Job ID = 14167211 SRX = SRX6407591 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5223418 spots for SRR9645782/SRR9645782.sra Written 5223418 spots for SRR9645782/SRR9645782.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167747 ("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: 00:02:21 5223418 reads; of these: 5223418 (100.00%) were unpaired; of these: 282433 (5.41%) aligned 0 times 4313212 (82.57%) aligned exactly 1 time 627773 (12.02%) aligned >1 times 94.59% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 408162 / 4940985 = 0.0826 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.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 @ Fri, 10 Dec 2021 11:07:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:07:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:07:30: 1000000 INFO @ Fri, 10 Dec 2021 11:07:38: 2000000 INFO @ Fri, 10 Dec 2021 11:07:46: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:07:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.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 @ Fri, 10 Dec 2021 11:07:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:07:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:07:54: 4000000 INFO @ Fri, 10 Dec 2021 11:07:58: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 11:07:58: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 11:07:58: #1 total tags in treatment: 4532823 INFO @ Fri, 10 Dec 2021 11:07:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:07:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:07:58: #1 tags after filtering in treatment: 4532823 INFO @ Fri, 10 Dec 2021 11:07:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:07:58: #1 finished! INFO @ Fri, 10 Dec 2021 11:07:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:07:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:07:59: #2 number of paired peaks: 3007 INFO @ Fri, 10 Dec 2021 11:07:59: start model_add_line... INFO @ Fri, 10 Dec 2021 11:07:59: start X-correlation... INFO @ Fri, 10 Dec 2021 11:07:59: end of X-cor INFO @ Fri, 10 Dec 2021 11:07:59: #2 finished! INFO @ Fri, 10 Dec 2021 11:07:59: #2 predicted fragment length is 209 bps INFO @ Fri, 10 Dec 2021 11:07:59: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 10 Dec 2021 11:07:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.05_model.r INFO @ Fri, 10 Dec 2021 11:07:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:07:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:08:01: 1000000 INFO @ Fri, 10 Dec 2021 11:08:09: 2000000 INFO @ Fri, 10 Dec 2021 11:08:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:08:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:08:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:08:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.05_summits.bed INFO @ Fri, 10 Dec 2021 11:08:14: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (5608 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:08:17: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.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 @ Fri, 10 Dec 2021 11:08:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:08:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:08:26: 4000000 INFO @ Fri, 10 Dec 2021 11:08:30: 1000000 INFO @ Fri, 10 Dec 2021 11:08:30: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 11:08:30: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 11:08:30: #1 total tags in treatment: 4532823 INFO @ Fri, 10 Dec 2021 11:08:30: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:08:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:08:30: #1 tags after filtering in treatment: 4532823 INFO @ Fri, 10 Dec 2021 11:08:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:08:30: #1 finished! INFO @ Fri, 10 Dec 2021 11:08:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:08:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:08:31: #2 number of paired peaks: 3007 INFO @ Fri, 10 Dec 2021 11:08:31: start model_add_line... INFO @ Fri, 10 Dec 2021 11:08:31: start X-correlation... INFO @ Fri, 10 Dec 2021 11:08:31: end of X-cor INFO @ Fri, 10 Dec 2021 11:08:31: #2 finished! INFO @ Fri, 10 Dec 2021 11:08:31: #2 predicted fragment length is 209 bps INFO @ Fri, 10 Dec 2021 11:08:31: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 10 Dec 2021 11:08:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.10_model.r INFO @ Fri, 10 Dec 2021 11:08:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:08:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:08:37: 2000000 INFO @ Fri, 10 Dec 2021 11:08:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:08:44: 3000000 INFO @ Fri, 10 Dec 2021 11:08:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:08:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:08:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.10_summits.bed INFO @ Fri, 10 Dec 2021 11:08:47: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (3393 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:08:51: 4000000 INFO @ Fri, 10 Dec 2021 11:08:54: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 11:08:54: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 11:08:54: #1 total tags in treatment: 4532823 INFO @ Fri, 10 Dec 2021 11:08:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:08:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:08:55: #1 tags after filtering in treatment: 4532823 INFO @ Fri, 10 Dec 2021 11:08:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:08:55: #1 finished! INFO @ Fri, 10 Dec 2021 11:08:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:08:55: #2 number of paired peaks: 3007 INFO @ Fri, 10 Dec 2021 11:08:55: start model_add_line... INFO @ Fri, 10 Dec 2021 11:08:55: start X-correlation... INFO @ Fri, 10 Dec 2021 11:08:55: end of X-cor INFO @ Fri, 10 Dec 2021 11:08:55: #2 finished! INFO @ Fri, 10 Dec 2021 11:08:55: #2 predicted fragment length is 209 bps INFO @ Fri, 10 Dec 2021 11:08:55: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 10 Dec 2021 11:08:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.20_model.r INFO @ Fri, 10 Dec 2021 11:08:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:08:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:09:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:09:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:09:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:09:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6407591/SRX6407591.20_summits.bed INFO @ Fri, 10 Dec 2021 11:09:11: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1504 records, 4 fields): 3 millis CompletedMACS2peakCalling