Job ID = 8069559 SRX = SRX7917382 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:34:46 prefetch.2.10.7: 1) Downloading 'SRR11312929'... 2020-08-08T03:34:46 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:35:10 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:35:10 prefetch.2.10.7: 'SRR11312929' is valid 2020-08-08T03:35:10 prefetch.2.10.7: 1) 'SRR11312929' was downloaded successfully Read 1679356 spots for SRR11312929/SRR11312929.sra Written 1679356 spots for SRR11312929/SRR11312929.sra fastq に変換しました。 bowtie でマッピング中... Your job 8069750 ("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: 00:01:58 1679356 reads; of these: 1679356 (100.00%) were paired; of these: 483963 (28.82%) aligned concordantly 0 times 1017878 (60.61%) aligned concordantly exactly 1 time 177515 (10.57%) aligned concordantly >1 times ---- 483963 pairs aligned concordantly 0 times; of these: 149921 (30.98%) aligned discordantly 1 time ---- 334042 pairs aligned 0 times concordantly or discordantly; of these: 668084 mates make up the pairs; of these: 536847 (80.36%) aligned 0 times 68945 (10.32%) aligned exactly 1 time 62292 (9.32%) aligned >1 times 84.02% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 522919 / 1337366 = 0.3910 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 12:38:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.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 12:38:21: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:38:21: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:38:27: 1000000 INFO @ Sat, 08 Aug 2020 12:38:32: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:38:32: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:38:32: #1 total tags in treatment: 704936 INFO @ Sat, 08 Aug 2020 12:38:32: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:38:32: #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 12:38:32: #1 tags after filtering in treatment: 548625 INFO @ Sat, 08 Aug 2020 12:38:32: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 08 Aug 2020 12:38:32: #1 finished! INFO @ Sat, 08 Aug 2020 12:38:32: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:38:32: #2 number of paired peaks: 4384 INFO @ Sat, 08 Aug 2020 12:38:32: start model_add_line... INFO @ Sat, 08 Aug 2020 12:38:32: start X-correlation... INFO @ Sat, 08 Aug 2020 12:38:32: end of X-cor INFO @ Sat, 08 Aug 2020 12:38:32: #2 finished! INFO @ Sat, 08 Aug 2020 12:38:32: #2 predicted fragment length is 213 bps INFO @ Sat, 08 Aug 2020 12:38:32: #2 alternative fragment length(s) may be 3,188,213 bps INFO @ Sat, 08 Aug 2020 12:38:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.05_model.r INFO @ Sat, 08 Aug 2020 12:38:32: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:38:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:38:33: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:38:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:38:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:38:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.05_summits.bed INFO @ Sat, 08 Aug 2020 12:38:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (21 records, 4 fields): 6 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 12:38:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.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 12:38:51: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:38:51: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:38:56: 1000000 INFO @ Sat, 08 Aug 2020 12:39:00: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:39:00: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:39:00: #1 total tags in treatment: 704936 INFO @ Sat, 08 Aug 2020 12:39:00: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:39:00: #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 12:39:00: #1 tags after filtering in treatment: 548625 INFO @ Sat, 08 Aug 2020 12:39:00: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 08 Aug 2020 12:39:00: #1 finished! INFO @ Sat, 08 Aug 2020 12:39:00: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:39:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:39:00: #2 number of paired peaks: 4384 INFO @ Sat, 08 Aug 2020 12:39:00: start model_add_line... INFO @ Sat, 08 Aug 2020 12:39:00: start X-correlation... INFO @ Sat, 08 Aug 2020 12:39:00: end of X-cor INFO @ Sat, 08 Aug 2020 12:39:00: #2 finished! INFO @ Sat, 08 Aug 2020 12:39:00: #2 predicted fragment length is 213 bps INFO @ Sat, 08 Aug 2020 12:39:00: #2 alternative fragment length(s) may be 3,188,213 bps INFO @ Sat, 08 Aug 2020 12:39:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.10_model.r INFO @ Sat, 08 Aug 2020 12:39:00: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:39:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:39:01: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:39:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:39:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:39:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.10_summits.bed INFO @ Sat, 08 Aug 2020 12:39:02: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 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 12:39:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.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 12:39:21: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:39:21: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:39:26: 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 12:39:30: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:39:30: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:39:30: #1 total tags in treatment: 704936 INFO @ Sat, 08 Aug 2020 12:39:30: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:39:30: #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 12:39:30: #1 tags after filtering in treatment: 548625 INFO @ Sat, 08 Aug 2020 12:39:30: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 08 Aug 2020 12:39:30: #1 finished! INFO @ Sat, 08 Aug 2020 12:39:30: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:39:30: #2 number of paired peaks: 4384 INFO @ Sat, 08 Aug 2020 12:39:30: start model_add_line... INFO @ Sat, 08 Aug 2020 12:39:30: start X-correlation... INFO @ Sat, 08 Aug 2020 12:39:30: end of X-cor INFO @ Sat, 08 Aug 2020 12:39:30: #2 finished! INFO @ Sat, 08 Aug 2020 12:39:30: #2 predicted fragment length is 213 bps INFO @ Sat, 08 Aug 2020 12:39:30: #2 alternative fragment length(s) may be 3,188,213 bps INFO @ Sat, 08 Aug 2020 12:39:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.20_model.r INFO @ Sat, 08 Aug 2020 12:39:30: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:39:31: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:39:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:39:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:39:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917382/SRX7917382.20_summits.bed INFO @ Sat, 08 Aug 2020 12:39:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling