Job ID = 5720788 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,512,497 reads read : 25,024,994 reads written : 25,024,994 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: 00:36:13 12512497 reads; of these: 12512497 (100.00%) were paired; of these: 2571798 (20.55%) aligned concordantly 0 times 7383973 (59.01%) aligned concordantly exactly 1 time 2556726 (20.43%) aligned concordantly >1 times ---- 2571798 pairs aligned concordantly 0 times; of these: 844808 (32.85%) aligned discordantly 1 time ---- 1726990 pairs aligned 0 times concordantly or discordantly; of these: 3453980 mates make up the pairs; of these: 1846062 (53.45%) aligned 0 times 782443 (22.65%) aligned exactly 1 time 825475 (23.90%) aligned >1 times 92.62% overall alignment rate Time searching: 00:36:13 Overall time: 00:36:13 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] 2431664 / 10348931 = 0.2350 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 02:21:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.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 02:21:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:21:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:21:06: 1000000 INFO @ Thu, 16 Apr 2020 02:21:11: 2000000 INFO @ Thu, 16 Apr 2020 02:21:17: 3000000 INFO @ Thu, 16 Apr 2020 02:21:22: 4000000 INFO @ Thu, 16 Apr 2020 02:21:28: 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 @ Thu, 16 Apr 2020 02:21:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.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 02:21:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:21:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:21:34: 6000000 INFO @ Thu, 16 Apr 2020 02:21:38: 1000000 INFO @ Thu, 16 Apr 2020 02:21:39: 7000000 INFO @ Thu, 16 Apr 2020 02:21:44: 2000000 INFO @ Thu, 16 Apr 2020 02:21:45: 8000000 INFO @ Thu, 16 Apr 2020 02:21:51: 9000000 INFO @ Thu, 16 Apr 2020 02:21:51: 3000000 INFO @ Thu, 16 Apr 2020 02:21:57: 10000000 INFO @ Thu, 16 Apr 2020 02:21:58: 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 02:22:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.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 02:22:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:22:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:22:02: 11000000 INFO @ Thu, 16 Apr 2020 02:22:05: 5000000 INFO @ Thu, 16 Apr 2020 02:22:07: 1000000 INFO @ Thu, 16 Apr 2020 02:22:08: 12000000 INFO @ Thu, 16 Apr 2020 02:22:12: 6000000 INFO @ Thu, 16 Apr 2020 02:22:14: 13000000 INFO @ Thu, 16 Apr 2020 02:22:14: 2000000 INFO @ Thu, 16 Apr 2020 02:22:19: 7000000 INFO @ Thu, 16 Apr 2020 02:22:20: 14000000 INFO @ Thu, 16 Apr 2020 02:22:21: 3000000 INFO @ Thu, 16 Apr 2020 02:22:25: 15000000 INFO @ Thu, 16 Apr 2020 02:22:26: 8000000 INFO @ Thu, 16 Apr 2020 02:22:28: 4000000 INFO @ Thu, 16 Apr 2020 02:22:31: 16000000 INFO @ Thu, 16 Apr 2020 02:22:33: 9000000 INFO @ Thu, 16 Apr 2020 02:22:35: 5000000 INFO @ Thu, 16 Apr 2020 02:22:37: 17000000 INFO @ Thu, 16 Apr 2020 02:22:40: 10000000 INFO @ Thu, 16 Apr 2020 02:22:42: 6000000 INFO @ Thu, 16 Apr 2020 02:22:43: 18000000 INFO @ Thu, 16 Apr 2020 02:22:45: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 02:22:45: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 02:22:45: #1 total tags in treatment: 7601302 INFO @ Thu, 16 Apr 2020 02:22:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:22:45: #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 02:22:45: #1 tags after filtering in treatment: 7265144 INFO @ Thu, 16 Apr 2020 02:22:45: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 02:22:45: #1 finished! INFO @ Thu, 16 Apr 2020 02:22:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:22:45: #2 number of paired peaks: 238 WARNING @ Thu, 16 Apr 2020 02:22:45: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Thu, 16 Apr 2020 02:22:45: start model_add_line... INFO @ Thu, 16 Apr 2020 02:22:45: start X-correlation... INFO @ Thu, 16 Apr 2020 02:22:45: end of X-cor INFO @ Thu, 16 Apr 2020 02:22:45: #2 finished! INFO @ Thu, 16 Apr 2020 02:22:45: #2 predicted fragment length is 154 bps INFO @ Thu, 16 Apr 2020 02:22:45: #2 alternative fragment length(s) may be 154 bps INFO @ Thu, 16 Apr 2020 02:22:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.05_model.r WARNING @ Thu, 16 Apr 2020 02:22:45: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:22:45: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Thu, 16 Apr 2020 02:22:45: #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 02:22:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:22:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:22:46: 11000000 INFO @ Thu, 16 Apr 2020 02:22:48: 7000000 INFO @ Thu, 16 Apr 2020 02:22:53: 12000000 INFO @ Thu, 16 Apr 2020 02:22:55: 8000000 INFO @ Thu, 16 Apr 2020 02:23:00: 13000000 INFO @ Thu, 16 Apr 2020 02:23:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:23:02: 9000000 INFO @ Thu, 16 Apr 2020 02:23:07: 14000000 INFO @ Thu, 16 Apr 2020 02:23:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:23:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:23:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.05_summits.bed INFO @ Thu, 16 Apr 2020 02:23:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1789 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:23:09: 10000000 INFO @ Thu, 16 Apr 2020 02:23:14: 15000000 INFO @ Thu, 16 Apr 2020 02:23:15: 11000000 INFO @ Thu, 16 Apr 2020 02:23:21: 16000000 INFO @ Thu, 16 Apr 2020 02:23:22: 12000000 INFO @ Thu, 16 Apr 2020 02:23:28: 17000000 INFO @ Thu, 16 Apr 2020 02:23:28: 13000000 INFO @ Thu, 16 Apr 2020 02:23:35: 14000000 INFO @ Thu, 16 Apr 2020 02:23:35: 18000000 INFO @ Thu, 16 Apr 2020 02:23:37: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 02:23:37: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 02:23:37: #1 total tags in treatment: 7601302 INFO @ Thu, 16 Apr 2020 02:23:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:23:37: #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 02:23:38: #1 tags after filtering in treatment: 7265144 INFO @ Thu, 16 Apr 2020 02:23:38: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 02:23:38: #1 finished! INFO @ Thu, 16 Apr 2020 02:23:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:23:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:23:38: #2 number of paired peaks: 238 WARNING @ Thu, 16 Apr 2020 02:23:38: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Thu, 16 Apr 2020 02:23:38: start model_add_line... INFO @ Thu, 16 Apr 2020 02:23:38: start X-correlation... INFO @ Thu, 16 Apr 2020 02:23:38: end of X-cor INFO @ Thu, 16 Apr 2020 02:23:38: #2 finished! INFO @ Thu, 16 Apr 2020 02:23:38: #2 predicted fragment length is 154 bps INFO @ Thu, 16 Apr 2020 02:23:38: #2 alternative fragment length(s) may be 154 bps INFO @ Thu, 16 Apr 2020 02:23:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.10_model.r WARNING @ Thu, 16 Apr 2020 02:23:38: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:23:38: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Thu, 16 Apr 2020 02:23:38: #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 02:23:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:23:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:23:41: 15000000 INFO @ Thu, 16 Apr 2020 02:23:48: 16000000 INFO @ Thu, 16 Apr 2020 02:23:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:23:54: 17000000 INFO @ Thu, 16 Apr 2020 02:24:00: 18000000 INFO @ Thu, 16 Apr 2020 02:24:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:24:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:24:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.10_summits.bed INFO @ Thu, 16 Apr 2020 02:24:01: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1079 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:24:02: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 02:24:02: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 02:24:02: #1 total tags in treatment: 7601302 INFO @ Thu, 16 Apr 2020 02:24:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:24:02: #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 02:24:02: #1 tags after filtering in treatment: 7265144 INFO @ Thu, 16 Apr 2020 02:24:02: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 02:24:02: #1 finished! INFO @ Thu, 16 Apr 2020 02:24:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:24:03: #2 number of paired peaks: 238 WARNING @ Thu, 16 Apr 2020 02:24:03: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Thu, 16 Apr 2020 02:24:03: start model_add_line... INFO @ Thu, 16 Apr 2020 02:24:03: start X-correlation... INFO @ Thu, 16 Apr 2020 02:24:03: end of X-cor INFO @ Thu, 16 Apr 2020 02:24:03: #2 finished! INFO @ Thu, 16 Apr 2020 02:24:03: #2 predicted fragment length is 154 bps INFO @ Thu, 16 Apr 2020 02:24:03: #2 alternative fragment length(s) may be 154 bps INFO @ Thu, 16 Apr 2020 02:24:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.20_model.r WARNING @ Thu, 16 Apr 2020 02:24:03: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:24:03: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Thu, 16 Apr 2020 02:24:03: #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 02:24:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:24:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:24:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:24:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:24:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:24:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246880/SRX5246880.20_summits.bed INFO @ Thu, 16 Apr 2020 02:24:26: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (597 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。