Job ID = 8069501 SRX = SRX7917363 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:33:44 prefetch.2.10.7: 1) Downloading 'SRR11312910'... 2020-08-08T03:33:44 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:37:53 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:37:53 prefetch.2.10.7: 1) 'SRR11312910' was downloaded successfully 2020-08-08T03:37:53 prefetch.2.10.7: 'SRR11312910' has 0 unresolved dependencies Read 103366080 spots for SRR11312910/SRR11312910.sra Written 103366080 spots for SRR11312910/SRR11312910.sra fastq に変換しました。 bowtie でマッピング中... Your job 8072385 ("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: 00:44:22 103366080 reads; of these: 103366080 (100.00%) were paired; of these: 102848374 (99.50%) aligned concordantly 0 times 394873 (0.38%) aligned concordantly exactly 1 time 122833 (0.12%) aligned concordantly >1 times ---- 102848374 pairs aligned concordantly 0 times; of these: 92225 (0.09%) aligned discordantly 1 time ---- 102756149 pairs aligned 0 times concordantly or discordantly; of these: 205512298 mates make up the pairs; of these: 192702612 (93.77%) aligned 0 times 9647159 (4.69%) aligned exactly 1 time 3162527 (1.54%) aligned >1 times 6.79% overall alignment rate Time searching: 00:44:22 Overall time: 00:44:22 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_sort_core] merging from 8 files... [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] 269130 / 600810 = 0.4479 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 13:33:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.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 13:33:54: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:33:54: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:33:59: 1000000 INFO @ Sat, 08 Aug 2020 13:34:05: 2000000 INFO @ Sat, 08 Aug 2020 13:34:10: 3000000 INFO @ Sat, 08 Aug 2020 13:34:15: 4000000 INFO @ Sat, 08 Aug 2020 13:34:21: 5000000 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 13:34:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.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 13:34:24: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:34:24: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:34:26: 6000000 INFO @ Sat, 08 Aug 2020 13:34:30: 1000000 INFO @ Sat, 08 Aug 2020 13:34:32: 7000000 INFO @ Sat, 08 Aug 2020 13:34:36: 2000000 INFO @ Sat, 08 Aug 2020 13:34:38: 8000000 INFO @ Sat, 08 Aug 2020 13:34:42: 3000000 INFO @ Sat, 08 Aug 2020 13:34:44: 9000000 INFO @ Sat, 08 Aug 2020 13:34:47: 4000000 INFO @ Sat, 08 Aug 2020 13:34:50: 10000000 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 13:34:53: 5000000 INFO @ Sat, 08 Aug 2020 13:34:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.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 13:34:54: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:34:54: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:34:56: 11000000 INFO @ Sat, 08 Aug 2020 13:34:59: 6000000 INFO @ Sat, 08 Aug 2020 13:35:00: 1000000 INFO @ Sat, 08 Aug 2020 13:35:02: 12000000 INFO @ Sat, 08 Aug 2020 13:35:05: 7000000 INFO @ Sat, 08 Aug 2020 13:35:06: 2000000 INFO @ Sat, 08 Aug 2020 13:35:08: 13000000 INFO @ Sat, 08 Aug 2020 13:35:11: #1 tag size is determined as 51 bps INFO @ Sat, 08 Aug 2020 13:35:11: #1 tag size = 51 INFO @ Sat, 08 Aug 2020 13:35:11: #1 total tags in treatment: 283816 INFO @ Sat, 08 Aug 2020 13:35:11: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:35:11: #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 13:35:11: #1 tags after filtering in treatment: 262324 INFO @ Sat, 08 Aug 2020 13:35:11: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:35:11: #1 finished! INFO @ Sat, 08 Aug 2020 13:35:11: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:35:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:35:11: #2 number of paired peaks: 3940 INFO @ Sat, 08 Aug 2020 13:35:11: start model_add_line... INFO @ Sat, 08 Aug 2020 13:35:11: start X-correlation... INFO @ Sat, 08 Aug 2020 13:35:11: end of X-cor INFO @ Sat, 08 Aug 2020 13:35:11: #2 finished! INFO @ Sat, 08 Aug 2020 13:35:11: #2 predicted fragment length is 249 bps INFO @ Sat, 08 Aug 2020 13:35:11: #2 alternative fragment length(s) may be 20,205,226,249 bps INFO @ Sat, 08 Aug 2020 13:35:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.05_model.r INFO @ Sat, 08 Aug 2020 