Job ID = 6627047 SRX = SRX8325353 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:36:37 prefetch.2.10.7: 1) Downloading 'SRR11772159'... 2020-07-14T00:36:37 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:38:37 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:38:38 prefetch.2.10.7: 'SRR11772159' is valid 2020-07-14T00:38:38 prefetch.2.10.7: 1) 'SRR11772159' was downloaded successfully 2020-07-14T00:38:38 prefetch.2.10.7: 'SRR11772159' has 0 unresolved dependencies Read 3204820 spots for SRR11772159/SRR11772159.sra Written 3204820 spots for SRR11772159/SRR11772159.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627273 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:50 3204820 reads; of these: 3204820 (100.00%) were paired; of these: 1111772 (34.69%) aligned concordantly 0 times 1673280 (52.21%) aligned concordantly exactly 1 time 419768 (13.10%) aligned concordantly >1 times ---- 1111772 pairs aligned concordantly 0 times; of these: 487997 (43.89%) aligned discordantly 1 time ---- 623775 pairs aligned 0 times concordantly or discordantly; of these: 1247550 mates make up the pairs; of these: 608673 (48.79%) aligned 0 times 355671 (28.51%) aligned exactly 1 time 283206 (22.70%) aligned >1 times 90.50% overall alignment rate Time searching: 00:08:51 Overall time: 00:08:51 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 8 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] 799577 / 2499624 = 0.3199 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 09:50:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.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 09:50:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:50:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:51:07: 1000000 INFO @ Tue, 14 Jul 2020 09:51:15: 2000000 INFO @ Tue, 14 Jul 2020 09:51:25: 3000000 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 09:51:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.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 09:51:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:51:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:51:35: 4000000 INFO @ Tue, 14 Jul 2020 09:51:37: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 09:51:37: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 09:51:37: #1 total tags in treatment: 1442506 INFO @ Tue, 14 Jul 2020 09:51:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:51:37: #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 09:51:37: #1 tags after filtering in treatment: 1380079 INFO @ Tue, 14 Jul 2020 09:51:37: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 09:51:37: #1 finished! INFO @ Tue, 14 Jul 2020 09:51:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:51:37: #2 number of paired peaks: 2014 INFO @ Tue, 14 Jul 2020 09:51:37: start model_add_line... INFO @ Tue, 14 Jul 2020 09:51:37: start X-correlation... INFO @ Tue, 14 Jul 2020 09:51:37: end of X-cor INFO @ Tue, 14 Jul 2020 09:51:37: #2 finished! INFO @ Tue, 14 Jul 2020 09:51:37: #2 predicted fragment length is 233 bps INFO @ Tue, 14 Jul 2020 09:51:37: #2 alternative fragment length(s) may be 233 bps INFO @ Tue, 14 Jul 2020 09:51:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.05_model.r WARNING @ Tue, 14 Jul 2020 09:51:37: #2 Since the d (233) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:51:37: #2 You may need to consider one of the other alternative d(s): 233 WARNING @ Tue, 14 Jul 2020 09:51:37: #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 09:51:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:51:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:51:40: 1000000 INFO @ Tue, 14 Jul 2020 09:51:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:51:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:51:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.05_summits.bed INFO @ Tue, 14 Jul 2020 09:51:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1681 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:51:50: 2000000 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 09:51:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.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 09:51:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:51:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:52:02: 3000000 INFO @ Tue, 14 Jul 2020 09:52:09: 1000000 INFO @ Tue, 14 Jul 2020 09:52:15: 4000000 INFO @ Tue, 14 Jul 2020 09:52:17: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 09:52:17: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 09:52:17: #1 total tags in treatment: 1442506 INFO @ Tue, 14 Jul 2020 09:52:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:52:17: #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 09:52:17: #1 tags after filtering in treatment: 1380079 INFO @ Tue, 14 Jul 2020 09:52:17: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 09:52:17: #1 finished! INFO @ Tue, 14 Jul 2020 09:52:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:52:18: #2 number of paired peaks: 2014 INFO @ Tue, 14 Jul 2020 09:52:18: start model_add_line... INFO @ Tue, 14 Jul 2020 09:52:18: start X-correlation... INFO @ Tue, 14 Jul 2020 09:52:18: end of X-cor INFO @ Tue, 14 Jul 2020 09:52:18: #2 finished! INFO @ Tue, 14 Jul 2020 09:52:18: #2 predicted fragment length is 233 bps INFO @ Tue, 14 Jul 2020 09:52:18: #2 alternative fragment length(s) may be 233 bps INFO @ Tue, 14 Jul 2020 09:52:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.10_model.r WARNING @ Tue, 14 Jul 2020 09:52:18: #2 Since the d (233) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:52:18: #2 You may need to consider one of the other alternative d(s): 233 WARNING @ Tue, 14 Jul 2020 09:52:18: #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 09:52:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:52:20: 2000000 INFO @ Tue, 14 Jul 2020 09:52:21: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:52:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:52:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:52:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.10_summits.bed INFO @ Tue, 14 Jul 2020 09:52:22: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (860 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:52:30: 3000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:52:39: 4000000 INFO @ Tue, 14 Jul 2020 09:52:41: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 09:52:41: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 09:52:41: #1 total tags in treatment: 1442506 INFO @ Tue, 14 Jul 2020 09:52:41: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:52:41: #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 09:52:41: #1 tags after filtering in treatment: 1380079 INFO @ Tue, 14 Jul 2020 09:52:41: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 09:52:41: #1 finished! INFO @ Tue, 14 Jul 2020 09:52:41: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:52:41: #2 number of paired peaks: 2014 INFO @ Tue, 14 Jul 2020 09:52:41: start model_add_line... INFO @ Tue, 14 Jul 2020 09:52:41: start X-correlation... INFO @ Tue, 14 Jul 2020 09:52:41: end of X-cor INFO @ Tue, 14 Jul 2020 09:52:41: #2 finished! INFO @ Tue, 14 Jul 2020 09:52:41: #2 predicted fragment length is 233 bps INFO @ Tue, 14 Jul 2020 09:52:41: #2 alternative fragment length(s) may be 233 bps INFO @ Tue, 14 Jul 2020 09:52:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.20_model.r WARNING @ Tue, 14 Jul 2020 09:52:41: #2 Since the d (233) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:52:41: #2 You may need to consider one of the other alternative d(s): 233 WARNING @ Tue, 14 Jul 2020 09:52:41: #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 09:52:41: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:52:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:52:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:52:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:52:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:52:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325353/SRX8325353.20_summits.bed INFO @ Tue, 14 Jul 2020 09:52:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 1 millis CompletedMACS2peakCalling