Job ID = 14171732 SRX = SRX10386227 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11841076 spots for SRR14009292/SRR14009292.sra Written 11841076 spots for SRR14009292/SRR14009292.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172164 ("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: 00:04:55 11841076 reads; of these: 11841076 (100.00%) were paired; of these: 9982244 (84.30%) aligned concordantly 0 times 1199565 (10.13%) aligned concordantly exactly 1 time 659267 (5.57%) aligned concordantly >1 times ---- 9982244 pairs aligned concordantly 0 times; of these: 54903 (0.55%) aligned discordantly 1 time ---- 9927341 pairs aligned 0 times concordantly or discordantly; of these: 19854682 mates make up the pairs; of these: 19708035 (99.26%) aligned 0 times 60370 (0.30%) aligned exactly 1 time 86277 (0.43%) aligned >1 times 16.78% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 200958 / 1902547 = 0.1056 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 @ Sat, 11 Dec 2021 12:45:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.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, 11 Dec 2021 12:45:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:45:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:45:38: 1000000 INFO @ Sat, 11 Dec 2021 12:45:44: 2000000 INFO @ Sat, 11 Dec 2021 12:45:49: 3000000 INFO @ Sat, 11 Dec 2021 12:45:52: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:45:52: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:45:52: #1 total tags in treatment: 1664241 INFO @ Sat, 11 Dec 2021 12:45:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:45:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:45:52: #1 tags after filtering in treatment: 1497024 INFO @ Sat, 11 Dec 2021 12:45:52: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 12:45:52: #1 finished! INFO @ Sat, 11 Dec 2021 12:45:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:45:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:45:52: #2 number of paired peaks: 1223 INFO @ Sat, 11 Dec 2021 12:45:52: start model_add_line... INFO @ Sat, 11 Dec 2021 12:45:53: start X-correlation... INFO @ Sat, 11 Dec 2021 12:45:53: end of X-cor INFO @ Sat, 11 Dec 2021 12:45:53: #2 finished! INFO @ Sat, 11 Dec 2021 12:45:53: #2 predicted fragment length is 82 bps INFO @ Sat, 11 Dec 2021 12:45:53: #2 alternative fragment length(s) may be 82 bps INFO @ Sat, 11 Dec 2021 12:45:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.05_model.r WARNING @ Sat, 11 Dec 2021 12:45:53: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:45:53: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Sat, 11 Dec 2021 12:45:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:45:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:45:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:45:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:45:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:45:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:45:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.05_summits.bed INFO @ Sat, 11 Dec 2021 12:45:57: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1520 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 12:46:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.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, 11 Dec 2021 12:46:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:46:03: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:46:08: 1000000 INFO @ Sat, 11 Dec 2021 12:46:14: 2000000 INFO @ Sat, 11 Dec 2021 12:46:19: 3000000 INFO @ Sat, 11 Dec 2021 12:46:23: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:46:23: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:46:23: #1 total tags in treatment: 1664241 INFO @ Sat, 11 Dec 2021 12:46:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:46:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:46:23: #1 tags after filtering in treatment: 1497024 INFO @ Sat, 11 Dec 2021 12:46:23: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 12:46:23: #1 finished! INFO @ Sat, 11 Dec 2021 12:46:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:46:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:46:23: #2 number of paired peaks: 1223 INFO @ Sat, 11 Dec 2021 12:46:23: start model_add_line... INFO @ Sat, 11 Dec 2021 12:46:23: start X-correlation... INFO @ Sat, 11 Dec 2021 12:46:23: end of X-cor INFO @ Sat, 11 Dec 2021 12:46:23: #2 finished! INFO @ Sat, 11 Dec 2021 12:46:23: #2 predicted fragment length is 82 bps INFO @ Sat, 11 Dec 2021 12:46:23: #2 alternative fragment length(s) may be 82 bps INFO @ Sat, 11 Dec 2021 12:46:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.10_model.r WARNING @ Sat, 11 Dec 2021 12:46:23: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:46:23: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Sat, 11 Dec 2021 12:46:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:46:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:46:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:46:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:46:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:46:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:46:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.10_summits.bed INFO @ Sat, 11 Dec 2021 12:46:28: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (833 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 12:46:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.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, 11 Dec 2021 12:46:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:46:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:46:38: 1000000 INFO @ Sat, 11 Dec 2021 12:46:44: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:46:50: 3000000 INFO @ Sat, 11 Dec 2021 12:46:53: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:46:53: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:46:53: #1 total tags in treatment: 1664241 INFO @ Sat, 11 Dec 2021 12:46:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:46:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:46:53: #1 tags after filtering in treatment: 1497024 INFO @ Sat, 11 Dec 2021 12:46:53: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 12:46:53: #1 finished! INFO @ Sat, 11 Dec 2021 12:46:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:46:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:46:53: #2 number of paired peaks: 1223 INFO @ Sat, 11 Dec 2021 12:46:53: start model_add_line... INFO @ Sat, 11 Dec 2021 12:46:53: start X-correlation... INFO @ Sat, 11 Dec 2021 12:46:53: end of X-cor INFO @ Sat, 11 Dec 2021 12:46:53: #2 finished! INFO @ Sat, 11 Dec 2021 12:46:53: #2 predicted fragment length is 82 bps INFO @ Sat, 11 Dec 2021 12:46:53: #2 alternative fragment length(s) may be 82 bps INFO @ Sat, 11 Dec 2021 12:46:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.20_model.r WARNING @ Sat, 11 Dec 2021 12:46:53: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:46:53: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Sat, 11 Dec 2021 12:46:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:46:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:46:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:46:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:46:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:46:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:46:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386227/SRX10386227.20_summits.bed INFO @ Sat, 11 Dec 2021 12:46:58: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (359 records, 4 fields): 2 millis CompletedMACS2peakCalling