Job ID = 6627052 SRX = SRX8347275 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18610212 spots for SRR11795458/SRR11795458.sra Written 18610212 spots for SRR11795458/SRR11795458.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627411 ("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: 00:55:33 18610212 reads; of these: 18610212 (100.00%) were paired; of these: 5244610 (28.18%) aligned concordantly 0 times 10725287 (57.63%) aligned concordantly exactly 1 time 2640315 (14.19%) aligned concordantly >1 times ---- 5244610 pairs aligned concordantly 0 times; of these: 1035259 (19.74%) aligned discordantly 1 time ---- 4209351 pairs aligned 0 times concordantly or discordantly; of these: 8418702 mates make up the pairs; of these: 7454121 (88.54%) aligned 0 times 387064 (4.60%) aligned exactly 1 time 577517 (6.86%) aligned >1 times 79.97% overall alignment rate Time searching: 00:55:33 Overall time: 00:55:33 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 24 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] 6971901 / 14345621 = 0.4860 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:46:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.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 @ Tue, 14 Jul 2020 10:46:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:46:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:46:46: 1000000 INFO @ Tue, 14 Jul 2020 10:46:56: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:47:05: 3000000 INFO @ Tue, 14 Jul 2020 10:47:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.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 @ Tue, 14 Jul 2020 10:47:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:47:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:47:15: 4000000 INFO @ Tue, 14 Jul 2020 10:47:16: 1000000 INFO @ Tue, 14 Jul 2020 10:47:25: 2000000 INFO @ Tue, 14 Jul 2020 10:47:26: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:47:35: 3000000 INFO @ Tue, 14 Jul 2020 10:47:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.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 @ Tue, 14 Jul 2020 10:47:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:47:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:47:38: 6000000 INFO @ Tue, 14 Jul 2020 10:47:45: 4000000 INFO @ Tue, 14 Jul 2020 10:47:47: 1000000 INFO @ Tue, 14 Jul 2020 10:47:49: 7000000 INFO @ Tue, 14 Jul 2020 10:47:55: 5000000 INFO @ Tue, 14 Jul 2020 10:47:59: 2000000 INFO @ Tue, 14 Jul 2020 10:47:59: 8000000 INFO @ Tue, 14 Jul 2020 10:48:05: 6000000 INFO @ Tue, 14 Jul 2020 10:48:09: 9000000 INFO @ Tue, 14 Jul 2020 10:48:10: 3000000 INFO @ Tue, 14 Jul 2020 10:48:16: 7000000 INFO @ Tue, 14 Jul 2020 10:48:20: 10000000 INFO @ Tue, 14 Jul 2020 10:48:21: 4000000 INFO @ Tue, 14 Jul 2020 10:48:27: 8000000 INFO @ Tue, 14 Jul 2020 10:48:31: 11000000 INFO @ Tue, 14 Jul 2020 10:48:32: 5000000 INFO @ Tue, 14 Jul 2020 10:48:37: 9000000 INFO @ Tue, 14 Jul 2020 10:48:43: 12000000 INFO @ Tue, 14 Jul 2020 10:48:43: 6000000 INFO @ Tue, 14 Jul 2020 10:48:47: 10000000 INFO @ Tue, 14 Jul 2020 10:48:54: 13000000 INFO @ Tue, 14 Jul 2020 10:48:54: 7000000 INFO @ Tue, 14 Jul 2020 10:48:57: 11000000 INFO @ Tue, 14 Jul 2020 10:49:03: 8000000 INFO @ Tue, 14 Jul 2020 10:49:05: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:49:08: 12000000 INFO @ Tue, 14 Jul 2020 10:49:14: 9000000 INFO @ Tue, 14 Jul 2020 10:49:17: 15000000 INFO @ Tue, 14 Jul 2020 10:49:18: 13000000 INFO @ Tue, 14 Jul 2020 10:49:25: 10000000 INFO @ Tue, 14 Jul 2020 10:49:26: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:49:26: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:49:26: #1 total tags in treatment: 6747243 INFO @ Tue, 14 Jul 2020 10:49:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:49:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:49:27: #1 tags after filtering in treatment: 6418062 INFO @ Tue, 14 Jul 2020 10:49:27: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 10:49:27: #1 finished! INFO @ Tue, 14 Jul 2020 10:49:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:49:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:49:27: #2 number of paired peaks: 1853 INFO @ Tue, 14 Jul 2020 10:49:27: start model_add_line... INFO @ Tue, 14 Jul 2020 10:49:27: start X-correlation... INFO @ Tue, 14 Jul 2020 10:49:27: end of X-cor INFO @ Tue, 14 Jul 2020 10:49:27: #2 finished! INFO @ Tue, 14 Jul 2020 10:49:27: #2 predicted fragment length is 236 bps INFO @ Tue, 14 Jul 2020 10:49:27: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 14 Jul 2020 10:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.05_model.r