Job ID = 5721081 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,105,680 reads read : 18,211,360 reads written : 18,211,360 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: 00:55:01 9105680 reads; of these: 9105680 (100.00%) were paired; of these: 2459591 (27.01%) aligned concordantly 0 times 2645608 (29.05%) aligned concordantly exactly 1 time 4000481 (43.93%) aligned concordantly >1 times ---- 2459591 pairs aligned concordantly 0 times; of these: 522989 (21.26%) aligned discordantly 1 time ---- 1936602 pairs aligned 0 times concordantly or discordantly; of these: 3873204 mates make up the pairs; of these: 1956052 (50.50%) aligned 0 times 754236 (19.47%) aligned exactly 1 time 1162916 (30.02%) aligned >1 times 89.26% overall alignment rate Time searching: 00:55:01 Overall time: 00:55:01 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 12 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] 3017940 / 6938712 = 0.4349 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 05:29:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.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 05:29:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:29:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:29:15: 1000000 INFO @ Thu, 16 Apr 2020 05:29:22: 2000000 INFO @ Thu, 16 Apr 2020 05:29:28: 3000000 INFO @ Thu, 16 Apr 2020 05:29:35: 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 05:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.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 05:29:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:29:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:29:42: 5000000 INFO @ Thu, 16 Apr 2020 05:29:45: 1000000 INFO @ Thu, 16 Apr 2020 05:29:48: 6000000 INFO @ Thu, 16 Apr 2020 05:29:52: 2000000 INFO @ Thu, 16 Apr 2020 05:29:55: 7000000 INFO @ Thu, 16 Apr 2020 05:29:59: 3000000 INFO @ Thu, 16 Apr 2020 05:30:02: 8000000 INFO @ Thu, 16 Apr 2020 05:30:06: 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 05:30:08: 9000000 INFO @ Thu, 16 Apr 2020 05:30:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.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 05:30:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:30:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:30:12: 5000000 INFO @ Thu, 16 Apr 2020 05:30:15: 10000000 INFO @ Thu, 16 Apr 2020 05:30:16: 1000000 INFO @ Thu, 16 Apr 2020 05:30:16: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:30:16: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:30:16: #1 total tags in treatment: 3711235 INFO @ Thu, 16 Apr 2020 05:30:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:30:16: #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 05:30:16: #1 tags after filtering in treatment: 3134381 INFO @ Thu, 16 Apr 2020 05:30:16: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 05:30:16: #1 finished! INFO @ Thu, 16 Apr 2020 05:30:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:30:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:30:17: #2 number of paired peaks: 4876 INFO @ Thu, 16 Apr 2020 05:30:17: start model_add_line... INFO @ Thu, 16 Apr 2020 05:30:17: start X-correlation... INFO @ Thu, 16 Apr 2020 05:30:17: end of X-cor INFO @ Thu, 16 Apr 2020 05:30:17: #2 finished! INFO @ Thu, 16 Apr 2020 05:30:17: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 05:30:17: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 05:30:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.05_model.r WARNING @ Thu, 16 Apr 2020 05:30:17: #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 05:30:17: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Thu, 16 Apr 2020 05:30:17: #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 05:30:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:30:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:30:19: 6000000 INFO @ Thu, 16 Apr 2020 05:30:24: 2000000 INFO @ Thu, 16 Apr 2020 05:30:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:30:26: 7000000 INFO @ Thu, 16 Apr 2020 05:30:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:30:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:30:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.05_summits.bed INFO @ Thu, 16 Apr 2020 05:30:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (10733 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:30:31: 3000000 INFO @ Thu, 16 Apr 2020 05:30:33: 8000000 INFO @ Thu, 16 Apr 2020 05:30:39: 4000000 INFO @ Thu, 16 Apr 2020 05:30:40: 9000000 INFO @ Thu, 16 Apr 2020 05:30:46: 10000000 INFO @ Thu, 16 Apr 2020 05:30:47: 5000000 INFO @ Thu, 16 Apr 2020 05:30:48: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:30:48: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:30:48: #1 total tags in treatment: 3711235 INFO @ Thu, 16 Apr 2020 05:30:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:30:48: #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 05:30:48: #1 tags after filtering in treatment: 3134381 INFO @ Thu, 16 Apr 2020 05:30:48: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 05:30:48: #1 finished! INFO @ Thu, 16 Apr 2020 05:30:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:30:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:30:48: #2 number of paired peaks: 4876 INFO @ Thu, 16 Apr 2020 05:30:48: start model_add_line... INFO @ Thu, 16 Apr 2020 05:30:48: start X-correlation... INFO @ Thu, 16 Apr 2020 05:30:48: end of X-cor INFO @ Thu, 16 Apr 2020 05:30:48: #2 finished! INFO @ Thu, 16 Apr 2020 05:30:48: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 05:30:48: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 05:30:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.10_model.r WARNING @ Thu, 16 Apr 2020 05:30:48: #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 05:30:48: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Thu, 16 Apr 2020 05:30:48: #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 05:30:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:30:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:30:54: 6000000 INFO @ Thu, 16 Apr 2020 05:30:56: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:31:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:31:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:31:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.10_summits.bed INFO @ Thu, 16 Apr 2020 05:31:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6503 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:31:02: 7000000 INFO @ Thu, 16 Apr 2020 05:31:10: 8000000 INFO @ Thu, 16 Apr 2020 05:31:17: 9000000 INFO @ Thu, 16 Apr 2020 05:31:25: 10000000 INFO @ Thu, 16 Apr 2020 05:31:26: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:31:26: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:31:26: #1 total tags in treatment: 3711235 INFO @ Thu, 16 Apr 2020 05:31:26: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:31:26: #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 05:31:26: #1 tags after filtering in treatment: 3134381 INFO @ Thu, 16 Apr 2020 05:31:26: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 05:31:26: #1 finished! INFO @ Thu, 16 Apr 2020 05:31:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:31:27: #2 number of paired peaks: 4876 INFO @ Thu, 16 Apr 2020 05:31:27: start model_add_line... INFO @ Thu, 16 Apr 2020 05:31:27: start X-correlation... INFO @ Thu, 16 Apr 2020 05:31:27: end of X-cor INFO @ Thu, 16 Apr 2020 05:31:27: #2 finished! INFO @ Thu, 16 Apr 2020 05:31:27: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 05:31:27: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 05:31:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.20_model.r WARNING @ Thu, 16 Apr 2020 05:31:27: #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 05:31:27: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Thu, 16 Apr 2020 05:31:27: #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 05:31:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:31:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:31:34: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:31:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:31:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:31:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448075/SRX6448075.20_summits.bed INFO @ Thu, 16 Apr 2020 05:31:38: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2597 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。