Job ID = 6626527 SRX = SRX6813067 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6158939 spots for SRR10080075/SRR10080075.sra Written 6158939 spots for SRR10080075/SRR10080075.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626644 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:51 6158939 reads; of these: 6158939 (100.00%) were unpaired; of these: 730875 (11.87%) aligned 0 times 4089031 (66.39%) aligned exactly 1 time 1339033 (21.74%) aligned >1 times 88.13% 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: 15 sequences. [bam_rmdupse_core] 594472 / 5428064 = 0.1095 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 07:23:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.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 07:23:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:23:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:24:01: 1000000 INFO @ Tue, 14 Jul 2020 07:24:07: 2000000 INFO @ Tue, 14 Jul 2020 07:24:13: 3000000 INFO @ Tue, 14 Jul 2020 07:24:19: 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 07:24:23: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:24:23: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:24:23: #1 total tags in treatment: 4833592 INFO @ Tue, 14 Jul 2020 07:24:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:24:23: #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 07:24:24: #1 tags after filtering in treatment: 4833592 INFO @ Tue, 14 Jul 2020 07:24:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:24:24: #1 finished! INFO @ Tue, 14 Jul 2020 07:24:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:24:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:24:24: #2 number of paired peaks: 3046 INFO @ Tue, 14 Jul 2020 07:24:24: start model_add_line... INFO @ Tue, 14 Jul 2020 07:24:24: start X-correlation... INFO @ Tue, 14 Jul 2020 07:24:24: end of X-cor INFO @ Tue, 14 Jul 2020 07:24:24: #2 finished! INFO @ Tue, 14 Jul 2020 07:24:24: #2 predicted fragment length is 233 bps INFO @ Tue, 14 Jul 2020 07:24:24: #2 alternative fragment length(s) may be 233 bps INFO @ Tue, 14 Jul 2020 07:24:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.05_model.r INFO @ Tue, 14 Jul 2020 07:24:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:24:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:24:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.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 07:24:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:24:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:24:31: 1000000 INFO @ Tue, 14 Jul 2020 07:24:37: 2000000 INFO @ Tue, 14 Jul 2020 07:24:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:24:42: 3000000 INFO @ Tue, 14 Jul 2020 07:24:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.05_summits.bed INFO @ Tue, 14 Jul 2020 07:24:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3001 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:24:48: 4000000 INFO @ Tue, 14 Jul 2020 07:24:53: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:24:53: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:24:53: #1 total tags in treatment: 4833592 INFO @ Tue, 14 Jul 2020 07:24:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:24:53: #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 07:24:53: #1 tags after filtering in treatment: 4833592 INFO @ Tue, 14 Jul 2020 07:24:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:24:53: #1 finished! INFO @ Tue, 14 Jul 2020 07:24:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:24:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:24:53: #2 number of paired peaks: 3046 INFO @ Tue, 14 Jul 2020 07:24:53: start model_add_line... BedGraph に変換中... INFO @ Tue, 14 Jul 2020 07:24:53: start X-correlation... INFO @ Tue, 14 Jul 2020 07:24:53: end of X-cor INFO @ Tue, 14 Jul 2020 07:24:53: #2 finished! INFO @ Tue, 14 Jul 2020 07:24:53: #2 predicted fragment length is 233 bps INFO @ Tue, 14 Jul 2020 07:24:53: #2 alternative fragment length(s) may be 233 bps INFO @ Tue, 14 Jul 2020 07:24:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.10_model.r 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 07:24:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:24:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:24:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.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 07:24:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:24:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:25:01: 1000000 INFO @ Tue, 14 Jul 2020 07:25:06: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:25:07: 2000000 INFO @ Tue, 14 Jul 2020 07:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.10_summits.bed INFO @ Tue, 14 Jul 2020 07:25:12: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1460 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:25:13: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:25:18: 4000000 INFO @ Tue, 14 Jul 2020 07:25:23: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:25:23: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:25:23: #1 total tags in treatment: 4833592 INFO @ Tue, 14 Jul 2020 07:25:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:25:23: #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 07:25:23: #1 tags after filtering in treatment: 4833592 INFO @ Tue, 14 Jul 2020 07:25:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:25:23: #1 finished! INFO @ Tue, 14 Jul 2020 07:25:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:25:24: #2 number of paired peaks: 3046 INFO @ Tue, 14 Jul 2020 07:25:24: start model_add_line... INFO @ Tue, 14 Jul 2020 07:25:24: start X-correlation... INFO @ Tue, 14 Jul 2020 07:25:24: end of X-cor INFO @ Tue, 14 Jul 2020 07:25:24: #2 finished! INFO @ Tue, 14 Jul 2020 07:25:24: #2 predicted fragment length is 233 bps INFO @ Tue, 14 Jul 2020 07:25:24: #2 alternative fragment length(s) may be 233 bps INFO @ Tue, 14 Jul 2020 07:25:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.20_model.r INFO @ Tue, 14 Jul 2020 07:25:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:25:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:25:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:25:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:25:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:25:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813067/SRX6813067.20_summits.bed INFO @ Tue, 14 Jul 2020 07:25:42: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (648 records, 4 fields): 22 millis CompletedMACS2peakCalling