Job ID = 8071313 SRX = SRX7917546 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T04:26:43 prefetch.2.10.7: 1) Downloading 'SRR11313127'... 2020-08-08T04:26:43 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T04:27:10 prefetch.2.10.7: HTTPS download succeed 2020-08-08T04:27:10 prefetch.2.10.7: 'SRR11313127' is valid 2020-08-08T04:27:10 prefetch.2.10.7: 1) 'SRR11313127' was downloaded successfully Read 2517841 spots for SRR11313127/SRR11313127.sra Written 2517841 spots for SRR11313127/SRR11313127.sra fastq に変換しました。 bowtie でマッピング中... Your job 8072369 ("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: 00:02:56 2517841 reads; of these: 2517841 (100.00%) were paired; of these: 461779 (18.34%) aligned concordantly 0 times 1799155 (71.46%) aligned concordantly exactly 1 time 256907 (10.20%) aligned concordantly >1 times ---- 461779 pairs aligned concordantly 0 times; of these: 233259 (50.51%) aligned discordantly 1 time ---- 228520 pairs aligned 0 times concordantly or discordantly; of these: 457040 mates make up the pairs; of these: 254936 (55.78%) aligned 0 times 107954 (23.62%) aligned exactly 1 time 94150 (20.60%) aligned >1 times 94.94% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 1044631 / 2281851 = 0.4578 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 13:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.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 13:31:45: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:31:45: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:31:50: 1000000 INFO @ Sat, 08 Aug 2020 13:31:55: 2000000 INFO @ Sat, 08 Aug 2020 13:31:58: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:31:58: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:31:58: #1 total tags in treatment: 1053010 INFO @ Sat, 08 Aug 2020 13:31:58: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:31:58: #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 13:31:58: #1 tags after filtering in treatment: 697514 INFO @ Sat, 08 Aug 2020 13:31:58: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 08 Aug 2020 13:31:58: #1 finished! INFO @ Sat, 08 Aug 2020 13:31:58: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:31:58: #2 number of paired peaks: 4361 INFO @ Sat, 08 Aug 2020 13:31:58: start model_add_line... INFO @ Sat, 08 Aug 2020 13:31:59: start X-correlation... INFO @ Sat, 08 Aug 2020 13:31:59: end of X-cor INFO @ Sat, 08 Aug 2020 13:31:59: #2 finished! INFO @ Sat, 08 Aug 2020 13:31:59: #2 predicted fragment length is 139 bps INFO @ Sat, 08 Aug 2020 13:31:59: #2 alternative fragment length(s) may be 2,139,175 bps INFO @ Sat, 08 Aug 2020 13:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.05_model.r INFO @ Sat, 08 Aug 2020 13:31:59: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:32:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.05_summits.bed INFO @ Sat, 08 Aug 2020 13:32:00: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (11 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 13:32:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.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 13:32:15: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:32:15: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:32:21: 1000000 INFO @ Sat, 08 Aug 2020 13:32:25: 2000000 INFO @ Sat, 08 Aug 2020 13:32:29: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:32:29: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:32:29: #1 total tags in treatment: 1053010 INFO @ Sat, 08 Aug 2020 13:32:29: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:32:29: #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 13:32:29: #1 tags after filtering in treatment: 697514 INFO @ Sat, 08 Aug 2020 13:32:29: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 08 Aug 2020 13:32:29: #1 finished! INFO @ Sat, 08 Aug 2020 13:32:29: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:32:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:32:29: #2 number of paired peaks: 4361 INFO @ Sat, 08 Aug 2020 13:32:29: start model_add_line... INFO @ Sat, 08 Aug 2020 13:32:29: start X-correlation... INFO @ Sat, 08 Aug 2020 13:32:29: end of X-cor INFO @ Sat, 08 Aug 2020 13:32:29: #2 finished! INFO @ Sat, 08 Aug 2020 13:32:29: #2 predicted fragment length is 139 bps INFO @ Sat, 08 Aug 2020 13:32:29: #2 alternative fragment length(s) may be 2,139,175 bps INFO @ Sat, 08 Aug 2020 13:32:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.10_model.r INFO @ Sat, 08 Aug 2020 13:32:29: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:32:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:32:30: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:32:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:32:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:32:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.10_summits.bed INFO @ Sat, 08 Aug 2020 13:32:31: 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 13:32:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.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 13:32:45: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:32:45: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:32:50: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:32:55: 2000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:32:58: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:32:58: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:32:58: #1 total tags in treatment: 1053010 INFO @ Sat, 08 Aug 2020 13:32:58: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:32:58: #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 13:32:58: #1 tags after filtering in treatment: 697514 INFO @ Sat, 08 Aug 2020 13:32:58: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 08 Aug 2020 13:32:58: #1 finished! INFO @ Sat, 08 Aug 2020 13:32:58: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:32:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:32:59: #2 number of paired peaks: 4361 INFO @ Sat, 08 Aug 2020 13:32:59: start model_add_line... INFO @ Sat, 08 Aug 2020 13:32:59: start X-correlation... INFO @ Sat, 08 Aug 2020 13:32:59: end of X-cor INFO @ Sat, 08 Aug 2020 13:32:59: #2 finished! INFO @ Sat, 08 Aug 2020 13:32:59: #2 predicted fragment length is 139 bps INFO @ Sat, 08 Aug 2020 13:32:59: #2 alternative fragment length(s) may be 2,139,175 bps INFO @ Sat, 08 Aug 2020 13:32:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.20_model.r INFO @ Sat, 08 Aug 2020 13:32:59: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:32:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:33:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:33:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:33:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:33:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917546/SRX7917546.20_summits.bed INFO @ Sat, 08 Aug 2020 13:33:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling