Job ID = 8069862 SRX = SRX7917472 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:57:24 prefetch.2.10.7: 1) Downloading 'SRR11313053'... 2020-08-08T03:57:24 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:57:49 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:57:50 prefetch.2.10.7: 'SRR11313053' is valid 2020-08-08T03:57:50 prefetch.2.10.7: 1) 'SRR11313053' was downloaded successfully Read 2500691 spots for SRR11313053/SRR11313053.sra Written 2500691 spots for SRR11313053/SRR11313053.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070937 ("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: 00:03:07 2500691 reads; of these: 2500691 (100.00%) were paired; of these: 716711 (28.66%) aligned concordantly 0 times 1495752 (59.81%) aligned concordantly exactly 1 time 288228 (11.53%) aligned concordantly >1 times ---- 716711 pairs aligned concordantly 0 times; of these: 175602 (24.50%) aligned discordantly 1 time ---- 541109 pairs aligned 0 times concordantly or discordantly; of these: 1082218 mates make up the pairs; of these: 840234 (77.64%) aligned 0 times 121555 (11.23%) aligned exactly 1 time 120429 (11.13%) aligned >1 times 83.20% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 900601 / 1953285 = 0.4611 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 @ Sat, 08 Aug 2020 13:02:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.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, 08 Aug 2020 13:02:28: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:02:28: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:02:34: 1000000 INFO @ Sat, 08 Aug 2020 13:02:39: 2000000 INFO @ Sat, 08 Aug 2020 13:02:41: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:02:41: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:02:41: #1 total tags in treatment: 917955 INFO @ Sat, 08 Aug 2020 13:02:41: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:02:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:02:41: #1 tags after filtering in treatment: 679054 INFO @ Sat, 08 Aug 2020 13:02:41: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 08 Aug 2020 13:02:41: #1 finished! INFO @ Sat, 08 Aug 2020 13:02:41: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:02:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:02:41: #2 number of paired peaks: 3002 INFO @ Sat, 08 Aug 2020 13:02:41: start model_add_line... INFO @ Sat, 08 Aug 2020 13:02:41: start X-correlation... INFO @ Sat, 08 Aug 2020 13:02:41: end of X-cor INFO @ Sat, 08 Aug 2020 13:02:41: #2 finished! INFO @ Sat, 08 Aug 2020 13:02:41: #2 predicted fragment length is 180 bps INFO @ Sat, 08 Aug 2020 13:02:41: #2 alternative fragment length(s) may be 2,123,144,180,234,258 bps INFO @ Sat, 08 Aug 2020 13:02:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.05_model.r INFO @ Sat, 08 Aug 2020 13:02:41: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:02:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:02:42: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:02:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:02:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:02:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.05_summits.bed INFO @ Sat, 08 Aug 2020 13:02:43: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Sat, 08 Aug 2020 13:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.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, 08 Aug 2020 13:02:58: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:02:58: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:03:03: 1000000 INFO @ Sat, 08 Aug 2020 13:03:08: 2000000 INFO @ Sat, 08 Aug 2020 13:03:10: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:03:10: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:03:10: #1 total tags in treatment: 917955 INFO @ Sat, 08 Aug 2020 13:03:10: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:03:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:03:10: #1 tags after filtering in treatment: 679054 INFO @ Sat, 08 Aug 2020 13:03:10: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 08 Aug 2020 13:03:10: #1 finished! INFO @ Sat, 08 Aug 2020 13:03:10: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:03:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:03:10: #2 number of paired peaks: 3002 INFO @ Sat, 08 Aug 2020 13:03:10: start model_add_line... INFO @ Sat, 08 Aug 2020 13:03:10: start X-correlation... INFO @ Sat, 08 Aug 2020 13:03:10: end of X-cor INFO @ Sat, 08 Aug 2020 13:03:10: #2 finished! INFO @ Sat, 08 Aug 2020 13:03:10: #2 predicted fragment length is 180 bps INFO @ Sat, 08 Aug 2020 13:03:10: #2 alternative fragment length(s) may be 2,123,144,180,234,258 bps INFO @ Sat, 08 Aug 2020 13:03:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.10_model.r INFO @ Sat, 08 Aug 2020 13:03:10: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:03:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:03:12: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.10_summits.bed INFO @ Sat, 08 Aug 2020 13:03:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling 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 @ Sat, 08 Aug 2020 13:03:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.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, 08 Aug 2020 13:03:28: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:03:28: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:03:34: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:03:40: 2000000 INFO @ Sat, 08 Aug 2020 13:03:42: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:03:42: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:03:42: #1 total tags in treatment: 917955 INFO @ Sat, 08 Aug 2020 13:03:42: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:03:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:03:42: #1 tags after filtering in treatment: 679054 INFO @ Sat, 08 Aug 2020 13:03:42: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 08 Aug 2020 13:03:42: #1 finished! INFO @ Sat, 08 Aug 2020 13:03:42: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:03:42: #2 number of paired peaks: 3002 INFO @ Sat, 08 Aug 2020 13:03:42: start model_add_line... INFO @ Sat, 08 Aug 2020 13:03:42: start X-correlation... INFO @ Sat, 08 Aug 2020 13:03:42: end of X-cor INFO @ Sat, 08 Aug 2020 13:03:42: #2 finished! INFO @ Sat, 08 Aug 2020 13:03:42: #2 predicted fragment length is 180 bps INFO @ Sat, 08 Aug 2020 13:03:42: #2 alternative fragment length(s) may be 2,123,144,180,234,258 bps INFO @ Sat, 08 Aug 2020 13:03:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.20_model.r INFO @ Sat, 08 Aug 2020 13:03:42: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:03:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:03:43: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:03:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:03:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:03:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917472/SRX7917472.20_summits.bed INFO @ Sat, 08 Aug 2020 13:03:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling