Job ID = 8069695 SRX = SRX7917424 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:45:42 prefetch.2.10.7: 1) Downloading 'SRR11313005'... 2020-08-08T03:45:42 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:46:09 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:46:09 prefetch.2.10.7: 'SRR11313005' is valid 2020-08-08T03:46:09 prefetch.2.10.7: 1) 'SRR11313005' was downloaded successfully Read 2572196 spots for SRR11313005/SRR11313005.sra Written 2572196 spots for SRR11313005/SRR11313005.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070399 ("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: 00:03:47 2572196 reads; of these: 2572196 (100.00%) were paired; of these: 463633 (18.02%) aligned concordantly 0 times 1771051 (68.85%) aligned concordantly exactly 1 time 337512 (13.12%) aligned concordantly >1 times ---- 463633 pairs aligned concordantly 0 times; of these: 203729 (43.94%) aligned discordantly 1 time ---- 259904 pairs aligned 0 times concordantly or discordantly; of these: 519808 mates make up the pairs; of these: 238711 (45.92%) aligned 0 times 141223 (27.17%) aligned exactly 1 time 139874 (26.91%) aligned >1 times 95.36% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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] 1078011 / 2305743 = 0.4675 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 12:51:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.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 12:51:37: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:51:37: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:51:42: 1000000 INFO @ Sat, 08 Aug 2020 12:51:48: 2000000 INFO @ Sat, 08 Aug 2020 12:51:52: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:51:52: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:51:52: #1 total tags in treatment: 1071607 INFO @ Sat, 08 Aug 2020 12:51:52: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:51:52: #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 12:51:52: #1 tags after filtering in treatment: 759213 INFO @ Sat, 08 Aug 2020 12:51:52: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 08 Aug 2020 12:51:52: #1 finished! INFO @ Sat, 08 Aug 2020 12:51:52: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:51:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:51:52: #2 number of paired peaks: 2385 INFO @ Sat, 08 Aug 2020 12:51:52: start model_add_line... INFO @ Sat, 08 Aug 2020 12:51:52: start X-correlation... INFO @ Sat, 08 Aug 2020 12:51:52: end of X-cor INFO @ Sat, 08 Aug 2020 12:51:52: #2 finished! INFO @ Sat, 08 Aug 2020 12:51:52: #2 predicted fragment length is 177 bps INFO @ Sat, 08 Aug 2020 12:51:52: #2 alternative fragment length(s) may be 2,31,73,118,156,177 bps INFO @ Sat, 08 Aug 2020 12:51:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.05_model.r INFO @ Sat, 08 Aug 2020 12:51:52: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:51:54: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:51:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:51:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:51:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.05_summits.bed INFO @ Sat, 08 Aug 2020 12:51:54: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 4 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 12:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.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 12:52:07: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:07: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:52:12: 1000000 INFO @ Sat, 08 Aug 2020 12:52:16: 2000000 INFO @ Sat, 08 Aug 2020 12:52:20: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:52:20: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:52:20: #1 total tags in treatment: 1071607 INFO @ Sat, 08 Aug 2020 12:52:20: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:52:20: #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 12:52:20: #1 tags after filtering in treatment: 759213 INFO @ Sat, 08 Aug 2020 12:52:20: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 08 Aug 2020 12:52:20: #1 finished! INFO @ Sat, 08 Aug 2020 12:52:20: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:52:20: #2 number of paired peaks: 2385 INFO @ Sat, 08 Aug 2020 12:52:20: start model_add_line... INFO @ Sat, 08 Aug 2020 12:52:20: start X-correlation... INFO @ Sat, 08 Aug 2020 12:52:20: end of X-cor INFO @ Sat, 08 Aug 2020 12:52:20: #2 finished! INFO @ Sat, 08 Aug 2020 12:52:20: #2 predicted fragment length is 177 bps INFO @ Sat, 08 Aug 2020 12:52:20: #2 alternative fragment length(s) may be 2,31,73,118,156,177 bps INFO @ Sat, 08 Aug 2020 12:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.10_model.r INFO @ Sat, 08 Aug 2020 12:52:20: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:52:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:52:21: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:52:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:52:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:52:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.10_summits.bed INFO @ Sat, 08 Aug 2020 12:52:22: 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 12:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.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 12:52:37: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:37: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:52:42: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:52:48: 2000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:52:52: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:52:52: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:52:52: #1 total tags in treatment: 1071607 INFO @ Sat, 08 Aug 2020 12:52:52: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:52:52: #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 12:52:52: #1 tags after filtering in treatment: 759213 INFO @ Sat, 08 Aug 2020 12:52:52: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 08 Aug 2020 12:52:52: #1 finished! INFO @ Sat, 08 Aug 2020 12:52:52: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:52:52: #2 number of paired peaks: 2385 INFO @ Sat, 08 Aug 2020 12:52:52: start model_add_line... INFO @ Sat, 08 Aug 2020 12:52:52: start X-correlation... INFO @ Sat, 08 Aug 2020 12:52:52: end of X-cor INFO @ Sat, 08 Aug 2020 12:52:52: #2 finished! INFO @ Sat, 08 Aug 2020 12:52:52: #2 predicted fragment length is 177 bps INFO @ Sat, 08 Aug 2020 12:52:52: #2 alternative fragment length(s) may be 2,31,73,118,156,177 bps INFO @ Sat, 08 Aug 2020 12:52:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.20_model.r INFO @ Sat, 08 Aug 2020 12:52:52: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:52:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:52:54: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:52:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:52:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:52:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917424/SRX7917424.20_summits.bed INFO @ Sat, 08 Aug 2020 12:52:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling