Job ID = 8069738 SRX = SRX7917436 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:48:57 prefetch.2.10.7: 1) Downloading 'SRR11313017'... 2020-08-08T03:48:57 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:49:19 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:49:19 prefetch.2.10.7: 'SRR11313017' is valid 2020-08-08T03:49:19 prefetch.2.10.7: 1) 'SRR11313017' was downloaded successfully Read 1304357 spots for SRR11313017/SRR11313017.sra Written 1304357 spots for SRR11313017/SRR11313017.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070474 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:11 1304357 reads; of these: 1304357 (100.00%) were paired; of these: 265129 (20.33%) aligned concordantly 0 times 835576 (64.06%) aligned concordantly exactly 1 time 203652 (15.61%) aligned concordantly >1 times ---- 265129 pairs aligned concordantly 0 times; of these: 90956 (34.31%) aligned discordantly 1 time ---- 174173 pairs aligned 0 times concordantly or discordantly; of these: 348346 mates make up the pairs; of these: 214547 (61.59%) aligned 0 times 66177 (19.00%) aligned exactly 1 time 67622 (19.41%) aligned >1 times 91.78% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 449844 / 1125686 = 0.3996 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 12:52:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.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 12:52:38: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:38: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:52:44: 1000000 INFO @ Sat, 08 Aug 2020 12:52:47: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:52:47: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:52:47: #1 total tags in treatment: 611593 INFO @ Sat, 08 Aug 2020 12:52:47: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:52:47: #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 12:52:47: #1 tags after filtering in treatment: 520614 INFO @ Sat, 08 Aug 2020 12:52:47: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 08 Aug 2020 12:52:47: #1 finished! INFO @ Sat, 08 Aug 2020 12:52:47: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:52:48: #2 number of paired peaks: 1128 INFO @ Sat, 08 Aug 2020 12:52:48: start model_add_line... INFO @ Sat, 08 Aug 2020 12:52:48: start X-correlation... INFO @ Sat, 08 Aug 2020 12:52:48: end of X-cor INFO @ Sat, 08 Aug 2020 12:52:48: #2 finished! INFO @ Sat, 08 Aug 2020 12:52:48: #2 predicted fragment length is 197 bps INFO @ Sat, 08 Aug 2020 12:52:48: #2 alternative fragment length(s) may be 1,148,172,197,224,256 bps INFO @ Sat, 08 Aug 2020 12:52:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.05_model.r INFO @ Sat, 08 Aug 2020 12:52:48: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:52:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:52:49: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:52:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:52:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:52:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.05_summits.bed INFO @ Sat, 08 Aug 2020 12:52:49: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 3 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 12:53:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.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 12:53:08: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:53:08: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:53:13: 1000000 INFO @ Sat, 08 Aug 2020 12:53:16: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:53:16: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:53:16: #1 total tags in treatment: 611593 INFO @ Sat, 08 Aug 2020 12:53:16: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:53:16: #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 12:53:16: #1 tags after filtering in treatment: 520614 INFO @ Sat, 08 Aug 2020 12:53:16: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 08 Aug 2020 12:53:16: #1 finished! INFO @ Sat, 08 Aug 2020 12:53:16: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:53:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:53:16: #2 number of paired peaks: 1128 INFO @ Sat, 08 Aug 2020 12:53:16: start model_add_line... INFO @ Sat, 08 Aug 2020 12:53:16: start X-correlation... INFO @ Sat, 08 Aug 2020 12:53:16: end of X-cor INFO @ Sat, 08 Aug 2020 12:53:16: #2 finished! INFO @ Sat, 08 Aug 2020 12:53:16: #2 predicted fragment length is 197 bps INFO @ Sat, 08 Aug 2020 12:53:16: #2 alternative fragment length(s) may be 1,148,172,197,224,256 bps INFO @ Sat, 08 Aug 2020 12:53:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.10_model.r INFO @ Sat, 08 Aug 2020 12:53:16: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:53:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:53:17: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.10_summits.bed INFO @ Sat, 08 Aug 2020 12:53:18: 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 12:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.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 12:53:38: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:53:38: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:53:44: 1000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:53:47: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:53:47: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:53:47: #1 total tags in treatment: 611593 INFO @ Sat, 08 Aug 2020 12:53:47: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:53:47: #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 12:53:47: #1 tags after filtering in treatment: 520614 INFO @ Sat, 08 Aug 2020 12:53:47: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 08 Aug 2020 12:53:47: #1 finished! INFO @ Sat, 08 Aug 2020 12:53:47: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:53:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:53:47: #2 number of paired peaks: 1128 INFO @ Sat, 08 Aug 2020 12:53:47: start model_add_line... INFO @ Sat, 08 Aug 2020 12:53:47: start X-correlation... INFO @ Sat, 08 Aug 2020 12:53:47: end of X-cor INFO @ Sat, 08 Aug 2020 12:53:47: #2 finished! INFO @ Sat, 08 Aug 2020 12:53:47: #2 predicted fragment length is 197 bps INFO @ Sat, 08 Aug 2020 12:53:47: #2 alternative fragment length(s) may be 1,148,172,197,224,256 bps INFO @ Sat, 08 Aug 2020 12:53:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.20_model.r INFO @ Sat, 08 Aug 2020 12:53:47: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:53:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:53:48: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:53:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:53:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:53:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917436/SRX7917436.20_summits.bed INFO @ Sat, 08 Aug 2020 12:53:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling