Job ID = 12266685 SRX = SRX8622120 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16007345 spots for SRR12096680/SRR12096680.sra Written 16007345 spots for SRR12096680/SRR12096680.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267079 ("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: 00:28:17 16007345 reads; of these: 16007345 (100.00%) were paired; of these: 15224232 (95.11%) aligned concordantly 0 times 526732 (3.29%) aligned concordantly exactly 1 time 256381 (1.60%) aligned concordantly >1 times ---- 15224232 pairs aligned concordantly 0 times; of these: 395342 (2.60%) aligned discordantly 1 time ---- 14828890 pairs aligned 0 times concordantly or discordantly; of these: 29657780 mates make up the pairs; of these: 29222775 (98.53%) aligned 0 times 115047 (0.39%) aligned exactly 1 time 319958 (1.08%) aligned >1 times 8.72% overall alignment rate Time searching: 00:28:17 Overall time: 00:28:17 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] 84945 / 1162331 = 0.0731 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 09:38:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.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 09:38:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:38:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:38:12: 1000000 INFO @ Sat, 03 Apr 2021 09:38:21: 2000000 INFO @ Sat, 03 Apr 2021 09:38:27: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:38:27: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:38:27: #1 total tags in treatment: 722304 INFO @ Sat, 03 Apr 2021 09:38:27: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:38:27: #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 09:38:27: #1 tags after filtering in treatment: 680077 INFO @ Sat, 03 Apr 2021 09:38:27: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 03 Apr 2021 09:38:27: #1 finished! INFO @ Sat, 03 Apr 2021 09:38:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:38:27: #2 number of paired peaks: 2012 INFO @ Sat, 03 Apr 2021 09:38:27: start model_add_line... INFO @ Sat, 03 Apr 2021 09:38:27: start X-correlation... INFO @ Sat, 03 Apr 2021 09:38:27: end of X-cor INFO @ Sat, 03 Apr 2021 09:38:27: #2 finished! INFO @ Sat, 03 Apr 2021 09:38:27: #2 predicted fragment length is 183 bps INFO @ Sat, 03 Apr 2021 09:38:27: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 03 Apr 2021 09:38:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.05_model.r WARNING @ Sat, 03 Apr 2021 09:38:27: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:38:27: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Sat, 03 Apr 2021 09:38:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:38:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:38:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:38:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:38:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:38:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:38:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.05_summits.bed INFO @ Sat, 03 Apr 2021 09:38:29: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (811 records, 4 fields): 2 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 09:38:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.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 09:38:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:38:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:38:42: 1000000 INFO @ Sat, 03 Apr 2021 09:38:52: 2000000 INFO @ Sat, 03 Apr 2021 09:38:59: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:38:59: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:38:59: #1 total tags in treatment: 722304 INFO @ Sat, 03 Apr 2021 09:38:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:38:59: #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 09:38:59: #1 tags after filtering in treatment: 680077 INFO @ Sat, 03 Apr 2021 09:38:59: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 03 Apr 2021 09:38:59: #1 finished! INFO @ Sat, 03 Apr 2021 09:38:59: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:38:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:38:59: #2 number of paired peaks: 2012 INFO @ Sat, 03 Apr 2021 09:38:59: start model_add_line... INFO @ Sat, 03 Apr 2021 09:38:59: start X-correlation... INFO @ Sat, 03 Apr 2021 09:38:59: end of X-cor INFO @ Sat, 03 Apr 2021 09:38:59: #2 finished! INFO @ Sat, 03 Apr 2021 09:38:59: #2 predicted fragment length is 183 bps INFO @ Sat, 03 Apr 2021 09:38:59: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 03 Apr 2021 09:38:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.10_model.r WARNING @ Sat, 03 Apr 2021 09:38:59: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:38:59: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Sat, 03 Apr 2021 09:38:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:38:59: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:38:59: #3 Pre-compute pvalue-qvalue table... 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 09:39:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:39:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:39:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:39:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.10_summits.bed INFO @ Sat, 03 Apr 2021 09:39:01: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (282 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:39:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.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 09:39:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:39:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:39:14: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:39:26: 2000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:39:33: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:39:33: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:39:33: #1 total tags in treatment: 722304 INFO @ Sat, 03 Apr 2021 09:39:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:39:33: #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 09:39:33: #1 tags after filtering in treatment: 680077 INFO @ Sat, 03 Apr 2021 09:39:33: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 03 Apr 2021 09:39:33: #1 finished! INFO @ Sat, 03 Apr 2021 09:39:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:39:33: #2 number of paired peaks: 2012 INFO @ Sat, 03 Apr 2021 09:39:33: start model_add_line... INFO @ Sat, 03 Apr 2021 09:39:33: start X-correlation... INFO @ Sat, 03 Apr 2021 09:39:33: end of X-cor INFO @ Sat, 03 Apr 2021 09:39:33: #2 finished! INFO @ Sat, 03 Apr 2021 09:39:33: #2 predicted fragment length is 183 bps INFO @ Sat, 03 Apr 2021 09:39:33: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 03 Apr 2021 09:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.20_model.r WARNING @ Sat, 03 Apr 2021 09:39:33: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:39:33: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Sat, 03 Apr 2021 09:39:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:39:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:39:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:39:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:39:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:39:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622120/SRX8622120.20_summits.bed INFO @ Sat, 03 Apr 2021 09:39:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (130 records, 4 fields): 2 millis CompletedMACS2peakCalling