13:35:11: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:35:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:35:11: 8000000 INFO @ Sat, 08 Aug 2020 13:35:11: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:35:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:35:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:35:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.05_summits.bed INFO @ Sat, 08 Aug 2020 13:35:12: Done! INFO @ Sat, 08 Aug 2020 13:35:12: 3000000 pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (310 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:35:17: 9000000 INFO @ Sat, 08 Aug 2020 13:35:18: 4000000 INFO @ Sat, 08 Aug 2020 13:35:23: 10000000 INFO @ Sat, 08 Aug 2020 13:35:24: 5000000 INFO @ Sat, 08 Aug 2020 13:35:29: 11000000 INFO @ Sat, 08 Aug 2020 13:35:29: 6000000 INFO @ Sat, 08 Aug 2020 13:35:35: 12000000 INFO @ Sat, 08 Aug 2020 13:35:35: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:35:41: 13000000 INFO @ Sat, 08 Aug 2020 13:35:41: 8000000 INFO @ Sat, 08 Aug 2020 13:35:44: #1 tag size is determined as 51 bps INFO @ Sat, 08 Aug 2020 13:35:44: #1 tag size = 51 INFO @ Sat, 08 Aug 2020 13:35:44: #1 total tags in treatment: 283816 INFO @ Sat, 08 Aug 2020 13:35:44: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:35:44: #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 13:35:44: #1 tags after filtering in treatment: 262324 INFO @ Sat, 08 Aug 2020 13:35:44: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:35:44: #1 finished! INFO @ Sat, 08 Aug 2020 13:35:44: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:35:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:35:44: #2 number of paired peaks: 3940 INFO @ Sat, 08 Aug 2020 13:35:44: start model_add_line... INFO @ Sat, 08 Aug 2020 13:35:44: start X-correlation... INFO @ Sat, 08 Aug 2020 13:35:44: end of X-cor INFO @ Sat, 08 Aug 2020 13:35:44: #2 finished! INFO @ Sat, 08 Aug 2020 13:35:44: #2 predicted fragment length is 249 bps INFO @ Sat, 08 Aug 2020 13:35:44: #2 alternative fragment length(s) may be 20,205,226,249 bps INFO @ Sat, 08 Aug 2020 13:35:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.10_model.r INFO @ Sat, 08 Aug 2020 13:35:44: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:35:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:35:44: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:35:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:35:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:35:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.10_summits.bed INFO @ Sat, 08 Aug 2020 13:35:45: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (67 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:35:47: 9000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:35:52: 10000000 INFO @ Sat, 08 Aug 2020 13:35:57: 11000000 INFO @ Sat, 08 Aug 2020 13:36:02: 12000000 INFO @ Sat, 08 Aug 2020 13:36:07: 13000000 INFO @ Sat, 08 Aug 2020 13:36:09: #1 tag size is determined as 51 bps INFO @ Sat, 08 Aug 2020 13:36:09: #1 tag size = 51 INFO @ Sat, 08 Aug 2020 13:36:09: #1 total tags in treatment: 283816 INFO @ Sat, 08 Aug 2020 13:36:09: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:36:09: #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 13:36:09: #1 tags after filtering in treatment: 262324 INFO @ Sat, 08 Aug 2020 13:36:09: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:36:09: #1 finished! INFO @ Sat, 08 Aug 2020 13:36:09: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:36:09: #2 number of paired peaks: 3940 INFO @ Sat, 08 Aug 2020 13:36:09: start model_add_line... INFO @ Sat, 08 Aug 2020 13:36:09: start X-correlation... INFO @ Sat, 08 Aug 2020 13:36:09: end of X-cor INFO @ Sat, 08 Aug 2020 13:36:09: #2 finished! INFO @ Sat, 08 Aug 2020 13:36:09: #2 predicted fragment length is 249 bps INFO @ Sat, 08 Aug 2020 13:36:09: #2 alternative fragment length(s) may be 20,205,226,249 bps INFO @ Sat, 08 Aug 2020 13:36:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.20_model.r INFO @ Sat, 08 Aug 2020 13:36:09: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:36:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:36:10: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917363/SRX7917363.20_summits.bed INFO @ Sat, 08 Aug 2020 13:36:10: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling