Job ID = 14172001 SRX = SRX10089736 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15986851 spots for SRR13700623/SRR13700623.sra Written 15986851 spots for SRR13700623/SRR13700623.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172524 ("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: 00:18:12 15986851 reads; of these: 15986851 (100.00%) were paired; of these: 1439704 (9.01%) aligned concordantly 0 times 11517221 (72.04%) aligned concordantly exactly 1 time 3029926 (18.95%) aligned concordantly >1 times ---- 1439704 pairs aligned concordantly 0 times; of these: 199176 (13.83%) aligned discordantly 1 time ---- 1240528 pairs aligned 0 times concordantly or discordantly; of these: 2481056 mates make up the pairs; of these: 1862594 (75.07%) aligned 0 times 411830 (16.60%) aligned exactly 1 time 206632 (8.33%) aligned >1 times 94.17% overall alignment rate Time searching: 00:18:12 Overall time: 00:18:12 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_sort_core] merging from 16 files... [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] 1636012 / 11225873 = 0.1457 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 14:14:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.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 14:14:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:14:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:14:07: 1000000 INFO @ Sat, 11 Dec 2021 14:14:14: 2000000 INFO @ Sat, 11 Dec 2021 14:14:21: 3000000 INFO @ Sat, 11 Dec 2021 14:14:28: 4000000 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 14:14:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.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 14:14:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:14:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:14:35: 5000000 INFO @ Sat, 11 Dec 2021 14:14:38: 1000000 INFO @ Sat, 11 Dec 2021 14:14:42: 6000000 INFO @ Sat, 11 Dec 2021 14:14:46: 2000000 INFO @ Sat, 11 Dec 2021 14:14:49: 7000000 INFO @ Sat, 11 Dec 2021 14:14:53: 3000000 INFO @ Sat, 11 Dec 2021 14:14:57: 8000000 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 14:15:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.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 14:15:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:15:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:15:01: 4000000 INFO @ Sat, 11 Dec 2021 14:15:04: 9000000 INFO @ Sat, 11 Dec 2021 14:15:08: 1000000 INFO @ Sat, 11 Dec 2021 14:15:08: 5000000 INFO @ Sat, 11 Dec 2021 14:15:12: 10000000 INFO @ Sat, 11 Dec 2021 14:15:16: 2000000 INFO @ Sat, 11 Dec 2021 14:15:16: 6000000 INFO @ Sat, 11 Dec 2021 14:15:19: 11000000 INFO @ Sat, 11 Dec 2021 14:15:23: 3000000 INFO @ Sat, 11 Dec 2021 14:15:23: 7000000 INFO @ Sat, 11 Dec 2021 14:15:27: 12000000 INFO @ Sat, 11 Dec 2021 14:15:31: 4000000 INFO @ Sat, 11 Dec 2021 14:15:31: 8000000 INFO @ Sat, 11 Dec 2021 14:15:34: 13000000 INFO @ Sat, 11 Dec 2021 14:15:38: 5000000 INFO @ Sat, 11 Dec 2021 14:15:39: 9000000 INFO @ Sat, 11 Dec 2021 14:15:41: 14000000 INFO @ Sat, 11 Dec 2021 14:15:46: 6000000 INFO @ Sat, 11 Dec 2021 14:15:46: 10000000 INFO @ Sat, 11 Dec 2021 14:15:49: 15000000 INFO @ Sat, 11 Dec 2021 14:15:53: 7000000 INFO @ Sat, 11 Dec 2021 14:15:54: 11000000 INFO @ Sat, 11 Dec 2021 14:15:56: 16000000 INFO @ Sat, 11 Dec 2021 14:16:01: 8000000 INFO @ Sat, 11 Dec 2021 14:16:01: 12000000 INFO @ Sat, 11 Dec 2021 14:16:04: 17000000 INFO @ Sat, 11 Dec 2021 14:16:08: 13000000 INFO @ Sat, 11 Dec 2021 14:16:08: 9000000 INFO @ Sat, 11 Dec 2021 14:16:11: 18000000 INFO @ Sat, 11 Dec 2021 14:16:16: 14000000 INFO @ Sat, 11 Dec 2021 14:16:16: 10000000 INFO @ Sat, 11 Dec 2021 14:16:19: 19000000 INFO @ Sat, 11 Dec 2021 14:16:23: 15000000 INFO @ Sat, 11 Dec 2021 14:16:23: 11000000 INFO @ Sat, 11 Dec 2021 14:16:26: 20000000 INFO @ Sat, 11 Dec 2021 14:16:30: 16000000 INFO @ Sat, 11 Dec 2021 14:16:31: 12000000 INFO @ Sat, 11 Dec 2021 14:16:33: 21000000 INFO @ Sat, 11 Dec 2021 14:16:38: 17000000 INFO @ Sat, 11 Dec 2021 14:16:39: 13000000 INFO @ Sat, 11 Dec 2021 14:16:40: 22000000 INFO @ Sat, 11 Dec 2021 14:16:45: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:16:46: 14000000 INFO @ Sat, 11 Dec 2021 14:16:48: 23000000 INFO @ Sat, 11 Dec 2021 14:16:52: 19000000 INFO @ Sat, 11 Dec 2021 14:16:54: 15000000 INFO @ Sat, 11 Dec 2021 14:16:55: 24000000 INFO @ Sat, 11 Dec 2021 14:16:59: 20000000 INFO @ Sat, 11 Dec 2021 14:17:01: 16000000 INFO @ Sat, 11 Dec 2021 14:17:03: 25000000 INFO @ Sat, 11 Dec 2021 14:17:07: 21000000 INFO @ Sat, 11 Dec 2021 14:17:09: 17000000 INFO @ Sat, 11 Dec 2021 14:17:10: 26000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:17:15: 22000000 INFO @ Sat, 11 Dec 2021 14:17:16: 18000000 INFO @ Sat, 11 Dec 2021 14:17:17: #1 tag size is determined as 67 bps INFO @ Sat, 11 Dec 2021 14:17:17: #1 tag size = 67 INFO @ Sat, 11 Dec 2021 14:17:17: #1 total tags in treatment: 12912971 INFO @ Sat, 11 Dec 2021 14:17:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:17:17: #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 14:17:17: #1 tags after filtering in treatment: 8292234 INFO @ Sat, 11 Dec 2021 14:17:17: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 11 Dec 2021 14:17:17: #1 finished! INFO @ Sat, 11 Dec 2021 14:17:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:17:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:17:18: #2 number of paired peaks: 4205 INFO @ Sat, 11 Dec 2021 14:17:18: start model_add_line... INFO @ Sat, 11 Dec 2021 14:17:18: start X-correlation... INFO @ Sat, 11 Dec 2021 14:17:18: end of X-cor INFO @ Sat, 11 Dec 2021 14:17:18: #2 finished! INFO @ Sat, 11 Dec 2021 14:17:18: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 14:17:18: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 11 Dec 2021 14:17:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.05_model.r WARNING @ Sat, 11 Dec 2021 14:17:18: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:17:18: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 11 Dec 2021 14:17:18: #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 14:17:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:17:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:17:23: 23000000 INFO @ Sat, 11 Dec 2021 14:17:24: 19000000 INFO @ Sat, 11 Dec 2021 14:17:31: 24000000 INFO @ Sat, 11 Dec 2021 14:17:31: 20000000 INFO @ Sat, 11 Dec 2021 14:17:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:17:38: 21000000 INFO @ Sat, 11 Dec 2021 14:17:39: 25000000 INFO @ Sat, 11 Dec 2021 14:17:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:17:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:17:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.05_summits.bed INFO @ Sat, 11 Dec 2021 14:17:44: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (16075 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:17:46: 22000000 INFO @ Sat, 11 Dec 2021 14:17:47: 26000000 INFO @ Sat, 11 Dec 2021 14:17:53: #1 tag size is determined as 67 bps INFO @ Sat, 11 Dec 2021 14:17:53: #1 tag size = 67 INFO @ Sat, 11 Dec 2021 14:17:53: #1 total tags in treatment: 12912971 INFO @ Sat, 11 Dec 2021 14:17:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:17:53: #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 14:17:53: 23000000 INFO @ Sat, 11 Dec 2021 14:17:53: #1 tags after filtering in treatment: 8292234 INFO @ Sat, 11 Dec 2021 14:17:53: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 11 Dec 2021 14:17:53: #1 finished! INFO @ Sat, 11 Dec 2021 14:17:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:17:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:17:54: #2 number of paired peaks: 4205 INFO @ Sat, 11 Dec 2021 14:17:54: start model_add_line... INFO @ Sat, 11 Dec 2021 14:17:54: start X-correlation... INFO @ Sat, 11 Dec 2021 14:17:54: end of X-cor INFO @ Sat, 11 Dec 2021 14:17:54: #2 finished! INFO @ Sat, 11 Dec 2021 14:17:54: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 14:17:54: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 11 Dec 2021 14:17:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.10_model.r WARNING @ Sat, 11 Dec 2021 14:17:54: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:17:54: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 11 Dec 2021 14:17:54: #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 14:17:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:17:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:18:00: 24000000 INFO @ Sat, 11 Dec 2021 14:18:08: 25000000 INFO @ Sat, 11 Dec 2021 14:18:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:18:15: 26000000 INFO @ Sat, 11 Dec 2021 14:18:20: #1 tag size is determined as 67 bps INFO @ Sat, 11 Dec 2021 14:18:20: #1 tag size = 67 INFO @ Sat, 11 Dec 2021 14:18:20: #1 total tags in treatment: 12912971 INFO @ Sat, 11 Dec 2021 14:18:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:18:20: #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 14:18:21: #1 tags after filtering in treatment: 8292234 INFO @ Sat, 11 Dec 2021 14:18:21: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 11 Dec 2021 14:18:21: #1 finished! INFO @ Sat, 11 Dec 2021 14:18:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:18:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:18:22: #2 number of paired peaks: 4205 INFO @ Sat, 11 Dec 2021 14:18:22: start model_add_line... INFO @ Sat, 11 Dec 2021 14:18:22: start X-correlation... INFO @ Sat, 11 Dec 2021 14:18:22: end of X-cor INFO @ Sat, 11 Dec 2021 14:18:22: #2 finished! INFO @ Sat, 11 Dec 2021 14:18:22: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 14:18:22: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 11 Dec 2021 14:18:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.20_model.r WARNING @ Sat, 11 Dec 2021 14:18:22: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:18:22: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 11 Dec 2021 14:18:22: #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 14:18:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:18:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:18:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:18:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:18:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.10_summits.bed INFO @ Sat, 11 Dec 2021 14:18:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10679 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:18:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:18:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:18:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:18:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089736/SRX10089736.20_summits.bed INFO @ Sat, 11 Dec 2021 14:18:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4773 records, 4 fields): 6 millis CompletedMACS2peakCalling