Job ID = 6626649 SRX = SRX6813072 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: 00:02:12 11071117 reads; of these: 11071117 (100.00%) were unpaired; of these: 3317632 (29.97%) aligned 0 times 6069491 (54.82%) aligned exactly 1 time 1683994 (15.21%) aligned >1 times 70.03% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 1066810 / 7753485 = 0.1376 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 08:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.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 08:13:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:13:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:13:07: 1000000 INFO @ Tue, 14 Jul 2020 08:13:13: 2000000 INFO @ Tue, 14 Jul 2020 08:13:18: 3000000 INFO @ Tue, 14 Jul 2020 08:13:24: 4000000 INFO @ Tue, 14 Jul 2020 08:13:29: 5000000 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 08:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.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 08:13:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:13:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:13:35: 6000000 INFO @ Tue, 14 Jul 2020 08:13:37: 1000000 INFO @ Tue, 14 Jul 2020 08:13:39: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:13:39: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:13:39: #1 total tags in treatment: 6686675 INFO @ Tue, 14 Jul 2020 08:13:39: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:13:39: #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 08:13:39: #1 tags after filtering in treatment: 6686599 INFO @ Tue, 14 Jul 2020 08:13:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:13:39: #1 finished! INFO @ Tue, 14 Jul 2020 08:13:39: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:13:39: #2 number of paired peaks: 1259 INFO @ Tue, 14 Jul 2020 08:13:39: start model_add_line... INFO @ Tue, 14 Jul 2020 08:13:39: start X-correlation... INFO @ Tue, 14 Jul 2020 08:13:39: end of X-cor INFO @ Tue, 14 Jul 2020 08:13:39: #2 finished! INFO @ Tue, 14 Jul 2020 08:13:39: #2 predicted fragment length is 216 bps INFO @ Tue, 14 Jul 2020 08:13:39: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 14 Jul 2020 08:13:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.05_model.r INFO @ Tue, 14 Jul 2020 08:13:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:13:42: 2000000 INFO @ Tue, 14 Jul 2020 08:13:47: 3000000 INFO @ Tue, 14 Jul 2020 08:13:52: 4000000 INFO @ Tue, 14 Jul 2020 08:13:55: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:13:57: 5000000 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 08:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.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 08:14:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:14:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:14:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:14:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:14:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.05_summits.bed INFO @ Tue, 14 Jul 2020 08:14:02: Done! pass1 - making usageList (397 chroms): 2 millis pass2 - checking and writing primary data (3455 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:14:02: 6000000 INFO @ Tue, 14 Jul 2020 08:14:06: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:14:06: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:14:06: #1 total tags in treatment: 6686675 INFO @ Tue, 14 Jul 2020 08:14:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:14:06: #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 08:14:06: #1 tags after filtering in treatment: 6686599 INFO @ Tue, 14 Jul 2020 08:14:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:14:06: #1 finished! INFO @ Tue, 14 Jul 2020 08:14:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:14:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:14:07: #2 number of paired peaks: 1259 INFO @ Tue, 14 Jul 2020 08:14:07: start model_add_line... INFO @ Tue, 14 Jul 2020 08:14:07: start X-correlation... INFO @ Tue, 14 Jul 2020 08:14:07: end of X-cor INFO @ Tue, 14 Jul 2020 08:14:07: #2 finished! INFO @ Tue, 14 Jul 2020 08:14:07: #2 predicted fragment length is 216 bps INFO @ Tue, 14 Jul 2020 08:14:07: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 14 Jul 2020 08:14:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.10_model.r INFO @ Tue, 14 Jul 2020 08:14:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:14:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:14:09: 1000000 INFO @ Tue, 14 Jul 2020 08:14:16: 2000000 INFO @ Tue, 14 Jul 2020 08:14:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:14:23: 3000000 INFO @ Tue, 14 Jul 2020 08:14:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:14:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:14:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.10_summits.bed INFO @ Tue, 14 Jul 2020 08:14:30: Done! pass1 - making usageList (308 chroms): 1 millis pass2 - checking and writing primary data (1934 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:14:30: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:14:35: 5000000 INFO @ Tue, 14 Jul 2020 08:14:42: 6000000 INFO @ Tue, 14 Jul 2020 08:14:46: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:14:46: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:14:46: #1 total tags in treatment: 6686675 INFO @ Tue, 14 Jul 2020 08:14:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:14:46: #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 08:14:46: #1 tags after filtering in treatment: 6686599 INFO @ Tue, 14 Jul 2020 08:14:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:14:46: #1 finished! INFO @ Tue, 14 Jul 2020 08:14:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:14:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:14:47: #2 number of paired peaks: 1259 INFO @ Tue, 14 Jul 2020 08:14:47: start model_add_line... INFO @ Tue, 14 Jul 2020 08:14:47: start X-correlation... INFO @ Tue, 14 Jul 2020 08:14:47: end of X-cor INFO @ Tue, 14 Jul 2020 08:14:47: #2 finished! INFO @ Tue, 14 Jul 2020 08:14:47: #2 predicted fragment length is 216 bps INFO @ Tue, 14 Jul 2020 08:14:47: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 14 Jul 2020 08:14:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.20_model.r INFO @ Tue, 14 Jul 2020 08:14:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:14:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:15:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:15:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:15:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:15:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6813072/SRX6813072.20_summits.bed INFO @ Tue, 14 Jul 2020 08:15:11: Done! pass1 - making usageList (226 chroms): 1 millis pass2 - checking and writing primary data (1193 records, 4 fields): 31 millis CompletedMACS2peakCalling