WARNING @ Tue, 14 Jul 2020 10:49:27: #2 Since the d (236) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:49:27: #2 You may need to consider one of the other alternative d(s): 236 WARNING @ Tue, 14 Jul 2020 10:49:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:49:27: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:49:28: 14000000 INFO @ Tue, 14 Jul 2020 10:49:36: 11000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:49:39: 15000000 INFO @ Tue, 14 Jul 2020 10:49:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:49:47: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:49:47: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:49:47: #1 total tags in treatment: 6747243 INFO @ Tue, 14 Jul 2020 10:49:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:49:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:49:47: #1 tags after filtering in treatment: 6418062 INFO @ Tue, 14 Jul 2020 10:49:47: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 10:49:47: #1 finished! INFO @ Tue, 14 Jul 2020 10:49:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:49:47: 12000000 INFO @ Tue, 14 Jul 2020 10:49:48: #2 number of paired peaks: 1853 INFO @ Tue, 14 Jul 2020 10:49:48: start model_add_line... INFO @ Tue, 14 Jul 2020 10:49:48: start X-correlation... INFO @ Tue, 14 Jul 2020 10:49:48: end of X-cor INFO @ Tue, 14 Jul 2020 10:49:48: #2 finished! INFO @ Tue, 14 Jul 2020 10:49:48: #2 predicted fragment length is 236 bps INFO @ Tue, 14 Jul 2020 10:49:48: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 14 Jul 2020 10:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.10_model.r WARNING @ Tue, 14 Jul 2020 10:49:48: #2 Since the d (236) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:49:48: #2 You may need to consider one of the other alternative d(s): 236 WARNING @ Tue, 14 Jul 2020 10:49:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:49:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:49:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:49:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:49:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.05_summits.bed INFO @ Tue, 14 Jul 2020 10:49:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6622 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:49:58: 13000000 INFO @ Tue, 14 Jul 2020 10:50:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:50:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:50:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:50:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.10_summits.bed INFO @ Tue, 14 Jul 2020 10:50:09: Done! INFO @ Tue, 14 Jul 2020 10:50:09: 14000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4204 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:50:19: 15000000 INFO @ Tue, 14 Jul 2020 10:50:27: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:50:27: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:50:27: #1 total tags in treatment: 6747243 INFO @ Tue, 14 Jul 2020 10:50:27: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:50:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:50:27: #1 tags after filtering in treatment: 6418062 INFO @ Tue, 14 Jul 2020 10:50:27: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 10:50:27: #1 finished! INFO @ Tue, 14 Jul 2020 10:50:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:50:28: #2 number of paired peaks: 1853 INFO @ Tue, 14 Jul 2020 10:50:28: start model_add_line... INFO @ Tue, 14 Jul 2020 10:50:28: start X-correlation... INFO @ Tue, 14 Jul 2020 10:50:28: end of X-cor INFO @ Tue, 14 Jul 2020 10:50:28: #2 finished! INFO @ Tue, 14 Jul 2020 10:50:28: #2 predicted fragment length is 236 bps INFO @ Tue, 14 Jul 2020 10:50:28: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 14 Jul 2020 10:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.20_model.r WARNING @ Tue, 14 Jul 2020 10:50:28: #2 Since the d (236) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:50:28: #2 You may need to consider one of the other alternative d(s): 236 WARNING @ Tue, 14 Jul 2020 10:50:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:50:28: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:50:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:50:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:50:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:50:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347275/SRX8347275.20_summits.bed INFO @ Tue, 14 Jul 2020 10:50:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2337 records, 4 fields): 3 millis CompletedMACS2peakCalling