Job ID = 8069541 SRX = SRX7917376 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:34:30 prefetch.2.10.7: 1) Downloading 'SRR11312923'... 2020-08-08T03:34:30 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:35:08 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:35:09 prefetch.2.10.7: 'SRR11312923' is valid 2020-08-08T03:35:09 prefetch.2.10.7: 1) 'SRR11312923' was downloaded successfully Read 2255389 spots for SRR11312923/SRR11312923.sra Written 2255389 spots for SRR11312923/SRR11312923.sra fastq に変換しました。 bowtie でマッピング中... Your job 8069832 ("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 2255389 reads; of these: 2255389 (100.00%) were paired; of these: 523982 (23.23%) aligned concordantly 0 times 1454359 (64.48%) aligned concordantly exactly 1 time 277048 (12.28%) aligned concordantly >1 times ---- 523982 pairs aligned concordantly 0 times; of these: 175482 (33.49%) aligned discordantly 1 time ---- 348500 pairs aligned 0 times concordantly or discordantly; of these: 697000 mates make up the pairs; of these: 454760 (65.25%) aligned 0 times 123077 (17.66%) aligned exactly 1 time 119163 (17.10%) aligned >1 times 89.92% 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] 861979 / 1900686 = 0.4535 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 12:39:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.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 12:39:45: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:39:45: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:39:52: 1000000 INFO @ Sat, 08 Aug 2020 12:39:58: 2000000 INFO @ Sat, 08 Aug 2020 12:40:00: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:40:00: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:40:00: #1 total tags in treatment: 903371 INFO @ Sat, 08 Aug 2020 12:40:00: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:40:00: #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 12:40:00: #1 tags after filtering in treatment: 666178 INFO @ Sat, 08 Aug 2020 12:40:00: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 08 Aug 2020 12:40:00: #1 finished! INFO @ Sat, 08 Aug 2020 12:40:00: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:40:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:40:00: #2 number of paired peaks: 3211 INFO @ Sat, 08 Aug 2020 12:40:00: start model_add_line... INFO @ Sat, 08 Aug 2020 12:40:00: start X-correlation... INFO @ Sat, 08 Aug 2020 12:40:00: end of X-cor INFO @ Sat, 08 Aug 2020 12:40:00: #2 finished! INFO @ Sat, 08 Aug 2020 12:40:00: #2 predicted fragment length is 228 bps INFO @ Sat, 08 Aug 2020 12:40:00: #2 alternative fragment length(s) may be 1,73,184,228 bps INFO @ Sat, 08 Aug 2020 12:40:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.05_model.r INFO @ Sat, 08 Aug 2020 12:40:00: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:40:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:40:02: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:40:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:40:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:40:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.05_summits.bed INFO @ Sat, 08 Aug 2020 12:40:02: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 25 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 12:40:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.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 12:40:15: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:40:15: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:40:21: 1000000 INFO @ Sat, 08 Aug 2020 12:40:26: 2000000 INFO @ Sat, 08 Aug 2020 12:40:28: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:40:28: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:40:28: #1 total tags in treatment: 903371 INFO @ Sat, 08 Aug 2020 12:40:28: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:40:28: #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 12:40:28: #1 tags after filtering in treatment: 666178 INFO @ Sat, 08 Aug 2020 12:40:28: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 08 Aug 2020 12:40:28: #1 finished! INFO @ Sat, 08 Aug 2020 12:40:28: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:40:28: #2 number of paired peaks: 3211 INFO @ Sat, 08 Aug 2020 12:40:28: start model_add_line... INFO @ Sat, 08 Aug 2020 12:40:28: start X-correlation... INFO @ Sat, 08 Aug 2020 12:40:28: end of X-cor INFO @ Sat, 08 Aug 2020 12:40:28: #2 finished! INFO @ Sat, 08 Aug 2020 12:40:28: #2 predicted fragment length is 228 bps INFO @ Sat, 08 Aug 2020 12:40:28: #2 alternative fragment length(s) may be 1,73,184,228 bps INFO @ Sat, 08 Aug 2020 12:40:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.10_model.r INFO @ Sat, 08 Aug 2020 12:40:28: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:40:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:40:29: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:40:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:40:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:40:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.10_summits.bed INFO @ Sat, 08 Aug 2020 12:40:30: Done! pass1 - making usageList (1 chroms): 1 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 12:40:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.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 12:40:45: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:40:45: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:40:51: 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 12:40:58: 2000000 INFO @ Sat, 08 Aug 2020 12:41:00: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:41:00: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:41:00: #1 total tags in treatment: 903371 INFO @ Sat, 08 Aug 2020 12:41:00: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:41:00: #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 12:41:00: #1 tags after filtering in treatment: 666178 INFO @ Sat, 08 Aug 2020 12:41:00: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 08 Aug 2020 12:41:00: #1 finished! INFO @ Sat, 08 Aug 2020 12:41:00: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:41:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:41:00: #2 number of paired peaks: 3211 INFO @ Sat, 08 Aug 2020 12:41:00: start model_add_line... INFO @ Sat, 08 Aug 2020 12:41:00: start X-correlation... INFO @ Sat, 08 Aug 2020 12:41:00: end of X-cor INFO @ Sat, 08 Aug 2020 12:41:00: #2 finished! INFO @ Sat, 08 Aug 2020 12:41:00: #2 predicted fragment length is 228 bps INFO @ Sat, 08 Aug 2020 12:41:00: #2 alternative fragment length(s) may be 1,73,184,228 bps INFO @ Sat, 08 Aug 2020 12:41:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.20_model.r INFO @ Sat, 08 Aug 2020 12:41:00: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:41:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:41:01: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:41:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:41:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:41:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917376/SRX7917376.20_summits.bed INFO @ Sat, 08 Aug 2020 12:41:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling