Job ID = 6626650 SRX = SRX6813073 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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 9352438 reads; of these: 9352438 (100.00%) were unpaired; of these: 3665618 (39.19%) aligned 0 times 4035355 (43.15%) aligned exactly 1 time 1651465 (17.66%) aligned >1 times 60.81% 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] 1285629 / 5686820 = 0.2261 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 @ Tue, 14 Jul 2020 08:12:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.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 @ Tue, 14 Jul 2020 08:12:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:12:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:12:10: 1000000 INFO @ Tue, 14 Jul 2020 08:12:16: 2000000 INFO @ Tue, 14 Jul 2020 08:12:22: 3000000 INFO @ Tue, 14 Jul 2020 08:12:29: 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 @ Tue, 14 Jul 2020 08:12:32: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:12:32: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:12:32: #1 total tags in treatment: 4401191 INFO @ Tue, 14 Jul 2020 08:12:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:12:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:12:32: #1 tags after filtering in treatment: 4401144 INFO @ Tue, 14 Jul 2020 08:12:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:12:32: #1 finished! INFO @ Tue, 14 Jul 2020 08:12:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:12:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:12:32: #2 number of paired peaks: 1384 INFO @ Tue, 14 Jul 2020 08:12:32: start model_add_line... INFO @ Tue, 14 Jul 2020 08:12:32: start X-correlation... INFO @ Tue, 14 Jul 2020 08:12:32: end of X-cor INFO @ Tue, 14 Jul 2020 08:12:32: #2 finished! INFO @ Tue, 14 Jul 2020 08:12:32: #2 predicted fragment length is 193 bps INFO @ Tue, 14 Jul 2020 08:12:32: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 14 Jul 2020 08:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.05_model.r INFO @ Tue, 14 Jul 2020 08:12:32: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.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 @ Tue, 14 Jul 2020 08:12:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:12:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:12:39: 1000000 INFO @ Tue, 14 Jul 2020 08:12:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:12:44: 2000000 INFO @ Tue, 14 Jul 2020 08:12:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:12:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:12:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.05_summits.bed INFO @ Tue, 14 Jul 2020 08:12:48: Done! pass1 - making usageList (613 chroms): 2 millis pass2 - checking and writing primary data (2312 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:12:49: 3000000 INFO @ Tue, 14 Jul 2020 08:12:55: 4000000 INFO @ Tue, 14 Jul 2020 08:12:58: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:12:58: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:12:58: #1 total tags in treatment: 4401191 INFO @ Tue, 14 Jul 2020 08:12:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:12:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:12:58: #1 tags after filtering in treatment: 4401144 INFO @ Tue, 14 Jul 2020 08:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:12:58: #1 finished! INFO @ Tue, 14 Jul 2020 08:12:58: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:12:58: #2 number of paired peaks: 1384 INFO @ Tue, 14 Jul 2020 08:12:58: start model_add_line... INFO @ Tue, 14 Jul 2020 08:12:58: start X-correlation... INFO @ Tue, 14 Jul 2020 08:12:58: end of X-cor INFO @ Tue, 14 Jul 2020 08:12:58: #2 finished! INFO @ Tue, 14 Jul 2020 08:12:58: #2 predicted fragment length is 193 bps INFO @ Tue, 14 Jul 2020 08:12:58: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 14 Jul 2020 08:12:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.10_model.r INFO @ Tue, 14 Jul 2020 08:12:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:12:58: #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 @ Tue, 14 Jul 2020 08:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.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 @ Tue, 14 Jul 2020 08:13:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:13:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:13:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:13:10: 1000000 INFO @ Tue, 14 Jul 2020 08:13:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:13:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:13:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.10_summits.bed INFO @ Tue, 14 Jul 2020 08:13:15: Done! pass1 - making usageList (423 chroms): 2 millis pass2 - checking and writing primary data (1493 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:13:15: 2000000 INFO @ Tue, 14 Jul 2020 08:13:21: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:13:27: 4000000 INFO @ Tue, 14 Jul 2020 08:13:29: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:13:29: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:13:29: #1 total tags in treatment: 4401191 INFO @ Tue, 14 Jul 2020 08:13:29: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:13:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:13:30: #1 tags after filtering in treatment: 4401144 INFO @ Tue, 14 Jul 2020 08:13:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:13:30: #1 finished! INFO @ Tue, 14 Jul 2020 08:13:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:13:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:13:30: #2 number of paired peaks: 1384 INFO @ Tue, 14 Jul 2020 08:13:30: start model_add_line... INFO @ Tue, 14 Jul 2020 08:13:30: start X-correlation... INFO @ Tue, 14 Jul 2020 08:13:30: end of X-cor INFO @ Tue, 14 Jul 2020 08:13:30: #2 finished! INFO @ Tue, 14 Jul 2020 08:13:30: #2 predicted fragment length is 193 bps INFO @ Tue, 14 Jul 2020 08:13:30: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 14 Jul 2020 08:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.20_model.r INFO @ Tue, 14 Jul 2020 08:13:30: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:13:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:13:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:13:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:13:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:13:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6813073/SRX6813073.20_summits.bed INFO @ Tue, 14 Jul 2020 08:13:46: Done! pass1 - making usageList (193 chroms): 1 millis pass2 - checking and writing primary data (831 records, 4 fields): 6 millis CompletedMACS2peakCalling