Job ID = 12264857 SRX = SRX3032256 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15085276 spots for SRR5863946/SRR5863946.sra Written 15085276 spots for SRR5863946/SRR5863946.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265023 ("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 15085276 reads; of these: 15085276 (100.00%) were unpaired; of these: 6681102 (44.29%) aligned 0 times 2553173 (16.92%) aligned exactly 1 time 5851001 (38.79%) aligned >1 times 55.71% 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] 6351039 / 8404174 = 0.7557 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 05:58:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.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 @ Sat, 03 Apr 2021 05:58:38: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:58:38: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 05:58:45: 1000000 INFO @ Sat, 03 Apr 2021 05:58:52: 2000000 INFO @ Sat, 03 Apr 2021 05:58:52: #1 tag size is determined as 20 bps INFO @ Sat, 03 Apr 2021 05:58:52: #1 tag size = 20 INFO @ Sat, 03 Apr 2021 05:58:52: #1 total tags in treatment: 2053135 INFO @ Sat, 03 Apr 2021 05:58:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 05:58:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 05:58:52: #1 tags after filtering in treatment: 2053135 INFO @ Sat, 03 Apr 2021 05:58:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 05:58:52: #1 finished! INFO @ Sat, 03 Apr 2021 05:58:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 05:58:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 05:58:53: #2 number of paired peaks: 3934 INFO @ Sat, 03 Apr 2021 05:58:53: start model_add_line... INFO @ Sat, 03 Apr 2021 05:58:53: start X-correlation... INFO @ Sat, 03 Apr 2021 05:58:53: end of X-cor INFO @ Sat, 03 Apr 2021 05:58:53: #2 finished! INFO @ Sat, 03 Apr 2021 05:58:53: #2 predicted fragment length is 76 bps INFO @ Sat, 03 Apr 2021 05:58:53: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 03 Apr 2021 05:58:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.05_model.r INFO @ Sat, 03 Apr 2021 05:58:53: #3 Call peaks... INFO @ Sat, 03 Apr 2021 05:58:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 05:58:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 05:59:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.05_peaks.xls INFO @ Sat, 03 Apr 2021 05:59:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 05:59:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.05_summits.bed INFO @ Sat, 03 Apr 2021 05:59:03: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6828 records, 4 fields): 22 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 05:59:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.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 @ Sat, 03 Apr 2021 05:59:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:59:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 05:59:14: 1000000 INFO @ Sat, 03 Apr 2021 05:59:20: 2000000 INFO @ Sat, 03 Apr 2021 05:59:21: #1 tag size is determined as 20 bps INFO @ Sat, 03 Apr 2021 05:59:21: #1 tag size = 20 INFO @ Sat, 03 Apr 2021 05:59:21: #1 total tags in treatment: 2053135 INFO @ Sat, 03 Apr 2021 05:59:21: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 05:59:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 05:59:21: #1 tags after filtering in treatment: 2053135 INFO @ Sat, 03 Apr 2021 05:59:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 05:59:21: #1 finished! INFO @ Sat, 03 Apr 2021 05:59:21: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 05:59:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 05:59:21: #2 number of paired peaks: 3934 INFO @ Sat, 03 Apr 2021 05:59:21: start model_add_line... INFO @ Sat, 03 Apr 2021 05:59:21: start X-correlation... INFO @ Sat, 03 Apr 2021 05:59:21: end of X-cor INFO @ Sat, 03 Apr 2021 05:59:21: #2 finished! INFO @ Sat, 03 Apr 2021 05:59:21: #2 predicted fragment length is 76 bps INFO @ Sat, 03 Apr 2021 05:59:21: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 03 Apr 2021 05:59:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.10_model.r INFO @ Sat, 03 Apr 2021 05:59:21: #3 Call peaks... INFO @ Sat, 03 Apr 2021 05:59:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 05:59:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 05:59:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.10_peaks.xls INFO @ Sat, 03 Apr 2021 05:59:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 05:59:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.10_summits.bed INFO @ Sat, 03 Apr 2021 05:59:31: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (3033 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 05:59:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.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 @ Sat, 03 Apr 2021 05:59:38: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:59:38: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 05:59:45: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 05:59:52: 2000000 INFO @ Sat, 03 Apr 2021 05:59:52: #1 tag size is determined as 20 bps INFO @ Sat, 03 Apr 2021 05:59:52: #1 tag size = 20 INFO @ Sat, 03 Apr 2021 05:59:52: #1 total tags in treatment: 2053135 INFO @ Sat, 03 Apr 2021 05:59:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 05:59:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 05:59:52: #1 tags after filtering in treatment: 2053135 INFO @ Sat, 03 Apr 2021 05:59:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 05:59:52: #1 finished! INFO @ Sat, 03 Apr 2021 05:59:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 05:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 05:59:53: #2 number of paired peaks: 3934 INFO @ Sat, 03 Apr 2021 05:59:53: start model_add_line... INFO @ Sat, 03 Apr 2021 05:59:53: start X-correlation... INFO @ Sat, 03 Apr 2021 05:59:53: end of X-cor INFO @ Sat, 03 Apr 2021 05:59:53: #2 finished! INFO @ Sat, 03 Apr 2021 05:59:53: #2 predicted fragment length is 76 bps INFO @ Sat, 03 Apr 2021 05:59:53: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 03 Apr 2021 05:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.20_model.r INFO @ Sat, 03 Apr 2021 05:59:53: #3 Call peaks... INFO @ Sat, 03 Apr 2021 05:59:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 05:59:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:00:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032256/SRX3032256.20_summits.bed INFO @ Sat, 03 Apr 2021 06:00:03: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (490 records, 4 fields): 3 millis CompletedMACS2peakCalling