Job ID = 14171212 SRX = SRX9555331 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6184335 spots for SRR13110829/SRR13110829.sra Written 6184335 spots for SRR13110829/SRR13110829.sra Read 5970382 spots for SRR13110830/SRR13110830.sra Written 5970382 spots for SRR13110830/SRR13110830.sra Read 6121637 spots for SRR13110831/SRR13110831.sra Written 6121637 spots for SRR13110831/SRR13110831.sra Read 5958864 spots for SRR13110832/SRR13110832.sra Written 5958864 spots for SRR13110832/SRR13110832.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171693 ("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: 00:05:55 24235218 reads; of these: 24235218 (100.00%) were paired; of these: 23606177 (97.40%) aligned concordantly 0 times 460614 (1.90%) aligned concordantly exactly 1 time 168427 (0.69%) aligned concordantly >1 times ---- 23606177 pairs aligned concordantly 0 times; of these: 8907 (0.04%) aligned discordantly 1 time ---- 23597270 pairs aligned 0 times concordantly or discordantly; of these: 47194540 mates make up the pairs; of these: 47128118 (99.86%) aligned 0 times 19044 (0.04%) aligned exactly 1 time 47378 (0.10%) aligned >1 times 2.77% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 10236 / 466913 = 0.0219 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 10:43:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.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 10:43:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:43:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:43:49: 1000000 INFO @ Sat, 11 Dec 2021 10:43:51: #1 tag size is determined as 78 bps INFO @ Sat, 11 Dec 2021 10:43:51: #1 tag size = 78 INFO @ Sat, 11 Dec 2021 10:43:51: #1 total tags in treatment: 618865 INFO @ Sat, 11 Dec 2021 10:43:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:43:51: #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 10:43:51: #1 tags after filtering in treatment: 584811 INFO @ Sat, 11 Dec 2021 10:43:51: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 10:43:51: #1 finished! INFO @ Sat, 11 Dec 2021 10:43:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:43:51: #2 number of paired peaks: 4349 INFO @ Sat, 11 Dec 2021 10:43:51: start model_add_line... INFO @ Sat, 11 Dec 2021 10:43:51: start X-correlation... INFO @ Sat, 11 Dec 2021 10:43:51: end of X-cor INFO @ Sat, 11 Dec 2021 10:43:51: #2 finished! INFO @ Sat, 11 Dec 2021 10:43:51: #2 predicted fragment length is 112 bps INFO @ Sat, 11 Dec 2021 10:43:51: #2 alternative fragment length(s) may be 112 bps INFO @ Sat, 11 Dec 2021 10:43:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.05_model.r WARNING @ Sat, 11 Dec 2021 10:43:51: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:43:51: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Sat, 11 Dec 2021 10:43:51: #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 10:43:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:43:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:43:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:43:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:43:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:43:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.05_summits.bed INFO @ Sat, 11 Dec 2021 10:43:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (981 records, 4 fields): 3 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 10:44:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.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 10:44:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:44:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:44:19: 1000000 INFO @ Sat, 11 Dec 2021 10:44:21: #1 tag size is determined as 78 bps INFO @ Sat, 11 Dec 2021 10:44:21: #1 tag size = 78 INFO @ Sat, 11 Dec 2021 10:44:21: #1 total tags in treatment: 618865 INFO @ Sat, 11 Dec 2021 10:44:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:44:21: #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 10:44:21: #1 tags after filtering in treatment: 584811 INFO @ Sat, 11 Dec 2021 10:44:21: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 10:44:21: #1 finished! INFO @ Sat, 11 Dec 2021 10:44:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:44:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:44:21: #2 number of paired peaks: 4349 INFO @ Sat, 11 Dec 2021 10:44:21: start model_add_line... INFO @ Sat, 11 Dec 2021 10:44:21: start X-correlation... INFO @ Sat, 11 Dec 2021 10:44:21: end of X-cor INFO @ Sat, 11 Dec 2021 10:44:21: #2 finished! INFO @ Sat, 11 Dec 2021 10:44:21: #2 predicted fragment length is 112 bps INFO @ Sat, 11 Dec 2021 10:44:21: #2 alternative fragment length(s) may be 112 bps INFO @ Sat, 11 Dec 2021 10:44:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.10_model.r WARNING @ Sat, 11 Dec 2021 10:44:21: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:44:21: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Sat, 11 Dec 2021 10:44:21: #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 10:44:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:44:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:44:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:44:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:44:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.10_summits.bed INFO @ Sat, 11 Dec 2021 10:44:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (248 records, 4 fields): 17 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 10:44:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.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 10:44:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:44:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:44:49: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 10:44:51: #1 tag size is determined as 78 bps INFO @ Sat, 11 Dec 2021 10:44:51: #1 tag size = 78 INFO @ Sat, 11 Dec 2021 10:44:51: #1 total tags in treatment: 618865 INFO @ Sat, 11 Dec 2021 10:44:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:44:51: #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 10:44:51: #1 tags after filtering in treatment: 584811 INFO @ Sat, 11 Dec 2021 10:44:51: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 10:44:51: #1 finished! INFO @ Sat, 11 Dec 2021 10:44:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:44:51: #2 number of paired peaks: 4349 INFO @ Sat, 11 Dec 2021 10:44:51: start model_add_line... INFO @ Sat, 11 Dec 2021 10:44:51: start X-correlation... INFO @ Sat, 11 Dec 2021 10:44:51: end of X-cor INFO @ Sat, 11 Dec 2021 10:44:51: #2 finished! INFO @ Sat, 11 Dec 2021 10:44:51: #2 predicted fragment length is 112 bps INFO @ Sat, 11 Dec 2021 10:44:51: #2 alternative fragment length(s) may be 112 bps INFO @ Sat, 11 Dec 2021 10:44:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.20_model.r WARNING @ Sat, 11 Dec 2021 10:44:51: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:44:51: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Sat, 11 Dec 2021 10:44:51: #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 10:44:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:44:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:44:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:44:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:44:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:44:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555331/SRX9555331.20_summits.bed INFO @ Sat, 11 Dec 2021 10:44:53: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。