Job ID = 6452443 SRX = SRX013063 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:31:42 prefetch.2.10.7: 1) Downloading 'SRR030329'... 2020-06-21T07:31:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:32:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:32:42 prefetch.2.10.7: 'SRR030329' is valid 2020-06-21T07:32:42 prefetch.2.10.7: 1) 'SRR030329' was downloaded successfully Read 6861895 spots for SRR030329/SRR030329.sra Written 6861895 spots for SRR030329/SRR030329.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: 00:01:02 6861895 reads; of these: 6861895 (100.00%) were unpaired; of these: 820887 (11.96%) aligned 0 times 5444951 (79.35%) aligned exactly 1 time 596057 (8.69%) aligned >1 times 88.04% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 1267107 / 6041008 = 0.2098 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 16:36:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.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 16:36:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:36:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:36:13: 1000000 INFO @ Sun, 21 Jun 2020 16:36:18: 2000000 INFO @ Sun, 21 Jun 2020 16:36:23: 3000000 INFO @ Sun, 21 Jun 2020 16:36:28: 4000000 INFO @ Sun, 21 Jun 2020 16:36:32: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:36:32: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:36:32: #1 total tags in treatment: 4773901 INFO @ Sun, 21 Jun 2020 16:36:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:36:32: #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 16:36:33: #1 tags after filtering in treatment: 4773712 INFO @ Sun, 21 Jun 2020 16:36:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:36:33: #1 finished! INFO @ Sun, 21 Jun 2020 16:36:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:36:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:36:34: #2 number of paired peaks: 8493 INFO @ Sun, 21 Jun 2020 16:36:34: start model_add_line... INFO @ Sun, 21 Jun 2020 16:36:34: start X-correlation... INFO @ Sun, 21 Jun 2020 16:36:34: end of X-cor INFO @ Sun, 21 Jun 2020 16:36:34: #2 finished! INFO @ Sun, 21 Jun 2020 16:36:34: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 16:36:34: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 16:36:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.05_model.r INFO @ Sun, 21 Jun 2020 16:36:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:36:34: #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 16:36:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.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 16:36:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:36:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:36:43: 1000000 INFO @ Sun, 21 Jun 2020 16:36:48: 2000000 INFO @ Sun, 21 Jun 2020 16:36:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:36:53: 3000000 INFO @ Sun, 21 Jun 2020 16:36:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:36:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:36:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.05_summits.bed INFO @ Sun, 21 Jun 2020 16:36:54: Done! pass1 - making usageList (95 chroms): 2 millis pass2 - checking and writing primary data (7237 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:36:59: 4000000 INFO @ Sun, 21 Jun 2020 16:37:03: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:37:03: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:37:03: #1 total tags in treatment: 4773901 INFO @ Sun, 21 Jun 2020 16:37:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:37:03: #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 16:37:03: #1 tags after filtering in treatment: 4773712 INFO @ Sun, 21 Jun 2020 16:37:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:37:03: #1 finished! INFO @ Sun, 21 Jun 2020 16:37:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:37:04: #2 number of paired peaks: 8493 INFO @ Sun, 21 Jun 2020 16:37:04: start model_add_line... INFO @ Sun, 21 Jun 2020 16:37:04: start X-correlation... INFO @ Sun, 21 Jun 2020 16:37:04: end of X-cor INFO @ Sun, 21 Jun 2020 16:37:04: #2 finished! INFO @ Sun, 21 Jun 2020 16:37:04: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 16:37:04: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 16:37:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.10_model.r INFO @ Sun, 21 Jun 2020 16:37:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:37:04: #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 16:37:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.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 16:37:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:37:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:37:13: 1000000 INFO @ Sun, 21 Jun 2020 16:37:18: 2000000 INFO @ Sun, 21 Jun 2020 16:37:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:37:22: 3000000 INFO @ Sun, 21 Jun 2020 16:37:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:37:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:37:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.10_summits.bed INFO @ Sun, 21 Jun 2020 16:37:25: Done! pass1 - making usageList (72 chroms): 2 millis pass2 - checking and writing primary data (6521 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:37:28: 4000000 INFO @ Sun, 21 Jun 2020 16:37:32: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:37:32: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:37:32: #1 total tags in treatment: 4773901 INFO @ Sun, 21 Jun 2020 16:37:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:37:32: #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 16:37:33: #1 tags after filtering in treatment: 4773712 INFO @ Sun, 21 Jun 2020 16:37:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:37:33: #1 finished! INFO @ Sun, 21 Jun 2020 16:37:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:37:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:37:34: #2 number of paired peaks: 8493 INFO @ Sun, 21 Jun 2020 16:37:34: start model_add_line... INFO @ Sun, 21 Jun 2020 16:37:34: start X-correlation... INFO @ Sun, 21 Jun 2020 16:37:34: end of X-cor INFO @ Sun, 21 Jun 2020 16:37:34: #2 finished! INFO @ Sun, 21 Jun 2020 16:37:34: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 16:37:34: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 16:37:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.20_model.r INFO @ Sun, 21 Jun 2020 16:37:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:37:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:37:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:37:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:37:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:37:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013063/SRX013063.20_summits.bed INFO @ Sun, 21 Jun 2020 16:37:54: Done! pass1 - making usageList (52 chroms): 2 millis pass2 - checking and writing primary data (5618 records, 4 fields): 11 millis CompletedMACS2peakCalling