Job ID = 6452394 SRX = SRX013031 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:47:15 prefetch.2.10.7: 1) Downloading 'SRR030297'... 2020-06-21T07:47:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:47:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:47:51 prefetch.2.10.7: 'SRR030297' is valid 2020-06-21T07:47:51 prefetch.2.10.7: 1) 'SRR030297' was downloaded successfully Read 2914436 spots for SRR030297/SRR030297.sra Written 2914436 spots for SRR030297/SRR030297.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: 00:00:27 2914436 reads; of these: 2914436 (100.00%) were unpaired; of these: 686064 (23.54%) aligned 0 times 1891008 (64.88%) aligned exactly 1 time 337364 (11.58%) aligned >1 times 76.46% overall alignment rate Time searching: 00:00:27 Overall time: 00:00:27 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] 109468 / 2228372 = 0.0491 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 16:49:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.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 16:49:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:49:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:49:34: 1000000 INFO @ Sun, 21 Jun 2020 16:49:39: 2000000 INFO @ Sun, 21 Jun 2020 16:49:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:49:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:49:40: #1 total tags in treatment: 2118904 INFO @ Sun, 21 Jun 2020 16:49:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:49:40: #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 16:49:41: #1 tags after filtering in treatment: 2118666 INFO @ Sun, 21 Jun 2020 16:49:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:49:41: #1 finished! INFO @ Sun, 21 Jun 2020 16:49:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:49:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:49:41: #2 number of paired peaks: 1070 INFO @ Sun, 21 Jun 2020 16:49:41: start model_add_line... INFO @ Sun, 21 Jun 2020 16:49:41: start X-correlation... INFO @ Sun, 21 Jun 2020 16:49:41: end of X-cor INFO @ Sun, 21 Jun 2020 16:49:41: #2 finished! INFO @ Sun, 21 Jun 2020 16:49:41: #2 predicted fragment length is 195 bps INFO @ Sun, 21 Jun 2020 16:49:41: #2 alternative fragment length(s) may be 195 bps INFO @ Sun, 21 Jun 2020 16:49:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.05_model.r INFO @ Sun, 21 Jun 2020 16:49:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:49:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:49:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:49:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:49:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:49:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.05_summits.bed INFO @ Sun, 21 Jun 2020 16:49:48: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (688 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 16:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.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 16:49:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:49:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:50:03: 1000000 INFO @ Sun, 21 Jun 2020 16:50:08: 2000000 INFO @ Sun, 21 Jun 2020 16:50:09: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:50:09: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:50:09: #1 total tags in treatment: 2118904 INFO @ Sun, 21 Jun 2020 16:50:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:50:09: #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 16:50:09: #1 tags after filtering in treatment: 2118666 INFO @ Sun, 21 Jun 2020 16:50:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:50:09: #1 finished! INFO @ Sun, 21 Jun 2020 16:50:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:50:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:50:09: #2 number of paired peaks: 1070 INFO @ Sun, 21 Jun 2020 16:50:09: start model_add_line... INFO @ Sun, 21 Jun 2020 16:50:09: start X-correlation... INFO @ Sun, 21 Jun 2020 16:50:09: end of X-cor INFO @ Sun, 21 Jun 2020 16:50:09: #2 finished! INFO @ Sun, 21 Jun 2020 16:50:09: #2 predicted fragment length is 195 bps INFO @ Sun, 21 Jun 2020 16:50:09: #2 alternative fragment length(s) may be 195 bps INFO @ Sun, 21 Jun 2020 16:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.10_model.r INFO @ Sun, 21 Jun 2020 16:50:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:50:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:50:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:50:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:50:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:50:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.10_summits.bed INFO @ Sun, 21 Jun 2020 16:50:17: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 2 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 16:50:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.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 16:50:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:50:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:50:33: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:50:38: 2000000 INFO @ Sun, 21 Jun 2020 16:50:39: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:50:39: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:50:39: #1 total tags in treatment: 2118904 INFO @ Sun, 21 Jun 2020 16:50:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:50:39: #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 16:50:39: #1 tags after filtering in treatment: 2118666 INFO @ Sun, 21 Jun 2020 16:50:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:50:39: #1 finished! INFO @ Sun, 21 Jun 2020 16:50:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:50:40: #2 number of paired peaks: 1070 INFO @ Sun, 21 Jun 2020 16:50:40: start model_add_line... INFO @ Sun, 21 Jun 2020 16:50:40: start X-correlation... INFO @ Sun, 21 Jun 2020 16:50:40: end of X-cor INFO @ Sun, 21 Jun 2020 16:50:40: #2 finished! INFO @ Sun, 21 Jun 2020 16:50:40: #2 predicted fragment length is 195 bps INFO @ Sun, 21 Jun 2020 16:50:40: #2 alternative fragment length(s) may be 195 bps INFO @ Sun, 21 Jun 2020 16:50:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.20_model.r INFO @ Sun, 21 Jun 2020 16:50:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:50:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:50:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:50:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:50:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:50:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013031/SRX013031.20_summits.bed INFO @ Sun, 21 Jun 2020 16:50:47: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 2 millis CompletedMACS2peakCalling