Job ID = 6626536 SRX = SRX6813075 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12601622 spots for SRR10080067/SRR10080067.sra Written 12601622 spots for SRR10080067/SRR10080067.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626658 ("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: 00:02:34 12601622 reads; of these: 12601622 (100.00%) were unpaired; of these: 3255855 (25.84%) aligned 0 times 8197871 (65.05%) aligned exactly 1 time 1147896 (9.11%) aligned >1 times 74.16% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 1268229 / 9345767 = 0.1357 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 07:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.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 07:27:52: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:27:52: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:27:57: 1000000 INFO @ Tue, 14 Jul 2020 07:28:03: 2000000 INFO @ Tue, 14 Jul 2020 07:28:08: 3000000 INFO @ Tue, 14 Jul 2020 07:28:14: 4000000 INFO @ Tue, 14 Jul 2020 07:28:19: 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 07:28:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.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 07:28:21: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:21: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:28:24: 6000000 INFO @ Tue, 14 Jul 2020 07:28:27: 1000000 INFO @ Tue, 14 Jul 2020 07:28:29: 7000000 INFO @ Tue, 14 Jul 2020 07:28:32: 2000000 INFO @ Tue, 14 Jul 2020 07:28:35: 8000000 INFO @ Tue, 14 Jul 2020 07:28:35: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:28:35: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:28:35: #1 total tags in treatment: 8077538 INFO @ Tue, 14 Jul 2020 07:28:35: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:28:35: #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 07:28:35: #1 tags after filtering in treatment: 8077538 INFO @ Tue, 14 Jul 2020 07:28:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:28:35: #1 finished! INFO @ Tue, 14 Jul 2020 07:28:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:28:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:28:36: #2 number of paired peaks: 7648 INFO @ Tue, 14 Jul 2020 07:28:36: start model_add_line... INFO @ Tue, 14 Jul 2020 07:28:36: start X-correlation... INFO @ Tue, 14 Jul 2020 07:28:36: end of X-cor INFO @ Tue, 14 Jul 2020 07:28:36: #2 finished! INFO @ Tue, 14 Jul 2020 07:28:36: #2 predicted fragment length is 229 bps INFO @ Tue, 14 Jul 2020 07:28:36: #2 alternative fragment length(s) may be 229 bps INFO @ Tue, 14 Jul 2020 07:28:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.05_model.r INFO @ Tue, 14 Jul 2020 07:28:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:28:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:28:38: 3000000 INFO @ Tue, 14 Jul 2020 07:28:43: 4000000 INFO @ Tue, 14 Jul 2020 07:28:49: 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 07:28:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.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 07:28:52: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:52: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:28:54: 6000000 INFO @ Tue, 14 Jul 2020 07:28:57: 1000000 INFO @ Tue, 14 Jul 2020 07:28:59: 7000000 INFO @ Tue, 14 Jul 2020 07:29:01: 2000000 INFO @ Tue, 14 Jul 2020 07:29:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:29:04: 8000000 INFO @ Tue, 14 Jul 2020 07:29:05: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:29:05: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:29:05: #1 total tags in treatment: 8077538 INFO @ Tue, 14 Jul 2020 07:29:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:29:05: #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 07:29:05: #1 tags after filtering in treatment: 8077538 INFO @ Tue, 14 Jul 2020 07:29:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:29:05: #1 finished! INFO @ Tue, 14 Jul 2020 07:29:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:29:06: #2 number of paired peaks: 7648 INFO @ Tue, 14 Jul 2020 07:29:06: start model_add_line... INFO @ Tue, 14 Jul 2020 07:29:06: start X-correlation... INFO @ Tue, 14 Jul 2020 07:29:06: end of X-cor INFO @ Tue, 14 Jul 2020 07:29:06: #2 finished! INFO @ Tue, 14 Jul 2020 07:29:06: #2 predicted fragment length is 229 bps INFO @ Tue, 14 Jul 2020 07:29:06: #2 alternative fragment length(s) may be 229 bps INFO @ Tue, 14 Jul 2020 07:29:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.10_model.r INFO @ Tue, 14 Jul 2020 07:29:06: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:29:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:29:06: 3000000 INFO @ Tue, 14 Jul 2020 07:29:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:29:11: 4000000 INFO @ Tue, 14 Jul 2020 07:29:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:29:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.05_summits.bed INFO @ Tue, 14 Jul 2020 07:29:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (6024 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:29:16: 5000000 INFO @ Tue, 14 Jul 2020 07:29:21: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:29:25: 7000000 INFO @ Tue, 14 Jul 2020 07:29:30: 8000000 INFO @ Tue, 14 Jul 2020 07:29:30: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:29:30: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:29:30: #1 total tags in treatment: 8077538 INFO @ Tue, 14 Jul 2020 07:29:30: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:29:30: #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 07:29:30: #1 tags after filtering in treatment: 8077538 INFO @ Tue, 14 Jul 2020 07:29:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:29:30: #1 finished! INFO @ Tue, 14 Jul 2020 07:29:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:29:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:29:31: #2 number of paired peaks: 7648 INFO @ Tue, 14 Jul 2020 07:29:31: start model_add_line... INFO @ Tue, 14 Jul 2020 07:29:32: start X-correlation... INFO @ Tue, 14 Jul 2020 07:29:32: end of X-cor INFO @ Tue, 14 Jul 2020 07:29:32: #2 finished! INFO @ Tue, 14 Jul 2020 07:29:32: #2 predicted fragment length is 229 bps INFO @ Tue, 14 Jul 2020 07:29:32: #2 alternative fragment length(s) may be 229 bps INFO @ Tue, 14 Jul 2020 07:29:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.20_model.r INFO @ Tue, 14 Jul 2020 07:29:32: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:29:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:29:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:29:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:29:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:29:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.10_summits.bed INFO @ Tue, 14 Jul 2020 07:29:42: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (3013 records, 4 fields): 270 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:29:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:30:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:30:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:30:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813075/SRX6813075.20_summits.bed INFO @ Tue, 14 Jul 2020 07:30:07: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1154 records, 4 fields): 14 millis CompletedMACS2peakCalling