Job ID = 8071238 SRX = SRX7917530 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T04:24:35 prefetch.2.10.7: 1) Downloading 'SRR11313111'... 2020-08-08T04:24:35 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T04:25:04 prefetch.2.10.7: HTTPS download succeed 2020-08-08T04:25:05 prefetch.2.10.7: 'SRR11313111' is valid 2020-08-08T04:25:05 prefetch.2.10.7: 1) 'SRR11313111' was downloaded successfully Read 1885195 spots for SRR11313111/SRR11313111.sra Written 1885195 spots for SRR11313111/SRR11313111.sra fastq に変換しました。 bowtie でマッピング中... Your job 8072204 ("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: 00:02:01 1885195 reads; of these: 1885195 (100.00%) were paired; of these: 419388 (22.25%) aligned concordantly 0 times 1289761 (68.42%) aligned concordantly exactly 1 time 176046 (9.34%) aligned concordantly >1 times ---- 419388 pairs aligned concordantly 0 times; of these: 172937 (41.24%) aligned discordantly 1 time ---- 246451 pairs aligned 0 times concordantly or discordantly; of these: 492902 mates make up the pairs; of these: 347813 (70.56%) aligned 0 times 76838 (15.59%) aligned exactly 1 time 68251 (13.85%) aligned >1 times 90.78% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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] 751519 / 1632787 = 0.4603 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 13:28:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.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 13:28:25: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:28:25: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:28:29: 1000000 INFO @ Sat, 08 Aug 2020 13:28:34: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:28:34: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:28:34: #1 total tags in treatment: 744440 INFO @ Sat, 08 Aug 2020 13:28:34: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:34: #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 13:28:34: #1 tags after filtering in treatment: 526323 INFO @ Sat, 08 Aug 2020 13:28:34: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 08 Aug 2020 13:28:34: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:34: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:34: #2 number of paired peaks: 5675 INFO @ Sat, 08 Aug 2020 13:28:34: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:34: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:34: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:34: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:34: #2 predicted fragment length is 183 bps INFO @ Sat, 08 Aug 2020 13:28:34: #2 alternative fragment length(s) may be 3,183 bps INFO @ Sat, 08 Aug 2020 13:28:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.05_model.r INFO @ Sat, 08 Aug 2020 13:28:34: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:28:35: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:28:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:28:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:28:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.05_summits.bed INFO @ Sat, 08 Aug 2020 13:28:35: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (19 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 13:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.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 13:28:55: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:28:55: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:28:59: 1000000 INFO @ Sat, 08 Aug 2020 13:29:04: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:29:04: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:29:04: #1 total tags in treatment: 744440 INFO @ Sat, 08 Aug 2020 13:29:04: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:29:04: #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 13:29:04: #1 tags after filtering in treatment: 526323 INFO @ Sat, 08 Aug 2020 13:29:04: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 08 Aug 2020 13:29:04: #1 finished! INFO @ Sat, 08 Aug 2020 13:29:04: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:29:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:29:04: #2 number of paired peaks: 5675 INFO @ Sat, 08 Aug 2020 13:29:04: start model_add_line... INFO @ Sat, 08 Aug 2020 13:29:04: start X-correlation... INFO @ Sat, 08 Aug 2020 13:29:04: end of X-cor INFO @ Sat, 08 Aug 2020 13:29:04: #2 finished! INFO @ Sat, 08 Aug 2020 13:29:04: #2 predicted fragment length is 183 bps INFO @ Sat, 08 Aug 2020 13:29:04: #2 alternative fragment length(s) may be 3,183 bps INFO @ Sat, 08 Aug 2020 13:29:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.10_model.r INFO @ Sat, 08 Aug 2020 13:29:04: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:29:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:29:05: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.10_summits.bed INFO @ Sat, 08 Aug 2020 13:29:05: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis 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 13:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.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 13:29:25: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:29:25: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:29:29: 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 13:29:34: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:29:34: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:29:34: #1 total tags in treatment: 744440 INFO @ Sat, 08 Aug 2020 13:29:34: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:29:34: #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 13:29:34: #1 tags after filtering in treatment: 526323 INFO @ Sat, 08 Aug 2020 13:29:34: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 08 Aug 2020 13:29:34: #1 finished! INFO @ Sat, 08 Aug 2020 13:29:34: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:29:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:29:34: #2 number of paired peaks: 5675 INFO @ Sat, 08 Aug 2020 13:29:34: start model_add_line... INFO @ Sat, 08 Aug 2020 13:29:34: start X-correlation... INFO @ Sat, 08 Aug 2020 13:29:34: end of X-cor INFO @ Sat, 08 Aug 2020 13:29:34: #2 finished! INFO @ Sat, 08 Aug 2020 13:29:34: #2 predicted fragment length is 183 bps INFO @ Sat, 08 Aug 2020 13:29:34: #2 alternative fragment length(s) may be 3,183 bps INFO @ Sat, 08 Aug 2020 13:29:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.20_model.r INFO @ Sat, 08 Aug 2020 13:29:34: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:29:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:29:35: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:29:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:29:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:29:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917530/SRX7917530.20_summits.bed INFO @ Sat, 08 Aug 2020 13:29:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling