INFO @ Sun, 21 Jun 2020 16:50:00: Done! pass1 - making usageList (636 chroms): 2 millis pass2 - checking and writing primary data (3692 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:50:03: 3000000 INFO @ Sun, 21 Jun 2020 16:50:09: 4000000 INFO @ Sun, 21 Jun 2020 16:50:12: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:50:12: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:50:12: #1 total tags in treatment: 4721477 INFO @ Sun, 21 Jun 2020 16:50:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:50:12: #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 16:50:13: #1 tags after filtering in treatment: 4721425 INFO @ Sun, 21 Jun 2020 16:50:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:50:13: #1 finished! INFO @ Sun, 21 Jun 2020 16:50:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:50:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:50:13: #2 number of paired peaks: 1057 INFO @ Sun, 21 Jun 2020 16:50:13: start model_add_line... INFO @ Sun, 21 Jun 2020 16:50:13: start X-correlation... INFO @ Sun, 21 Jun 2020 16:50:13: end of X-cor INFO @ Sun, 21 Jun 2020 16:50:13: #2 finished! INFO @ Sun, 21 Jun 2020 16:50:13: #2 predicted fragment length is 259 bps INFO @ Sun, 21 Jun 2020 16:50:13: #2 alternative fragment length(s) may be 259 bps INFO @ Sun, 21 Jun 2020 16:50:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.10_model.r INFO @ Sun, 21 Jun 2020 16:50:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:50:13: #3 Pre-compute pvalue-qvalue table... 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 16:50:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.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 16:50:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:50:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:50:23: 1000000 INFO @ Sun, 21 Jun 2020 16:50:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:50:28: 2000000 INFO @ Sun, 21 Jun 2020 16:50:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:50:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:50:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.10_summits.bed INFO @ Sun, 21 Jun 2020 16:50:30: Done! pass1 - making usageList (394 chroms): 2 millis pass2 - checking and writing primary data (1581 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:50:33: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:50:39: 4000000 INFO @ Sun, 21 Jun 2020 16:50:43: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:50:43: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:50:43: #1 total tags in treatment: 4721477 INFO @ Sun, 21 Jun 2020 16:50:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:50:43: #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 16:50:43: #1 tags after filtering in treatment: 4721425 INFO @ Sun, 21 Jun 2020 16:50:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:50:43: #1 finished! INFO @ Sun, 21 Jun 2020 16:50:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:50:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:50:43: #2 number of paired peaks: 1057 INFO @ Sun, 21 Jun 2020 16:50:43: start model_add_line... INFO @ Sun, 21 Jun 2020 16:50:43: start X-correlation... INFO @ Sun, 21 Jun 2020 16:50:43: end of X-cor INFO @ Sun, 21 Jun 2020 16:50:43: #2 finished! INFO @ Sun, 21 Jun 2020 16:50:43: #2 predicted fragment length is 259 bps INFO @ Sun, 21 Jun 2020 16:50:43: #2 alternative fragment length(s) may be 259 bps INFO @ Sun, 21 Jun 2020 16:50:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.20_model.r INFO @ Sun, 21 Jun 2020 16:50:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:50:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:50:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:51:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:51:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:51:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016142/SRX016142.20_summits.bed INFO @ Sun, 21 Jun 2020 16:51:00: Done! pass1 - making usageList (141 chroms): 1 millis pass2 - checking and writing primary data (544 records, 4 fields): 6 millis CompletedMACS2peakCalling