Job ID = 5721062 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,264,418 reads read : 10,528,836 reads written : 10,528,836 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:15 5264418 reads; of these: 5264418 (100.00%) were paired; of these: 528252 (10.03%) aligned concordantly 0 times 3252168 (61.78%) aligned concordantly exactly 1 time 1483998 (28.19%) aligned concordantly >1 times ---- 528252 pairs aligned concordantly 0 times; of these: 238102 (45.07%) aligned discordantly 1 time ---- 290150 pairs aligned 0 times concordantly or discordantly; of these: 580300 mates make up the pairs; of these: 227910 (39.27%) aligned 0 times 100584 (17.33%) aligned exactly 1 time 251806 (43.39%) aligned >1 times 97.84% overall alignment rate Time searching: 00:21:15 Overall time: 00:21:15 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] 649922 / 4915120 = 0.1322 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 @ Thu, 16 Apr 2020 04:28:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.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 @ Thu, 16 Apr 2020 04:28:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:28:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:28:45: 1000000 INFO @ Thu, 16 Apr 2020 04:28:51: 2000000 INFO @ Thu, 16 Apr 2020 04:28:58: 3000000 INFO @ Thu, 16 Apr 2020 04:29:04: 4000000 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 @ Thu, 16 Apr 2020 04:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.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 @ Thu, 16 Apr 2020 04:29:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:29:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:29:11: 5000000 INFO @ Thu, 16 Apr 2020 04:29:15: 1000000 INFO @ Thu, 16 Apr 2020 04:29:18: 6000000 INFO @ Thu, 16 Apr 2020 04:29:22: 2000000 INFO @ Thu, 16 Apr 2020 04:29:25: 7000000 INFO @ Thu, 16 Apr 2020 04:29:29: 3000000 INFO @ Thu, 16 Apr 2020 04:29:31: 8000000 INFO @ Thu, 16 Apr 2020 04:29:36: 4000000 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 @ Thu, 16 Apr 2020 04:29:38: 9000000 INFO @ Thu, 16 Apr 2020 04:29:38: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:29:38: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:29:38: #1 total tags in treatment: 4105266 INFO @ Thu, 16 Apr 2020 04:29:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:29:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:29:38: #1 tags after filtering in treatment: 3921519 INFO @ Thu, 16 Apr 2020 04:29:38: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 04:29:38: #1 finished! INFO @ Thu, 16 Apr 2020 04:29:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:29:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.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 @ Thu, 16 Apr 2020 04:29:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:29:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:29:39: #2 number of paired peaks: 1181 INFO @ Thu, 16 Apr 2020 04:29:39: start model_add_line... INFO @ Thu, 16 Apr 2020 04:29:39: start X-correlation... INFO @ Thu, 16 Apr 2020 04:29:39: end of X-cor INFO @ Thu, 16 Apr 2020 04:29:39: #2 finished! INFO @ Thu, 16 Apr 2020 04:29:39: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 04:29:39: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 04:29:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.05_model.r WARNING @ Thu, 16 Apr 2020 04:29:39: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:29:39: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Thu, 16 Apr 2020 04:29:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 04:29:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:29:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:29:43: 5000000 INFO @ Thu, 16 Apr 2020 04:29:46: 1000000 INFO @ Thu, 16 Apr 2020 04:29:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:29:49: 6000000 INFO @ Thu, 16 Apr 2020 04:29:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:29:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:29:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.05_summits.bed INFO @ Thu, 16 Apr 2020 04:29:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1544 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:29:53: 2000000 INFO @ Thu, 16 Apr 2020 04:29:56: 7000000 INFO @ Thu, 16 Apr 2020 04:30:00: 3000000 INFO @ Thu, 16 Apr 2020 04:30:03: 8000000 INFO @ Thu, 16 Apr 2020 04:30:07: 4000000 INFO @ Thu, 16 Apr 2020 04:30:10: 9000000 INFO @ Thu, 16 Apr 2020 04:30:10: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:30:10: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:30:10: #1 total tags in treatment: 4105266 INFO @ Thu, 16 Apr 2020 04:30:10: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:30:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:30:10: #1 tags after filtering in treatment: 3921519 INFO @ Thu, 16 Apr 2020 04:30:10: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 04:30:10: #1 finished! INFO @ Thu, 16 Apr 2020 04:30:10: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:30:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:30:11: #2 number of paired peaks: 1181 INFO @ Thu, 16 Apr 2020 04:30:11: start model_add_line... INFO @ Thu, 16 Apr 2020 04:30:11: start X-correlation... INFO @ Thu, 16 Apr 2020 04:30:11: end of X-cor INFO @ Thu, 16 Apr 2020 04:30:11: #2 finished! INFO @ Thu, 16 Apr 2020 04:30:11: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 04:30:11: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 04:30:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.10_model.r WARNING @ Thu, 16 Apr 2020 04:30:11: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:30:11: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Thu, 16 Apr 2020 04:30:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 04:30:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:30:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:30:13: 5000000 INFO @ Thu, 16 Apr 2020 04:30:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:30:20: 6000000 INFO @ Thu, 16 Apr 2020 04:30:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:30:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:30:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.10_summits.bed INFO @ Thu, 16 Apr 2020 04:30:24: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (911 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:30:27: 7000000 INFO @ Thu, 16 Apr 2020 04:30:33: 8000000 INFO @ Thu, 16 Apr 2020 04:30:40: 9000000 INFO @ Thu, 16 Apr 2020 04:30:40: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:30:40: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:30:40: #1 total tags in treatment: 4105266 INFO @ Thu, 16 Apr 2020 04:30:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:30:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:30:40: #1 tags after filtering in treatment: 3921519 INFO @ Thu, 16 Apr 2020 04:30:40: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 04:30:40: #1 finished! INFO @ Thu, 16 Apr 2020 04:30:40: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:30:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:30:41: #2 number of paired peaks: 1181 INFO @ Thu, 16 Apr 2020 04:30:41: start model_add_line... INFO @ Thu, 16 Apr 2020 04:30:41: start X-correlation... INFO @ Thu, 16 Apr 2020 04:30:41: end of X-cor INFO @ Thu, 16 Apr 2020 04:30:41: #2 finished! INFO @ Thu, 16 Apr 2020 04:30:41: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 04:30:41: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 04:30:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.20_model.r WARNING @ Thu, 16 Apr 2020 04:30:41: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:30:41: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Thu, 16 Apr 2020 04:30:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 04:30:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:30:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:30:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:30:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:30:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:30:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448060/SRX6448060.20_summits.bed INFO @ Thu, 16 Apr 2020 04:30:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (467 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。